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Initial commit: digital-patients pipeline (clean, no large files)

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Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
This commit is contained in:
Olamide Isreal
2026-03-26 15:15:23 +01:00
commit 9e6a16c19b
45 changed files with 7207 additions and 0 deletions
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gnomad.genomes.v4.1.sites.female.txt filter=lfs diff=lfs merge=lfs -text
gnomad.genomes.v4.1.sites.male.txt filter=lfs diff=lfs merge=lfs -text
gnomad.genomes.v4.1.sites.* filter=lfs diff=lfs merge=lfs -text
app_filter/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz filter=lfs diff=lfs merge=lfs -text

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/work
.nextflow
.nextflow.*
sample/
*.swp
*.pid
*.log
# Large files (baked into Docker images or staged to S3)
ensemble_reference.fasta
go_df_work.csv
MANE_transcipts_reference.fasta
reference.fasta
MANE.GRCh38.v1.3.update.tsv
go_term_protein_expression_model.pth
CIBERSORTx-fractionshires/
TPM_NO_MUTATIONS.csv
name_transcipt_map.csv
LM22_sourceGEP_ensg.txt
regulon.rda
impute-me_wget_ukbb_variants.sh
ncbiRefSeq_subset.pickle
prot_subset.pickle
app_filter/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz

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[submodule "ecotyper"]
path = ecotyper
url = https://gitlab.com/omic/next/registry/tools/ecotyper

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FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
cuda-toolkit-12-2 \
ca-certificates \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
# main conda env (borzoi)
RUN conda create -n borzoi python=3.9
ENV PATH "$PATH:/opt/conda/envs/borzoi/bin"
RUN echo "source activate borzoi" >> ~/.bashrc
RUN conda clean --all -f -y
# Install borzoi
RUN git clone https://github.com/calico/baskerville.git
WORKDIR /home/omic/baskerville
RUN /opt/conda/envs/borzoi/bin/python3 -m pip install -e .
WORKDIR /home/omic
RUN git clone https://github.com/calico/borzoi.git
WORKDIR /home/omic/borzoi
RUN /opt/conda/envs/borzoi/bin/python3 -m pip install -e .
# Install pretrained models
RUN mkdir -p /home/omic/borzoi/saved_models
WORKDIR /home/omic/borzoi/saved_models
RUN mkdir -p f0 && mkdir -p f1 && mkdir -p f2 && mkdir -p f3
RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f0/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f0/model0_best.h5
RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f1/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f1/model0_best.h5
RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f2/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f2/model0_best.h5
RUN wget --no-check-certificate -O /home/omic/borzoi/saved_models/f3/model0_best.h5 https://storage.googleapis.com/seqnn-share/borzoi/f3/model0_best.h5
WORKDIR /home/omic/borzoi
# Get hg38
RUN wget -O - https://hgdownload2.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa
# Get other supporting data
RUN wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf
RUN wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz
RUN wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz
# Index the reference
RUN /opt/conda/envs/borzoi/bin/python3 -m pip install pyfaidx
RUN /opt/conda/envs/borzoi/bin/python3 -c "import pyfaidx; pyfaidx.Faidx('hg38.fa')"
#Install samtools
RUN apt-get update -y && apt-get install -y libz-dev liblzma-dev libbz2-dev libcurl4-gnutls-dev
WORKDIR /home/omic
RUN git clone --recurse-submodules https://github.com/samtools/htslib.git
RUN git clone https://github.com/samtools/bcftools.git
WORKDIR /home/omic/bcftools
# The following is optional:
#RUN autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
RUN make
RUN export BCFTOOLS_PLUGINS=/home/omic/bcftools
WORKDIR /home/omic/borzoi
COPY ncbiRefSeq_bigger.csv .
COPY ncbiRefSeq_subset.pickle .
#copy MANE data
COPY prot_bigger.csv .
COPY prot_subset.pickle .
COPY TPM_NO_MUTATIONS.csv .
# test

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# Start with Ubuntu base
FROM ubuntu:22.04
USER root
SHELL ["/bin/bash", "-c"]
# Set environment variables
ENV DEBIAN_FRONTEND=noninteractive \
TZ=Etc/UTC \
PATH="/opt/conda/bin:/opt/conda/condabin:/opt/conda/envs/ecotyper/bin:$PATH" \
R_LIBS="/opt/conda/envs/ecotyper/lib/R/library:/ecotyper/R/library" \
ECOTYPER_HOME="/ecotyper"
# Install system dependencies
RUN apt-get update && apt-get install -y --no-install-recommends \
wget \
ca-certificates \
git \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
build-essential \
r-base \
r-base-dev \
libcairo2-dev \
libxt-dev \
libgraphicsmagick1-dev \
default-jdk \
xvfb \
xauth \
xfonts-base \
&& rm -rf /var/lib/apt/lists/*
# Set up R environment
RUN echo "options(repos = c(CRAN = 'https://cloud.r-project.org'))" > /root/.Rprofile
# Install Conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
mkdir -p /opt && \
bash miniconda.sh -b -p /opt/conda && \
rm miniconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc && \
find /opt/conda/ -follow -type f -name '*.a' -delete && \
find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
/opt/conda/bin/conda clean -afy
ENV PATH=/opt/conda/bin:$PATH
# Update conda and create environment
RUN conda update -y -n base -c defaults conda && \
conda create -n ecotyper -c conda-forge -c bioconda \
python=3.8 \
r-base=4.1.3 \
r-matrix \
r-mass \
r-nmf \
r-rcpp \
r-data.table \
r-reshape2 \
r-plyr \
r-stringr \
r-ggplot2 \
r-rcolorbrewer \
r-circlize \
r-cowplot \
r-viridis \
r-gridextra \
r-ggpubr \
r-cluster \
r-matrixtests \
r-doparallel \
r-foreach \
r-optparse \
r-argparse \
r-config \
r-colorspace \
r-rjson \
bioconductor-biobase \
bioconductor-complexheatmap \
bioconductor-genomicranges \
-y && \
conda clean -afy
# Clone EcoTyper and setup directory structure
RUN git clone --depth 1 https://github.com/digitalcytometry/ecotyper.git /ecotyper && \
cd /ecotyper && \
mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Analysis/rank_selection && \
mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Analysis/rank_selection && \
mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Cell_States/recovery && \
mkdir -p EcoTyper/Carcinoma/Carcinoma_Fractions/Ecotypes/recovery && \
mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Cell_States/recovery && \
mkdir -p EcoTyper/Lymphoma/Lymphoma_Fractions/Ecotypes/recovery && \
chmod -R +x pipeline/*.R && \
chmod -R +x *.R
# Setup EcoTyper permissions
RUN cd /ecotyper && \
ln -sf /ecotyper/pipeline pipeline && \
chmod -R 755 /ecotyper/EcoTyper && \
chmod -R 755 /ecotyper/pipeline
# Setup CIBERSORTx
RUN mkdir -p /src
WORKDIR /src
# Copy CIBERSORTx files
COPY ./CIBERSORTx-fractionshires/ /src/
# Install R dependencies for CIBERSORTx
RUN R -e "if (!require('BiocManager', quietly=TRUE)) install.packages('BiocManager', repos='https://cloud.r-project.org/')" && \
Rscript /src/install_R_dependencies.R
# Add src to PATH
ENV PATH="/src:${PATH}"
# Setup final environment
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate ecotyper" >> ~/.bashrc
#Add pandas
RUN conda install -n ecotyper anaconda::pandas
# Set default command
CMD ["/bin/bash"]

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FROM r-base:latest
WORKDIR /usr/src/app
# Install system dependencies
RUN apt-get update && apt-get install -y \
git \
libcurl4-gnutls-dev \
libssl-dev \
libxml2-dev \
procps # Adding procps for the 'ps' command
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (rpy2)
RUN conda create -n rpy2 python=3.9
ENV PATH "$PATH:/opt/conda/envs/rpy2/bin"
RUN echo "source activate rpy2" >> ~/.bashrc
RUN conda clean --all -f -y
RUN conda install -y -n rpy2 -c anaconda pandas
RUN conda install -y -n rpy2 -c anaconda numpy
# Install R packages
RUN Rscript -e "install.packages('remotes', dependencies=TRUE)" \
&& Rscript -e "remotes::install_github('federicogiorgi/corto')" \
&& Rscript -e "install.packages('data.table', dependencies=TRUE)" \
&& Rscript -e "install.packages('BiocManager')" \
&& Rscript -e "BiocManager::install('DESeq2')"
# Test commands to validate installation
RUN Rscript -e "library(corto)"
# Clone the corto repository (optional, based on your needs)
RUN git clone https://github.com/federicogiorgi/corto.git
CMD ["/bin/bash"]

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ARG CUDA=11.7
FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
python3-pip \
python3-dev \
python3-opencv \
libglib2.0-0 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Add the NVIDIA GPG key directly
RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
RUN apt-get -y update && \
apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (rna2protexpresson)
RUN conda create -n rna2protexpresson python=3.9
ENV PATH "$PATH:/opt/conda/envs/rna2protexpresson/bin"
RUN echo "source activate rna2protexpresson" >> ~/.bashrc
RUN conda clean --all -f -y
# Upgrade apt-get
RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
# Upgrade pip
RUN python3 -m pip install --upgrade pip
# Install PyTorch and torchvision
RUN /opt/conda/envs/rna2protexpresson/bin/python3 -m pip install torch torchvision torchaudio -f https://download.pytorch.org/whl/cu111/torch_stable.html
#Inatall packages
RUN /opt/conda/envs/rna2protexpresson/bin/python3 -m pip install axial_attention thefuzz
RUN conda install -n rna2protexpresson -c anaconda pandas numpy scikit-learn joblib
RUN /opt/conda/envs/rna2protexpresson/bin/python3 -m pip install argparse
# make rna2protexpresson
RUN mkdir -p /home/omic/rna2protexpresson
WORKDIR /home/omic/rna2protexpresson
# Package into python script for running in nextflow
COPY rna2protexpression.py /home/omic/rna2protexpression/rna2protexpression.py
RUN chmod +x /home/omic/rna2protexpression/rna2protexpression.py
#COPY model &˛ preprocessing
COPY tissue2number.joblib .
COPY ensg2number.joblib .
COPY go_df_work.csv .
COPY go_term_protein_expression_model.pth .

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FROM ubuntu:latest
ARG DEBIAN_FRONTEND=noninteractive
USER root
# Install gradle and JDK
RUN apt -y update && apt-get -y update
RUN apt install -y build-essential openjdk-8-jdk wget git python3 python3-pip tabix
# install conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
mkdir -p /opt && \
sh miniconda.sh -b -p /opt/conda && \
rm miniconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc && \
find /opt/conda/ -follow -type f -name '*.a' -delete && \
find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
/opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
# main conda env (synthea)
RUN conda create -n synthea
ENV PATH "$PATH:/opt/conda/envs/synthea/bin"
RUN echo "source activate synthea" >> ~/.bashrc
# Install pandas and numpy
RUN python3 -m pip install --upgrade pip
RUN python3 -m pip install pandas numpy fuzzywuzzy python-Levenshtein requests
# Install synthea from latest release
RUN wget https://github.com/synthetichealth/synthea/archive/refs/tags/master-branch-latest.tar.gz
RUN tar xzf master-branch-latest.tar.gz && mv synthea-master-branch-latest synthea
WORKDIR /synthea
ARG PATH $PATH:/synthea
ENV PATH $PATH:/synthea
RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge
# Install samtools
RUN conda install -n synthea -c bioconda samtools
# Install UCSC Liftover
RUN conda install -n synthea -c bioconda ucsc-liftover
RUN conda install -n synthea -c bioconda gatk4
RUN conda install -n synthea -c bioconda bedtools
RUN apt-get -y install vcftools
# DNA to Protein Sequence code
WORKDIR /synthea
RUN git clone https://github.com/prestevez/dna2proteins.git
RUN mv dna2proteins/dna2proteins.py .
RUN rm -r dna2proteins
RUN apt install -y 2to3
RUN 2to3 -w dna2proteins.py
#Test
# RUN ./gradlew build check test
RUN ./run_synthea -p 10 --exporter.csv.export true
# use -a for age range e.g. 30-40 and -g for gender M/F

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#FROM nvidia/cuda:12.2.2-cudnn8-runtime-ubuntu22.04
FROM rust:1.61
USER root
SHELL ["/bin/bash", "-c"]
#SHELL [ "/bin/sh", "-s", ".", "$HOME/.cargo/env" ]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y software-properties-common --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
libopenblas-dev \
libgsl-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Get Rust
#RUN curl https://sh.rustup.rs -sSf | bash -s -- --default-toolchain nightly -y
#RUN source $HOME/.cargo/env
#RUN echo 'source $HOME/.cargo/env' >> $HOME/.bashrc
# Install vcf2prot
RUN git clone https://github.com/ikmb/vcf2prot.git
WORKDIR /home/omic/vcf2prot
RUN cargo build --release
WORKDIR /home/omic/vcf2prot/target/release
RUN export DEBUG_CPU_EXEC=TRUE
RUN export INSPECT_TXP=TRUE
RUN export INSPECT_INS_GEN=TRUE
#Test
RUN ./vcf2prot -h
WORKDIR /home/omic/vcf2prot
RUN gunzip examples/reference_sequences.fasta.gz
COPY reference.fasta .
#install bcftools
WORKDIR /home/omic/
# install conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
mkdir -p /opt && \
bash miniconda.sh -b -p /opt/conda && \
rm miniconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc && \
find /opt/conda/ -follow -type f -name '*.a' -delete && \
find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
/opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
## update conda
RUN conda update -y -n base -c defaults conda
# main conda env (vcf2prot)
RUN conda create -n vcf2prot python=3.9
ENV PATH "$PATH:/opt/conda/envs/vcf2prot/bin"
RUN echo "source activate vcf2prot" >> ~/.bashrc
RUN conda install -y -n vcf2prot -c bioconda openssl
RUN conda install -y -n vcf2prot -c conda-forge libgcc-ng
RUN conda install -y -n vcf2prot -c bioconda bcftools==1.20
#Install beagle
#RUN wget https://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jar
#Get data
RUN wget https://ftp.ensembl.org/pub/release-112/gff3/homo_sapiens/Homo_sapiens.GRCh38.112.gff3.gz
RUN gunzip Homo_sapiens.GRCh38.112.gff3.gz
#RUN wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
#RUN gunzip hg38.fa.gz
RUN wget https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
RUN gunzip Homo_sapiens.GRCh38.dna.toplevel.fa.gz
WORKDIR /home/omic/vcf2prot
RUN conda install -y -n vcf2prot numpy pandas
COPY MANE_transcipts_reference.fasta .

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FROM ensemblorg/ensembl-vep:release_115.2

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{
"cells": [
{
"cell_type": "code",
"execution_count": 10,
"id": "e2d83e35-e69f-456e-a2fb-77a05b42f43a",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import io\n",
"import os\n",
"import pandas as pd\n",
"import gzip\n",
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "900349f6-d73f-4584-b949-42c1f770d696",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"#create names of all chromosome\n",
"chr_list = [str(i+1) for i in range(22)]\n",
"chr_list.extend(['X','Y'])"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "0bca1990-db14-4f99-a57a-1132515fa21f",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2024-11-04 13:33:40-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr15.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.211.251, 142.251.33.91, 142.250.217.91, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.211.251|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 16904431253 (16G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr15.vcf.bgz.1’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 15.74G 78.2MB/s in 4m 34s \n",
"\n",
"2024-11-04 13:38:15 (58.9 MB/s) - ‘gnomad.genomes.v4.1.sites.chr15.vcf.bgz.1’ saved [16904431253/16904431253]\n",
"\n",
"--2024-11-04 13:38:15-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr16.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.250.217.123, 142.251.215.251, 172.217.14.251, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.250.217.123|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 18918703003 (18G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr16.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 17.62G 77.1MB/s in 4m 7s \n",
"\n",
"2024-11-04 13:42:23 (73.1 MB/s) - ‘gnomad.genomes.v4.1.sites.chr16.vcf.bgz’ saved [18918703003/18918703003]\n",
"\n",
"--2024-11-04 13:42:23-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr17.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.215.251, 172.217.14.251, 142.250.69.219, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.215.251|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 17412317144 (16G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr17.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 16.22G 67.9MB/s in 4m 1s \n",
"\n",
"2024-11-04 13:46:24 (68.9 MB/s) - ‘gnomad.genomes.v4.1.sites.chr17.vcf.bgz’ saved [17412317144/17412317144]\n",
"\n",
"--2024-11-04 13:46:25-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr18.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.33.123, 142.251.211.251, 142.251.33.91, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.33.123|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 14430177524 (13G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr18.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 13.44G 72.8MB/s in 3m 19s \n",
"\n",
"2024-11-04 13:49:45 (69.0 MB/s) - ‘gnomad.genomes.v4.1.sites.chr18.vcf.bgz’ saved [14430177524/14430177524]\n",
"\n",
"--2024-11-04 13:49:45-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr19.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.250.69.219, 142.251.33.123, 142.251.211.251, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.250.69.219|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 13679473477 (13G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr19.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 12.74G 74.2MB/s in 3m 1s \n",
"\n",
"2024-11-04 13:52:46 (72.0 MB/s) - ‘gnomad.genomes.v4.1.sites.chr19.vcf.bgz’ saved [13679473477/13679473477]\n",
"\n",
"--2024-11-04 13:52:47-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr20.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.211.251, 142.251.33.91, 142.250.217.91, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.211.251|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 11838569571 (11G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr20.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 11.03G 79.9MB/s in 2m 38s \n",
"\n",
"2024-11-04 13:55:26 (71.2 MB/s) - ‘gnomad.genomes.v4.1.sites.chr20.vcf.bgz’ saved [11838569571/11838569571]\n",
"\n",
"--2024-11-04 13:55:26-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr21.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.211.251, 142.251.33.91, 142.250.217.91, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.211.251|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 7758981978 (7.2G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr21.vcf.bgz.1’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 7.23G 72.4MB/s in 1m 50s \n",
"\n",
"2024-11-04 13:57:16 (67.2 MB/s) - ‘gnomad.genomes.v4.1.sites.chr21.vcf.bgz.1’ saved [7758981978/7758981978]\n",
"\n",
"--2024-11-04 13:57:16-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr22.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.215.251, 172.217.14.219, 142.250.69.219, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.215.251|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 8731339280 (8.1G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chr22.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 8.13G 81.2MB/s in 2m 0s \n",
"\n",
"2024-11-04 13:59:16 (69.7 MB/s) - ‘gnomad.genomes.v4.1.sites.chr22.vcf.bgz’ saved [8731339280/8731339280]\n",
"\n",
"--2024-11-04 13:59:17-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chrX.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.33.123, 142.251.211.251, 142.251.33.91, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.33.123|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 22908335319 (21G) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chrX.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 21.33G 76.7MB/s in 5m 6s \n",
"\n",
"2024-11-04 14:04:23 (71.5 MB/s) - ‘gnomad.genomes.v4.1.sites.chrX.vcf.bgz’ saved [22908335319/22908335319]\n",
"\n",
"--2024-11-04 14:04:23-- https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chrY.vcf.bgz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 172.217.14.219, 142.250.69.219, 142.251.33.123, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|172.217.14.219|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 599108494 (571M) [application/octet-stream]\n",
"Saving to: ‘gnomad.genomes.v4.1.sites.chrY.vcf.bgz’\n",
"\n",
"gnomad.genomes.v4.1 100%[===================>] 571.35M 78.3MB/s in 8.9s \n",
"\n",
"2024-11-04 14:04:32 (64.4 MB/s) - ‘gnomad.genomes.v4.1.sites.chrY.vcf.bgz’ saved [599108494/599108494]\n",
"\n"
]
}
],
"source": [
"#download gnomad vcf v4\n",
"for i in chr_list: \n",
" !wget https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr{i}.vcf.bgz\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "68ba24a1-d60d-4097-8827-7599a1cc705d",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"#rewrite files to only extract alleles with frequency above freq_filter\n",
"\n",
"def rewrite(chr_name, freq_filter):\n",
" file_neme = f'gnomad.genomes.v4.1.sites.chr{chr_name}.vcf.bgz'\n",
" file_male_name=f'gnomad.genomes.v4.1.sites.chr{chr_name}.male.txt'\n",
" file_female_name=f'gnomad.genomes.v4.1.sites.chr{chr_name}.female.txt'\n",
" \n",
" #delete old male female files if they exist\n",
" try:\n",
" os.remove(file_male_name)\n",
" except OSError:\n",
" pass\n",
" try:\n",
" os.remove(file_female_name)\n",
" except OSError:\n",
" pass\n",
"\n",
" with open(file_male_name, 'a') as m_file, open(file_female_name, 'a') as f_file:\n",
" m_file.write('#CHROM,POS,ID,REF,ALT,QUAL,AF_XY\\n')\n",
" f_file.write('#CHROM,POS,ID,REF,ALT,QUAL,AF_XX\\n')\n",
" with gzip.open(file_neme, 'r') as f:\n",
" for l in f:\n",
" if not str(l)[2:3]=='#':\n",
" vcf_pos = str(l)[2:-1]\n",
" pos = vcf_pos.split('\\\\t')\n",
" info = pos[-1].split(';')\n",
" pos = pos[:6]\n",
" af_XX = list(np.array(info)[[i[:5]=='AF_XX' for i in info]])\n",
" af_XY = list(np.array(info)[[i[:5]=='AF_XY' for i in info]])\n",
" #some positions don't have allele frequency\n",
" if len(af_XX)==1:\n",
" assert af_XX[0][:5]=='AF_XX'\n",
" af_XX = af_XX[0].split('=')[1] \n",
" if float(af_XX)>=freq_filter:\n",
" f_file.write((',').join(pos)+','+af_XX+'\\n')\n",
" if len(af_XY)==1:\n",
" assert af_XY[0][:5]=='AF_XY'\n",
" af_XY = af_XY[0].split('=')[1] \n",
" if float(af_XY)>=freq_filter:\n",
" m_file.write((',').join(pos)+','+af_XY+'\\n')\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2fdac0b3-f8f3-4540-b050-408672fee807",
"metadata": {},
"outputs": [],
"source": [
"freq_filter = 0.005\n",
"[rewrite(i, freq_filter) for i in chr_list]"
]
},
{
"cell_type": "code",
"execution_count": 21,
"id": "fb349e47-38d4-4fb2-af02-9a522c64b3fc",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"#concat all chr to one file\n",
"def concat_all_chr_to_m_f(chr_list):\n",
" file_male_name = f'gnomad.genomes.v4.1.sites.male.txt'\n",
" file_female_name = f'gnomad.genomes.v4.1.sites.female.txt'\n",
" \n",
" #delete old male female files if they exist\n",
" try:\n",
" os.remove(file_male_name)\n",
" except OSError:\n",
" pass\n",
" try:\n",
" os.remove(file_female_name)\n",
" except OSError:\n",
" pass\n",
" \n",
" with open(file_male_name, 'a') as m_file, open(file_female_name, 'a') as f_file:\n",
" m_file.write('#CHROM,POS,ID,REF,ALT,QUAL,AF_XY\\n')\n",
" f_file.write('#CHROM,POS,ID,REF,ALT,QUAL,AF_XX\\n')\n",
" for chr_n in chr_list:\n",
" file_male=f'gnomad.genomes.v4.1.sites.chr{chr_n}.male.txt'\n",
" with open(file_male) as infile:\n",
" next(infile)\n",
" for line in infile:\n",
" m_file.write(line)\n",
" if chr_n != 'Y':\n",
" file_female=f'gnomad.genomes.v4.1.sites.chr{chr_n}.female.txt'\n",
" with open(file_female) as infile:\n",
" next(infile)\n",
" for line in infile:\n",
" f_file.write(line)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e170368a-9738-49af-9898-ac85bbe72385",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"concat_all_chr_to_m_f(chr_list)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

7
Notes.txt Normal file
View File

@@ -0,0 +1,7 @@
add rna splice step
fix borzoi - muatation step (main_borzoi;PREDICT_EXPRESSION;create_mut()) onyl POINT MUTATIONS add INDEL MUATAIONS
Borzoi can have alternativ chromosoms and chrUn_* as well, VCF2PROT CAN NOT have them. This will cause discrepancies in the code.
Name output files from borzoi ==> need to have patients name/id

210
README.md Normal file
View File

@@ -0,0 +1,210 @@
# Digital Patient and Drug Response Pipeline - Comprehensive Implementation Plan
## Pipeline Overview
```mermaid
flowchart TB
subgraph Patient["Patient Profile Generation"]
A1[1. Medical Records Creation] --> A2[2. Disease-specific Genome]
A2 --> A3[3. Disease-specific Protein Variants]
A3 --> A4[4. Disease-specific Transcriptome]
A4 --> A5[5. Disease-specific Proteome]
A5 --> A6[6. Disease-specific Metabolome]
A6 --> A7[7. Disease-specific Immunome]
end
subgraph Drug["Drug Analysis & Modeling"]
B1[8. Drug-Target PK] --> B1a[8a. Binding Site Prediction]
B1a --> B1b[8b. Drug-Target Docking]
B1b --> B2[9. Drug-Proteome Screening]
B2 --> B3[10. Off-target Analysis]
B3 --> B4[11. Drug-Compound Screening]
B4 --> B5[12. Drug-Genome Sensitivity]
end
subgraph Response["Response Prediction"]
C1[13. Transcriptomic Changes] --> C2[14. Disease Stage Evaluation]
C2 --> C3[15-16. Proteomic & Metabolomic Changes]
C3 --> C4[17-19. Biological & Immune Response]
C4 --> C5[20-21. ADMET & Toxicity]
end
Patient --> Drug
Drug --> Response
```
## Part 1: Digital Patient Generation
### Implementation Status Overview
| Step | Status | Tool/Method | Input | Output | Location | Validation Data | Dependencies/Notes |
|------|--------|-------------|--------|---------|-----------|-----------------|-------------------|
| 1. Medical Records | ✓ | Synthea | - | Demographics, records | /Workspace/next/registry/tools/synthea | Target: 1000 patients/disease | - |
| 2. Disease Genome | ✓ | Omic-UKBB | Alleles, positions, frequencies | VCF (hg38) | Part of Synthea repo | - | Only storing variants |
| 3. Protein Variants | ✓ | vcf2prot | VCF | Protein fasta | Part of Synthea repo (tbc) | - | Multi-tissue support needed |
| 4. Transcriptome | 🚧 | borzoi | Genomic sequences | RNAseq (TPM) | - | ENCODE, GTEx (E-MTAB-6814) | NIH ENCODE standards |
| 5. Proteome | 🚧 | clei2block | RNAseq (log2-FC) | Fold-change | github.com/stasaki/clei2block | CellModelPassport, TCGA | Requires GTEx training |
| 6. Metabolome | ⏳ | corto | RNAseq (TPM) | Metabolite profiles | github.com/federicogiorgi/corto | CCLE, NCI-60 | - |
| 7. Immunome | ⏳ | Ecotyper | RNAseq | Cell type profiles | - | SPICA30, SPICA17 | - |
### Active Implementation Tasks
#### Transcriptome Generation
Current goal: Establish accurate transcriptome prediction pipeline
- [x] Implement and evaluate primary models:
* ~~enformer~~
* ~~basenji~~
* borzoi ~~for RNAseq profiles~~, built on basenji and enformer
- [x] Add SequenceModelBenchmark ridge regression - built into borzoi (tbc)
- [ ] Validate against ENCODE standards
- [ ] Implement GTEx validation pipeline
#### Multi-omic Integration
Current goal: Create robust data transformation pipeline
- [ ] Proteome prediction (clei2block):
* Implement GTEx training pipeline
* Add multi-tissue support
* Create validation framework against CellModelPassport
- [ ] Metabolome generation (corto):
* Setup CCLE data integration
* Implement NCI-60 validation
- [ ] Immunome profiling:
* ~~Evaluate Ecotyper vs CIBERTSORTx~~ CIBERTSORTx incorporated within Ecotyper
* Integrate SPICA datasets
* Setup immune cell validation pipeline
## Part 2: Drug Discovery and Response
### Drug Development Tools
Current goal: Establish comprehensive drug analysis pipeline
- [ ] Molecule Processing:
* SELFIES library for biologics/peptides conversion
* Implement molecule validation checks
* Setup standardization pipeline
- [ ] Structure Analysis:
* DreamDock + ConPlex score pipeline
* LightDock for membrane binding
* Validation framework with crystal structures
### Binding Site Prediction
Current goal: Create consensus model for binding site prediction
- [ ] Benchmark tools:
* DiffDock implementation and testing
* Qvina2 evaluation
* P2Rank integration
* FPocket analysis
- [ ] Specific considerations:
* Allosteric site detection
* Multiple binding site handling
* Protein flexibility modeling
- [ ] Validation:
* BindingDB integration
* Crystal structure comparison pipeline
* Edge case testing suite
### Drug-Target Analysis
Current goal: Robust docking and interaction prediction
- [ ] Primary docking pipeline:
* Uni-mol integration
* DreamDock implementation
* Path4Drug integration for pathways
- [ ] Molecule type-specific handling:
* Small molecule pipeline
* Biologics pathway
* PROTACs specific analysis
* Prodrug processing
- [ ] Interaction analysis:
* Agonist vs antagonist classification
* Protein-protein interaction integration
* Chemical_checker for bioactivity signatures
### Chemical Property Prediction
Current goal: Comprehensive property prediction system
- [ ] Model implementation:
* Chemprop evaluation
* Soltrannet integration
* Custom ADMET model development
- [ ] Property coverage:
* Solubility prediction
* BBB penetration
* Chemical stability
* Metabolic processing
### Toxicity Prediction Pipeline
Current goal: Multi-faceted toxicity assessment system
- [ ] Core modules:
* Cardiotoxicity (ion channel) prediction
* Hepatotoxicity (Phase 1/2 proteins)
* Nephrotoxicity assessment
* Lung toxicity prediction
* Neurotoxicity (BBB criteria)
* Inflammatory response modeling
* Bleeding/clotting risk analysis
- [ ] Integration components:
* Human Protein Atlas tissue proportion estimation
* Reactome pathway analysis
* Industry model benchmarking
### Drug Response Analysis
Current goal: Integrated response prediction system
- [ ] Transcriptomic response:
* LINCS data integration
* Expression change prediction
* Tissue-specific effects
- [ ] Multi-omic response:
* Proteomic change modeling
* Metabolomic adjustment prediction
* Immune response profiling
- [ ] Special cases:
* Multi-drug combinations
* Time-dependent effects
* Population-specific responses
## Critical Dependencies & Requirements
| Category | Component | Status | Notes |
|----------|-----------|---------|--------|
| **External Data** | BindingDB | ✓ Available | Binding affinities |
| | LINCS | ✓ Available | Compound effects |
| | PharmGKB | ⏳ Pending | Variant annotations |
| | Human Cell Atlas | ⏳ Pending | Tissue-specific data |
| **Compute** | GPU Cluster | 🚧 Scaling | For enformer/basenji |
| | Storage | ✓ Configured | For variant data |
| | Distribution | ⏳ Planned | For processing |
## Validation Framework
| Dataset | Usage | Status | Notes |
|---------|--------|---------|--------|
| ENCODE | Transcriptomics | ✓ Ready | Primary validation |
| GTEx | Tissue-specific | ✓ Ready | E-MTAB-6814 |
| CCLE/GDSC2 | Cell lines | 🚧 In Progress | Cancer validation |
| TDC | ADMET | ⏳ Planned | Benchmark data |
| Cross-species | Conservation | ⏳ Planned | Evolutionary validation |
| Time-series | Metabolics | ⏳ Planned | Kinetic validation |
## Edge Cases & Special Considerations
### Complex Scenarios
| Scenario | Implementation Status | Handling Strategy |
|----------|---------------------|-------------------|
| Rare variants | 🚧 In Progress | Population frequency weighting |
| Multi-drug combinations | ⏳ Planned | Interaction matrix modeling |
| Time-dependent effects | ⏳ Planned | PK/PD time series modeling |
| Population specificity | 🚧 In Progress | Demographic stratification |
### Special Drug Classes
| Class | Special Requirements | Status |
|-------|---------------------|---------|
| Biologics | Membrane modeling, immunogenicity | ⏳ Planned |
| Prodrugs | Metabolite prediction, activation | 🚧 In Progress |
| Combination therapy | Interaction prediction, timing | ⏳ Planned |
| PROTACs | Protein degradation modeling | ⏳ Planned |
## Case Studies & Validation Examples
| Drug | Outcome | Learning Points | Implementation Status |
|------|---------|----------------|----------------------|
| Amcenestrant | Efficacy failure | Target validation importance | ✓ Integrated |
| Flupirtine | Liver toxicity | Metabolite prediction crucial | 🚧 In Progress |
| Ranitidine | NDMA formation | Chemical stability prediction | ⏳ Planned |
| Multi-drug Examples | Variable | Interaction modeling needed | ⏳ Planned |

5
app_filter/README.md Normal file
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@@ -0,0 +1,5 @@
Run command
```
vep --config vep.ini -i ${input_vcf} -o ${input_vcf.simpleName}_cosmic.vcf
```

56
app_filter/filter_transcriptome.py Normal file
View File

@@ -0,0 +1,56 @@
from argparse import ArgumentParser
import pandas as pd
import numpy as np
from pathlib import Path
def make_argparser():
parser = ArgumentParser(
description="Filter Transcriptome using mutated and non-mutated TPM values, and MANE dataset"
)
parser.add_argument(
"--mutated",
type=Path,
required=True,
help="The .csv file with mutated TPM."
)
parser.add_argument(
"--non-mutated",
type=Path,
required=True,
help="The .csv file with base (non-mutated) TPM"
)
parser.add_argument(
"--mane-data",
type=Path,
required=True,
help="The .tsv file with MANE data"
)
return parser
def main(mutated : Path, non_mutated : Path, mane_data : Path):
name = mutated.stem
df_mut = pd.read_csv(mutated)
df_nomut = pd.read_csv(non_mutated)
df_mane = pd.read_csv(mane_data, sep="\t")
df_mane["ENSG"] = [i.split('.')[0] for i in df_mane["Ensembl_Gene"]]
df_mane_map = df_mane[['symbol','ENSG']]
df_nomut_mapped = df_mane_map.merge(df_nomut, left_on='symbol', right_on='Unnamed: 0').dropna().drop_duplicates(subset=['symbol']).drop(["symbol", "Unnamed: 0"],axis=1)
df_merge = df_nomut_mapped.merge(df_mut, on="ENSG", suffixes=("_nomut","_mut"))
cols = df_mut.columns[1:]
df_res = pd.DataFrame({"ENSG": df_merge["ENSG"]} | {col:np.log2(df_merge[col + "_mut"] / df_merge[col + "_nomut"]) for col in cols})
df_res.to_csv(f"{name}_log2fc.csv", index=None)
if __name__ == "__main__":
parser = make_argparser()
args = parser.parse_args()
main(mutated=args.mutated, non_mutated=args.non_mutated, mane_data=args.mane_data)

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cache 1
dir_cache /data
assembly 'GRCh38'
offline 1
force_overwrite 1
custom file=/opt/vep/.vep/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz,short_name=COSMIC,format=vcf,type=exact,fields=LEGACY_ID%CNT
# Functional impact predictions
sift b # CALCULATE 1 - score
polyphen b # THESE TWO CAN BE AVERAGED
plugin REVEL,/opt/vep/.vep/REVEL/new_tabbed_revel_grch38.tsv.gz
# TODO: CALCUALTE THEIR L2 NORM
# plugin CADD,/opt/vep/.vep/CADD/GRCh38/whole_genome_SNVs.tsv.gz,/opt/vep/.vep/CADD/GRCh38/InDels.tsv.gz
# Clinical significance
check_existing
clinvar
# Allele frequencies
af
af_1kg
af_gnomade
af_gnomadg
max_af
# Additional useful flags
numbers
hgvs
symbol
canonical

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### Create reference file for borzoi-immun cibersortx step
import pandas as pd
MANE_data = pd.read_csv("MANE.GRCh38.v1.3.update.tsv", sep = '\t')
LM22_sourceGEP = pd.read_csv("LM22_sourceGEP.txt", sep = '\t')
MANE_data['ENSG'] = [i.split('.')[0] for i in MANE_data['Ensembl_Gene']]
mane_map = MANE_data[['symbol','ENSG']]
LM22_sourceGEP_ensg = mane_map.merge(LM22_sourceGEP, left_on='symbol', right_on='genesinput').dropna().drop_duplicates(subset=['symbol'])
LM22_sourceGEP_ensg = LM22_sourceGEP_ensg.drop(['symbol', 'genesinput'],axis = 1)
LM22_sourceGEP_ensg.to_csv('LM22_sourceGEP_ensg.txt', sep = '\t', index=False)

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docker-compose.yml Normal file
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services:
borzoi:
build:
context: .
dockerfile: Dockerfile_borzoi
image: harbor.cluster.omic.ai/omic/digital-patients/borzoi:latest
deploy:
resources:
reservations:
devices:
- driver: nvidia
count: all
capabilities: [gpu]
vcf2prot:
build:
context: .
dockerfile: Dockerfile_vcf2prot
image: harbor.cluster.omic.ai/omic/digital-patients/vcf2prot:latest
rna2protexpression:
build:
context: .
dockerfile: Dockerfile_rna2protexpression
image: harbor.cluster.omic.ai/omic/digital-patients/rna2protexpression:latest
corto:
build:
context: .
dockerfile: Dockerfile_corto
image: harbor.cluster.omic.ai/omic/digital-patients/corto:latest
ecotyper:
build:
context: .
dockerfile: Dockerfile_ecotyper
image: harbor.cluster.omic.ai/omic/digital-patients/ecotyper:latest
synthea:
build:
context: .
dockerfile: Dockerfile_synthea
image: harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf
vep:
build:
context: .
dockerfile: Dockerfile_vep
image: harbor.cluster.omic.ai/omic/digital-patients/vep:1.0.0
volumes:
- ./app_filter/sample:/sample
- /data/vep_data:/data
# export IMAGE_NAME=synthea:cudf && docker tag $IMAGE_NAME harbor.cluster.omic.ai/omic/digital-patients/$IMAGE_NAME && retry_command.sh docker --config ~/.config/bugra push harbor.cluster.omic.ai/omic/digital-patients/$IMAGE_NAME

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# access the current workspace
kubectl exec -it -n bioinformatics $(kubectl get pod -l app=digital-patient-nextflow -n bioinformatics | grep Run | awk '{ print $1 }') -- bash
nextflow run test.nf -profile k8s
# DEPRECATE: cleanup error pods in bioinformatics
kubectl get pod -n bioinformatics | grep -E "Pending|Error" | awk '{print $1}' | xargs -P 10 -I {} kubectl delete pod -n bioinformatics {}
# sync data (/data/bugra/similarity-search/utility/vec_db/nf_fingerptint) from node to workspace
kubectl delete -f k8s/job-copy-node-to-pvc.yaml; kubectl apply -f k8s/job-copy-node-to-pvc.yaml
# run the actual nextflow jobs
kubectl apply -f k8s/job-nextflow-digital-patient.yaml
# [WARNING] destroy the curent nextflow job
kubectl delete -f k8s/job-nextflow-digital-patient.yaml

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apiVersion: apps/v1
kind: Deployment
metadata:
name: digital-patient-nextflow
namespace: bioinformatics
spec:
progressDeadlineSeconds: 600
replicas: 1
revisionHistoryLimit: 10
selector:
matchLabels:
app: digital-patient-nextflow
strategy:
rollingUpdate:
maxSurge: 25%
maxUnavailable: 25%
type: RollingUpdate
template:
metadata:
creationTimestamp: null
labels:
app: digital-patient-nextflow
spec:
containers:
- command:
- sleep
- infinity
image: nextflow/nextflow:25.04.6
imagePullPolicy: IfNotPresent
name: nextflow
workingDir: /mnt/dreamdock-data/digital-patient-data
resources:
limits:
cpu: "2"
memory: 4Gi
requests:
cpu: "1"
memory: 2Gi
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /mnt/Avatar
name: avatar-new-volume
- mountPath: /mnt/dreamdock-data/
name: dreamdock-volume
dnsPolicy: ClusterFirst
restartPolicy: Always
schedulerName: default-scheduler
securityContext: {}
serviceAccount: nextflow-sa
serviceAccountName: nextflow-sa
terminationGracePeriodSeconds: 30
volumes:
- name: avatar-new-volume
persistentVolumeClaim:
claimName: avatar-new # CHANGE ME, RELATE TO nextflow.params.input
- name: dreamdock-volume
persistentVolumeClaim:
claimName: dreamdock-data # CHANGE ME, RELATE TO nextflow.params.input
# ---
# apiVersion: v1
# kind: PersistentVolumeClaim
# metadata:
# name: digital-patient-data
# namespace: bioinformatics
# spec:
# accessModes:
# - ReadWriteMany
# resources:
# requests:
# storage: 6000Gi
# storageClassName: truenas-nfs

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apiVersion: v1
kind: Pod
metadata:
name: gpu-test-pod
namespace: bioinformatics
spec:
restartPolicy: Never
nodeSelector:
gpu: 'yes'
gpu-type: 'geforce-rtx-3090'
containers:
- name: cuda-test
# Using a standard, lightweight NVIDIA CUDA image to test the runtime
image: nvidia/cuda:11.8.0-base-ubuntu22.04
command: ["nvidia-smi"]
resources:
limits:
nvidia.com/gpu: 1

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k8s/job-copy-node-to-pvc.yaml Normal file
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apiVersion: batch/v1
kind: Job
metadata:
name: job-data-copy-digital-patient-node-to-pvc
namespace: bioinformatics
spec:
backoffLimit: 6
completionMode: NonIndexed
completions: 1
manualSelector: false
parallelism: 1
suspend: false
template:
spec:
containers:
- args:
- |
apk add --no-cache rsync
mkdir -p /target
rsync -av --exclude .git/ --exclude .git-old/ --exclude work/ /source/ /target/digital-patient-data
command:
- /bin/sh
- -c
image: alpine
imagePullPolicy: Always
name: data-copy
resources: {}
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /source
name: k8s-node
- mountPath: /target
name: pvc-volume
dnsPolicy: ClusterFirst
nodeSelector:
kubernetes.io/hostname: k8s-node23
restartPolicy: Never
schedulerName: default-scheduler
securityContext: {}
terminationGracePeriodSeconds: 30
tolerations:
- effect: NoExecute
key: omic-app
operator: Equal
value: similarity-search
volumes:
- name: pvc-volume
persistentVolumeClaim:
claimName: dreamdock-data
- hostPath:
path: /data/bugra/digital_patient ## CHANGE ME
type: ""
name: k8s-node

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apiVersion: batch/v1
kind: Job
metadata:
name: job-nextflow-digital-patient
namespace: bioinformatics
spec:
backoffLimit: 1
completionMode: NonIndexed
completions: 1
manualSelector: false
parallelism: 1
podReplacementPolicy: TerminatingOrFailed
suspend: false
template:
spec:
containers:
- command:
- /bin/bash
- -c
- cd /mnt/dreamdock-data/digital-patient-data && nextflow run test.nf -profile k8s
image: nextflow/nextflow:25.04.6
imagePullPolicy: IfNotPresent
name: nextflow
resources:
limits:
cpu: "4"
memory: 8Gi
requests:
cpu: "2"
memory: 4Gi
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /mnt/Avatar
name: avatar-nas-volume
- mountPath: /mnt/dreamdock-data/
name: dreamdock-volume
dnsPolicy: ClusterFirst
restartPolicy: Never
schedulerName: default-scheduler
securityContext: {}
serviceAccount: nextflow-sa
serviceAccountName: nextflow-sa
terminationGracePeriodSeconds: 30
volumes:
- name: avatar-nas-volume
hostPath:
path: /mnt/Avatar-NAS
type: Directory
- name: dreamdock-volume
persistentVolumeClaim:
claimName: dreamdock-data # CHANGE ME, RELATE TO nextflow.params.input

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nextflow.enable.dsl=2
process FILTER_VCF {
memory 4.GB
container "${params.container_borzoi}"
containerOptions "${params.containerOptions}"
debug true
// maxForks 1
input:
path MANE
path vcf_filtered
output:
path "*.vcf" , emit: expression_output
script:
"""
#!/opt/conda/envs/borzoi/bin/python
#Filter VCF to extract only mutations in coding sequences plus 1000 upstream regulatory elements
import numpy as np
import pandas as pd
import pickle
#If ncbiRefSeq data need to be filtered in different manner change commented part
#This part is needed if we want to change ncbiRefSeq filtering
#column_names = [
# "bin", "name", "chrom", "strand", "txStart", "txEnd",
# "cdsStart", "cdsEnd", "exonCount", "exonStarts", "exonEnds",
# "score", "name2", "cdsStartStat", "cdsEndStat", "exonFrames"
#]
#ncbiRefSeq = pd.read_csv("{ncbiRefSeq}", sep='\t', names=column_names) #dollar sign is missing
##Get onyl protein coding genes (ncbiRefSeq['cdsStartStat'] != 'none')
#ncbiRefSeq = ncbiRefSeq[ncbiRefSeq['cdsStartStat'] != 'none']
##Remove duplicates
#ncbiRefSeq = ncbiRefSeq.drop_duplicates()
##Filter out isoforms for longest DNA sequenc. Filter by protein name and chromosom(differnet version of some shromosoms)
#ncbiRefSeq_filtered = []
#for i in np.unique(ncbiRefSeq['name2']):
# prot = ncbiRefSeq[ncbiRefSeq['name2'] == i]
# for j in np.unique(prot['chrom']):
# prot_chr = prot[prot['chrom'] == j]
# d1 = [prot_chr['txEnd'].astype(int).max(), prot_chr['txStart'].astype(int).min()] #get lowest starting position and maximum stop position
# max_len = np.argmax(prot_chr['txEnd'].astype(int) - prot_chr['txStart'].astype(int))
# position = prot_chr.iloc[max_len]
# position['txEnd'] = str(d1[0]) #end for isoform can be loaded from exonEnds
# position['txStart'] = str(d1[1]) #start for isoform can be loaded from exonStarts
# ncbiRefSeq_filtered.append(position)
#
#ncbiRefSeq = pd.DataFrame(ncbiRefSeq_filtered).reset_index().drop('index', axis = 1)
##protrin coding genes only 23314, all genes 48420
#Load ncbiRefSeq filtered
MANE_data = pd.read_csv("${MANE}", sep = '\t')
#Load vcf
with open("${vcf_filtered}") as f:
lines = f.readlines()
#Remove header/start of vcf file
vcf = []
for i in lines:
if i[:2] != '##':
vcf.append(i[:-1].split('\t'))
vcf = pd.DataFrame(vcf[1:], columns=vcf[0])
# Assuming 'vcf' and 'ncbiRefSeq' are already loaded DataFrames.
vcf['POS'] = vcf['POS'].astype(int)
vcf['#CHROM'] = vcf['#CHROM'].astype('category')
MANE_data['chrom'] = MANE_data['chrom'].astype('category')
MANE_data_renamed = MANE_data.rename(columns={'chrom': '#CHROM', 'chr_start': 'Start', 'chr_end': 'End', 'chr_strand': 'strand'})
relevant_chromosomes = vcf['#CHROM'].unique()
MANE_data_renamed = MANE_data_renamed[MANE_data_renamed['#CHROM'].isin(relevant_chromosomes)]
dataset = []
#Filter VCF
for chrom in relevant_chromosomes:
chrom_MANE = MANE_data_renamed[MANE_data_renamed['#CHROM'] == chrom]
# Find the indices in `vcf` that match the conditions for the current chromosome
for name, strand, start, end in chrom_MANE[['symbol', 'strand', 'Start', 'End']].itertuples(index=False):
condition = (vcf['#CHROM'] == chrom) & (vcf['POS'] >= start) & (vcf['POS'] <= end)
if np.sum(condition) != 0:
if strand == '+':
start_ = start - 1000
end_ = end
else:
end_ = end + 1000
start_ = start
dataset.append([[name, strand, start_, end_], np.array(vcf[condition]).tolist()])
#sort vcf by length
len_ = []
for vcf_entery in dataset:
len_.append(vcf_entery[0][3] - vcf_entery[0][2])
dataset = [dataset[index] for index in np.argsort(len_)]
#save vcf
#get name
patient_name = "${vcf_filtered}".split('/')[-1].split('_variants.vcf')[0]
with open(f"{patient_name}_rna_coding_vcf_with_mutations.vcf", "wb") as fp:
pickle.dump(dataset, fp)
"""
}
process PREDICT_EXPRESSION {
accelerator 1
memory 4.GB
container "${params.container_borzoi}"
label 'gpu_process'
// containerOptions "${params.containerOptions_borzoi}"
// debug true
maxForks 1 // TODO: COMMENT THIS IN KUBERNETES
input:
path vcf_filtered
path MANE
//path ncbiRefSeq_bigger
//path ncbiRefSeq_subset
output:
path "*_TPM.csv", emit: expression_output
script:
"""
#!/opt/conda/envs/borzoi/bin/python
#Predict expression based on mutation
import json
import os
import time
import warnings
import pickle
from itertools import compress
import h5py
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import numpy as np
import pandas as pd
import pysam
import pyfaidx
import tensorflow as tf
from baskerville import seqnn
from baskerville import gene as bgene
from baskerville import dna
import sys
sys.path.append( '/home/omic/borzoi' )
from examples.borzoi_helpers import *
#Load VCF and mutation files
#ncbiRefSeq_bigger = pd.read_csv("{ncbiRefSeq_bigger}")
#with open("{ncbiRefSeq_subset}", "rb") as fp:
# ncbiRefSeq_subset = pickle.load(fp)
prot_bigger = pd.read_csv("/home/omic/borzoi/prot_bigger.csv")
with open("/home/omic/borzoi/prot_subset.pickle", "rb") as fp:
prot_subset = pickle.load(fp)
with open("${vcf_filtered}", "rb") as fp:
vcf_file = pickle.load(fp)
MANE_data = pd.read_csv("${MANE}", sep = '\t')
batch_size = 4
#Define batch size and stop if batch size is to small for big transcripts
#min_batch_size = max(((np.array(ncbiRefSeq_bigger['txEnd']).astype('int')-np.array(ncbiRefSeq_bigger['txStart']).astype('int'))/524288).astype('int')+1)
#if min_batch_size > batch_size:
# print('batch size is ',batch_size,'and min_batch_size is ',min_batch_size)
# sys.exit('Batch size has to be bigger or same as number of big trnascripts split into chunks')
#Model configuration
params_file = '/home/omic/borzoi/examples/params_pred.json'
targets_file = '/home/omic/borzoi/examples/targets_gtex.txt' #Subset of targets_human.txt
n_folds = 1 #4 #To use only one model fold, set to 'n_folds = 1'. To use all four folds, set 'n_folds = 4'.
rc = True #Average across reverse-complement prediction
#Read model parameters
with open(params_file) as params_open :
params = json.load(params_open)
params_model = params['model']
params_train = params['train']
#Read targets
targets_df = pd.read_csv(targets_file, index_col=0, sep='\t')
target_index = targets_df.index
#Create local index of strand_pair (relative to sliced targets)
if rc :
strand_pair = targets_df.strand_pair
target_slice_dict = {ix : i for i, ix in enumerate(target_index.values.tolist())}
slice_pair = np.array([
target_slice_dict[ix] if ix in target_slice_dict else ix for ix in strand_pair.values.tolist()
], dtype='int32')
#Initialize model ensemble
models = []
for fold_ix in range(n_folds) :
model_file = "/home/omic/borzoi/saved_models/f" + str(fold_ix) + "/model0_best.h5"
seqnn_model = seqnn.SeqNN(params_model)
seqnn_model.restore(model_file, 0)
seqnn_model.build_slice(target_index)
if rc :
seqnn_model.strand_pair.append(slice_pair)
seqnn_model.build_ensemble(rc, [0]) #changed '0' to [0]
models.append(seqnn_model)
fasta_open = pysam.Fastafile('/home/omic/borzoi/hg38.fa')
#Create mutations(s) from WT
def create_mut(sequence_one_hot, poses, alts, start):
sequence_one_hot_mut = np.copy(sequence_one_hot_wt)
for pos, alt in zip(poses, alts) :
alt_ix = -1
if alt == 'A' :
alt_ix = 0
elif alt == 'C' :
alt_ix = 1
elif alt == 'G' :
alt_ix = 2
elif alt == 'T' :
alt_ix = 3
sequence_one_hot_mut[pos-start-1] = 0.
sequence_one_hot_mut[pos-start-1, alt_ix] = 1.
return sequence_one_hot_mut
#Make predictions/ run model
def predict_tracks(models, sequence_one_hot):
predicted_tracks = []
for fold_ix in range(len(models)):
yh = models[fold_ix](sequence_one_hot)[:, None, ...].astype("float16")
predicted_tracks.append(yh)
predicted_tracks = np.concatenate(predicted_tracks, axis=1)
return predicted_tracks
#calculate TPM from borzoi
def CalTPM(borzoi_data, start, cluster, prot_data, targets_df, plot = False):
TPM_list = []
#loop over all protrin in cluster
for i in range(len(cluster)):
#get exon start and end
ex_st = [(int(i)-(start + (32*16)))//32 for i in np.array(prot_data[prot_data['symbol'] == cluster[i]]['exonStarts'])[0].split(',')]
ex_en = [(int(i)-(start + (32*16)))//32 for i in np.array(prot_data[prot_data['symbol'] == cluster[i]]['exonEnds'])[0].split(',')]
#exon bool mask
exon_mask = np.zeros(borzoi_data.shape[-2])
for s,n in zip(ex_st,ex_en):
exon_mask = exon_mask + ((np.arange(borzoi_data.shape[-2]) >= s) & (np.arange(borzoi_data.shape[-2]) <= n))
#protrin TPM per person per tissue
TPM_per_tissue_replicates = np.sum(borzoi_data[:,exon_mask== 1], axis = 1)
#Plot proteins with exon marks if needed
if plot == True:
#Will plot only first adipose_tissue borzoi_data[0,:,x] change x for different tissue
plt.plot(borzoi_data[0,:,0])
plt.vlines(x = ex_st, ymin=0, ymax=3.5, colors='red', ls='--', lw=2, label='vline_multiple - full height')
plt.vlines(x = ex_en, ymin=0, ymax=3.5, colors='blue', ls='--', lw=2, label='vline_multiple - full height')
plt.xlim(ex_st[0]-100, ex_en[-1]+100)
plt.show()
#Get average for tissue replicates
TPM_per_tissue = [np.mean(i) for i in np.split(TPM_per_tissue_replicates[0], np.unique(targets_df['description'], return_index=True)[1][1:])]
TPM_list.append(TPM_per_tissue)
#cretae Datafreame
TPM_dataframe = pd.DataFrame(TPM_list,cluster,np.unique(targets_df['description'], return_index=True)[0])
return(TPM_dataframe)
#Protrin cluster list of list
protein_clusters = [np.array(i[2]) for i in prot_subset]
#Get all proteins from VCF
proteins_with_mutations = [i[0][0] for i in vcf_file]
proteins_with_mutations_working = proteins_with_mutations
TPM = []
#run until the expression of all proteins is predicted
while len(proteins_with_mutations_working) > 0:
TPM_dfs = []
sequences_one_hot_muts = []
st = []
cl = []
#append proteins to a list until equal to batch size if protein is smaller, if it's big just run borzoi for it (don't append)
while len(sequences_one_hot_muts) < batch_size and len(proteins_with_mutations_working) > 0:
#get work protein
protein = proteins_with_mutations_working[0]
#print(protein)
#get cluster
mask = [protein in i for i in protein_clusters]
cluster = list(compress(protein_clusters, mask))
#run borzoi for big proteins
if protein in np.array(prot_bigger['symbol']):
sequences_one_hot_muts_big = []
proteins_with_mutations_working = proteins_with_mutations_working[1:]
protein_data = prot_bigger[prot_bigger['symbol'] == protein]
prot_start = np.array(protein_data['chr_start']).astype('int')[0] - (16*32) - np.array(protein_data['chr_strand'] == '+')[0] * 1000
prot_end = np.array(protein_data['chr_end']).astype('int')[0] + (16*32) + np.array(protein_data['chr_strand'] == '-')[0] * 1000
mutations_ = np.array(list(compress(vcf_file, np.array(proteins_with_mutations) == protein))[0][1])
#only use one reference chromosom, in case mutations are maped to multiple chr/ cosenquence of lifover
mutations_ = mutations_[[i[0]== mutations_[0,0] for i in mutations_]]
chrom = mutations_[0,0]
all_poses = mutations_[:,1].astype('int')
all_alts = mutations_[:,4]
star = prot_start
st_big = star
while star < prot_end:
end = star + 524288
poses = all_poses[(all_poses > star) & (all_poses < end)]
alts = all_alts[(all_poses > star) & (all_poses < end)]
sequence_one_hot_wt = process_sequence(fasta_open, chrom, star, end, seq_len = 524288)
sequence_one_hot_mut = create_mut(sequence_one_hot_wt, poses, alts, star)
sequences_one_hot_muts_big.append(sequence_one_hot_mut)
star = end - (32*32)
sequences_one_hot_muts_big = np.array(sequences_one_hot_muts_big)
#if number of protein splits is begger than batch size
#print(sequences_one_hot_muts_big.shape)
if sequences_one_hot_muts_big.shape[0] > batch_size:
borzoi_pred_list = []
for seq_slice in np.array_split(sequences_one_hot_muts_big, np.ceil(sequences_one_hot_muts_big.shape[0]/batch_size)):
borzoi_pred_list.append(predict_tracks(models, seq_slice))
y_mut = np.concatenate(borzoi_pred_list)
else:
y_mut = predict_tracks(models, sequences_one_hot_muts_big)
y_mut = np.reshape(y_mut, [1,1,-1,89])
TPM.append(CalTPM(y_mut[0], st_big, [protein], MANE_data, targets_df))
#np.save('expression_predictions_%s.npy' %protein, y_mut)
else:
#append to a list of proteins to run
#get star and end of the cluste
star, end = (list(compress(prot_subset, mask))[0][:2])
#get mutated proteins in the cluster
mask = [i in cluster[0] for i in proteins_with_mutations_working]
proteins_in_cluster = list(compress(proteins_with_mutations_working, mask))
#remove cluster proteins from the ptoein list
proteins_with_mutations_working = list(compress(proteins_with_mutations_working, ~np.array(mask)))
#print(proteins_in_cluster)
mutations_ = [list(compress(vcf_file, [np.array(proteins_with_mutations) == i][0]))[0][1] for i in proteins_in_cluster]
mutations_ = np.concatenate([np.array(i) for i in mutations_],0)
#only use one reference chromosom, in case mutations are maped to multiple chr/ cosenquence of lifover
mutations_ = mutations_[[i[0]== mutations_[0,0] for i in mutations_]]
chrom = mutations_[0,0]
poses = mutations_[:,1].astype('int')
alts = mutations_[:,4]
sequence_one_hot_wt = process_sequence(fasta_open, chrom, star, end, seq_len = 524288)
sequence_one_hot_mut = create_mut(sequence_one_hot_wt, poses, alts, star)
sequences_one_hot_muts.append(sequence_one_hot_mut)
st.append(star)
cl.append(cluster)
### Test wt
#sequences_one_hot_muts.append(sequence_one_hot_wt)
###
sequences_one_hot_muts = np.array(sequences_one_hot_muts)
#run borzoi for smaller proteins, if list is empty isn't empty(can be empty for last step)
if sequences_one_hot_muts.shape != (0,):
y_mut = predict_tracks(models, sequences_one_hot_muts)
for i in range(len(y_mut)):
TPM_dfs.append(CalTPM(y_mut[i], st[i], cl[i][0], MANE_data, targets_df))
TPM_dfs = pd.concat(TPM_dfs)
TPM.append(TPM_dfs)
#np.save('expression_predictions_%s.npy' %protein, y_mut)
TPM = pd.concat(TPM)
#add RNA expression for positions with no mutations
#load reference genome expression
tpm_no_mut = pd.read_csv('/home/omic/borzoi/TPM_NO_MUTATIONS.csv',index_col=0)
#concat missing expression
TPM = pd.concat([TPM, tpm_no_mut.loc[list(set(tpm_no_mut.index) - set(TPM.index))]])
#change symbol to ENSG
TPM.index.names = ['RNA']
MANE_data['ENSG'] = [i.split('.')[0] for i in MANE_data['Ensembl_Gene']]
mane_map = MANE_data[['symbol','ENSG']]
TPM = mane_map.merge(TPM, left_on='symbol', right_on='RNA').dropna().drop_duplicates(subset=['symbol'])
#drop duplicates
TPM =TPM.drop_duplicates()
TPM = TPM.iloc[:,2:].set_index(TPM.iloc[:,1])
#save TPM
#get name
patient_name = "${vcf_filtered}".split('/')[-1].split('_rna_coding_vcf_with_mutations.vcf')[0]
TPM.to_csv(f'{patient_name}_TPM.csv')
gpu_stats = tf.config.experimental.get_memory_info('GPU:0')
print(f"Current VRAM usage: {gpu_stats['current'] / 1e9:.2f} GB")
print(f"Peak VRAM usage: {gpu_stats['peak'] / 1e9:.2f} GB")
"""
}
process CREATE_PROTEIN_CLUSTER {
container "${params.container_borzoi}"
containerOptions "${params.containerOptions}"
debug true
input:
path MANE
output:
path "prot_bigger.csv"
path "prot_subset.pickle"
script:
"""
#!/opt/conda/envs/borzoi/bin/python
# Use this if new RNAs transcripts need to be added to list of predicted RNAs
import numpy as np
import pandas as pd
import pickle
data = pd.read_csv("${MANE}", sep='\t')
data_subset = []
data_bigger = []
for ch in np.unique(data['chrom']):
data_working = data[data['chrom']==ch]
arg = np.argsort(np.array(data_working['chr_start']).astype('int'))
data_working = data_working.iloc[arg]
#protrin start poistion wirh regulatori elements negativ 1000 from start for + strand, plus 1000 from end for - strand
#add (16*32) as buffer because borzoi will cut tham
prot_start = np.array(data_working['chr_start']).astype('int') - (16*32) - np.array(data_working['chr_strand'] == '+') * 1000
prot_end = np.array(data_working['chr_end']).astype('int') + (16*32) + np.array(data_working['chr_strand'] == '-') * 1000
input_start = prot_start
input_end = input_start + 524288
while len(input_start) > 0:
st = input_start[0]
en = input_end[0]
mask = (prot_start >= st) & (prot_end <= en)
data_mask = data_working[mask]
data_subset.append([st, en, data_mask['symbol']])
#ncbiRefSeq_subset.append(ncbiRefSeq_working[mask])
if mask[0] == False:
data_bigger.append(data_working.iloc[0])
mask[0] = True
data_working = data_working[~mask]
arg = np.argsort(np.array(data_working['chr_start']).astype('int'))
data_working = data_working.iloc[arg]
prot_start = np.array(data_working['chr_start']).astype('int') - (16*32) - np.array(data_working['chr_strand'] == '+') * 1000
prot_end = np.array(data_working['chr_end']).astype('int') + (16*32) + np.array(data_working['chr_strand'] == '-') * 1000
input_start = prot_start
input_end = input_start + 524288
prot_bigger = pd.DataFrame(data_bigger)
prot_bigger.to_csv('prot_bigger.csv')
with open("prot_subset.pickle", "wb") as fp:
pickle.dump(data_subset, fp)
gpu_stats = tf.config.experimental.get_memory_info('GPU:0')
print(f"Current VRAM usage: {gpu_stats['current'] / 1e9:.2f} GB")
print(f"Peak VRAM usage: {gpu_stats['peak'] / 1e9:.2f} GB")
"""
}

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nextflow.enable.dsl=2
process CONVERT_TO_TXT {
memory 1.GB
container = "${params.container_ecotyper}"
containerOptions = "${params.containerOptions}"
publishDir "${params.ecotyper_outdir}/fractions", mode: 'copy'
// debug true
input:
path input_expression
output:
path '*.txt', emit: input_expression_txt
script:
"""
#!/bin/bash
name="\$(basename $input_expression .csv)"
sed -E 's/("([^"]*)")?,/\\2\\t/g' $input_expression > \${name}.txt
"""
}
process CIBERSORTx_FRACTIONS {
memory 4.GB
container = "${params.container_ecotyper}"
containerOptions = "${params.containerOptions}"
publishDir "${params.ecotyper_outdir}/fractions", mode: 'copy'
// debug true
input:
path input_expression, stageAs: 'input.txt'
path signature_matrix, stageAs: 'signature.txt'
output:
path "CIBERSORTx_Results.txt", emit: fractions_results
script:
"""
#!/bin/bash
set -ex
echo "Starting CIBERSORTx Fractions analysis..."
mkdir -p /src/data /src/outdir || { echo "Failed to create directories"; exit 1; }
# Prepare input files
echo "Preparing input files..."
sed 's/"//g' "input.txt" | tr -d '\\r' > /src/data/mixture.txt || { echo "Failed to prepare mixture file"; exit 1; }
sed 's/"//g' "signature.txt" | tr -d '\\r' > /src/data/signature.txt || { echo "Failed to prepare signature file"; exit 1; }
echo "Running CIBERSORTx Fractions"
/src/CIBERSORTxFractions \\
--mixture /src/data/mixture.txt \\
--sigmatrix /src/data/signature.txt \\
--outdir /src/outdir \\
--username "${params.cibersortx_username}" \\
--token "${params.cibersortx_token}"
if [ -f /src/outdir/CIBERSORTx_Results.txt ]; then
cp /src/outdir/CIBERSORTx_Results.txt .
else
echo "Error: CIBERSORTx_Results.txt not found"
ls -la /src/outdir/
exit 1
fi
"""
}
process CIBERSORTx_HIRES {
memory 1.GB
container = "${params.container_ecotyper}"
containerOptions = "${params.containerOptions}"
publishDir "${params.ecotyper_outdir}/hires", mode: 'copy'
// debug true
input:
path expression_matrix, stageAs: 'expression.txt'
path fractions_results, stageAs: 'fractions.txt'
path signature_matrix, stageAs: 'signature.txt'
output:
path "CIBERSORTx_HiRes_Matrix.txt", emit: hires_matrix
script:
"""
#!/opt/conda/envs/ecotyper/bin/python3
import pandas as pd
import numpy as np
import os
import glob
import subprocess
from pathlib import Path
# Create directories
print("Starting CIBERSORTx HiRes analysis...")
for dir_name in ['/src/data', '/src/outdir', '/src/intermediate', '/src/temp']:
Path(dir_name).mkdir(parents=True, exist_ok=True)
# Read input files
print("=== READING INPUT FILES ===")
mixture_df = pd.read_csv('expression.txt', sep='\t', index_col=0)
signature_df = pd.read_csv('signature.txt', sep='\t', index_col=0)
fractions_df = pd.read_csv('fractions.txt', sep='\t')
# Data quality checks
print("=== DATA QUALITY CHECKS ===")
def check_data_quality(df, name):
print(f"Checking {name}:")
print(f" NaN values: {df.isna().sum().sum()}")
print(f" Negative values: {(df < 0).sum().sum()}")
print(f" Zero values: {(df == 0).sum().sum()}")
print(f" Sample stats:")
print(df.describe().round(3))
check_data_quality(mixture_df, "Mixture")
check_data_quality(signature_df, "Signature")
# Clean and normalize gene names
print("=== PROCESSING GENE NAMES ===")
def normalize_gene_name(x):
return str(x).strip().upper()
mixture_df.index = mixture_df.index.map(normalize_gene_name)
signature_df.index = signature_df.index.map(normalize_gene_name)
# Find common genes with exact matching
print("=== FINDING COMMON GENES ===")
common_genes = sorted(set(mixture_df.index) & set(signature_df.index))
print(f"Number of common genes found: {len(common_genes)}")
if len(common_genes) == 0:
raise ValueError("No common genes found between mixture and signature files")
# Create aligned matrices with exact same gene order
mixture_filtered = mixture_df.loc[common_genes].copy()
signature_filtered = signature_df.loc[common_genes].copy()
# Verify gene order matches exactly
if not (mixture_filtered.index == signature_filtered.index).all():
raise ValueError("Gene order mismatch after filtering")
# Replace any NaN values with 0
mixture_filtered = mixture_filtered.fillna(0)
signature_filtered = signature_filtered.fillna(0)
# Prepare output files
print("=== PREPARING OUTPUT FILES ===")
# Save mixture file
mixture_filtered.index.name = 'genesinput'
mixture_filtered.to_csv('/src/data/mixture.txt', sep='\t', float_format='%.6f')
# Save signature file (no transpose)
signature_filtered.index.name = 'genesinput'
signature_filtered.to_csv('/src/data/signature.txt', sep='\t', float_format='%.6f')
# Process and save weights file
meta_cols = ['Mixture', 'P-value', 'Correlation', 'RMSE']
data_cols = [col for col in fractions_df.columns if col not in meta_cols]
weights_df = fractions_df[data_cols].copy()
weights_df.fillna(0, inplace=True)
weights_df.to_csv('/src/outdir/CIBERSORTxGEP_NA_Weights.txt', sep='\t', index=False)
# Print dimensions and verify
print("=== MATRIX VALIDATION ===")
print(f"Matrix dimensions:")
print(f" Mixture: {mixture_filtered.shape[0]} genes x {mixture_filtered.shape[1]} samples")
print(f" Signature: {signature_filtered.shape[0]} genes x {signature_filtered.shape[1]} samples")
print(f" Weights: {len(data_cols)} cols")
if len(data_cols) < 1:
raise ValueError(f"Invalid weights columns count: {len(data_cols)}")
# Additional validations
if not np.isfinite(mixture_filtered.values).all():
raise ValueError("Non-finite values found in mixture matrix")
if not np.isfinite(signature_filtered.values).all():
raise ValueError("Non-finite values found in signature matrix")
if not np.isfinite(weights_df.values).all():
raise ValueError("Non-finite values found in weights matrix")
window_size = len(data_cols)
print(f"Using window size: {window_size}")
# Run CIBERSORTx
print("=== RUNNING CIBERSORTX HIRES ===")
cmd = [
'/src/CIBERSORTxHiRes',
'--mixture', '/src/data/mixture.txt',
'--sigmatrix', '/src/data/signature.txt',
'--cibresults', '/src/outdir/CIBERSORTxGEP_NA_Weights.txt',
'--outdir', '/src/outdir',
'--window', str(window_size),
'--username', '${params.cibersortx_username}',
'--token', '${params.cibersortx_token}',
'--QN', 'true'
]
result = subprocess.run(cmd, check=True)
# List all files in output directory
print("=== CHECKING OUTPUT FILES ===")
output_dir = Path('/src/outdir')
print("Files in output directory:")
for f in output_dir.glob('*'):
print(f" {f.name} ({f.stat().st_size} bytes)")
# Try to find any file that might be our result
gep_files = list(output_dir.glob('*GEP*.txt'))
if not gep_files:
filtered_files = list(output_dir.glob('*Filtered*.txt'))
if filtered_files:
result_file = filtered_files[0]
else:
all_txt_files = list(output_dir.glob('*.txt'))
if all_txt_files:
result_file = max(all_txt_files, key=lambda x: x.stat().st_size)
else:
raise FileNotFoundError("No suitable output files found")
else:
result_file = gep_files[0]
print(f"Using result file: {result_file}")
subprocess.run(['cp', str(result_file), 'CIBERSORTx_HiRes_Matrix.txt'], check=True)
"""
}
process ADD_TISSUE_NAMES_TO_CIBERSORTX{
memory 1.GB
container = "${params.container_ecotyper}"
containerOptions = "${params.containerOptions}"
publishDir "${params.ecotyper_outdir}/hires", mode: 'copy'
// debug true
input:
path EXPRESSION_MATRIX
path CIBERSORTx_HIRES
output:
path '*_immune_cells.csv'
script:
"""
#!/opt/conda/envs/ecotyper/bin/python3
import pandas as pd
cibersort_df = pd.read_csv('${CIBERSORTx_HIRES}', sep='\t')
expression_df = pd.read_csv('${EXPRESSION_MATRIX}', sep='\t', index_col=0)
pat_name = '${EXPRESSION_MATRIX}'.split('_TPM.txt')[0]
tissue_name = [i.split(':')[1] for i in expression_df.columns]
cibersort_df = cibersort_df.set_index(pd.Index(tissue_name, dtype='str'))
cibersort_df.index.name = 'Tissues'
cibersort_df.to_csv(pat_name + '_immune_cells.csv')
"""
}

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nextflow.enable.dsl=2
process CORTO {
memory 1.GB
container "${params.container_corto}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
// debug true
// maxForks 1
stageInMode 'copy'
input:
path TPM
path regulon
// path TPM_ref
// Define output channels
output:
path "*_metabolome.csv", emit: csv_metabol
script:
"""
#!/usr/bin/Rscript
library(corto)
library(data.table)
TPM <- as.matrix(fread("$TPM"),rownames=1)
#TPM_ref <- as.matrix(fread("TPM_ref"),rownames=1) #dollar sign is missing
#try normalization; dont use
#TPM <- scale(TPM)
#TPM_log2 = log2(TPM + 1)
load("$regulon")
predicted<-mra(TPM, regulon=regulon)
#use this if we want to compare patients and reference TPM, data formet output is not csv -> work on data saving if needed
#predicted<-mra(TPM, path TPM_ref, regulon=regulon)
name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])], split = "_TPM.csv")[[1]][1]
name = paste(name, "_metabolome.csv", sep="")
write.csv(predicted, name)
"""
}

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nextflow.enable.dsl=2
// ==================== FILTER VARIANTS ====================
process FILTER_VARIANTS {
memory 16.GB
container "${params.container_synthea}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path vcf
output:
path "*_filtered_variants.vcf", emit: filtered_vcf
path "*_filtered_variants_summary.csv", emit: variants_summary
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import pandas as pd
import numpy as np
import sys
patient_name = "${vcf}".replace('.vcf', '')
print(f"Processing VCF file: ${vcf}", file=sys.stderr)
# Read VCF file header
header = []
with open("${vcf}") as f:
for line in f:
if line.startswith('#'):
header.append(line)
else:
break
print(f"Header has {len(header)} lines", file=sys.stderr)
# Count total variants first
total_variants = 0
with open("${vcf}") as f:
for line in f:
if not line.startswith('#'):
total_variants += 1
print(f"Total variants: {total_variants}", file=sys.stderr)
if total_variants == 0:
print("No variants found, creating empty output", file=sys.stderr)
# Create empty output files
with open(f"{patient_name}_filtered_variants.vcf", 'w') as f:
f.writelines(header)
pd.DataFrame(columns=['CHROM', 'POS', 'REF', 'ALT', 'QUAL']).to_csv(
f"{patient_name}_filtered_variants_summary.csv", index=False
)
else:
# Read VCF data in chunks to avoid memory issues
vcf_columns = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']
chunk_size = 100000
print(f"Reading VCF in chunks of {chunk_size}", file=sys.stderr)
# Read file and process in chunks
df_list = []
with open("${vcf}") as f:
chunk = []
for line in f:
if not line.startswith('#'):
chunk.append(line.strip().split('\\t'))
if len(chunk) >= chunk_size:
df_chunk = pd.DataFrame(chunk, columns=vcf_columns)
df_chunk['QUAL_numeric'] = pd.to_numeric(df_chunk['QUAL'], errors='coerce')
df_list.append(df_chunk[['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'QUAL_numeric', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']])
chunk = []
print(f"Processed {len(df_list) * chunk_size} variants", file=sys.stderr)
# Process remaining chunk
if chunk:
df_chunk = pd.DataFrame(chunk, columns=vcf_columns)
df_chunk['QUAL_numeric'] = pd.to_numeric(df_chunk['QUAL'], errors='coerce')
df_list.append(df_chunk[['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'QUAL_numeric', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']])
print(f"Concatenating {len(df_list)} chunks", file=sys.stderr)
df = pd.concat(df_list, ignore_index=True)
print(f"Sorting by QUAL score", file=sys.stderr)
# Sort by QUAL score (proxy for clinical significance)
df_sorted = df.sort_values('QUAL_numeric', ascending=False)
# Take top N variants
top_n = min(${params.top_n_variants}, len(df_sorted))
df_filtered = df_sorted.head(top_n)
print(f"Selected top {top_n} variants", file=sys.stderr)
# Write filtered VCF (keep original VCF columns only)
print(f"Writing filtered VCF", file=sys.stderr)
with open(f"{patient_name}_filtered_variants.vcf", 'w') as f:
f.writelines(header)
for _, row in df_filtered.iterrows():
vcf_line = '\\t'.join(str(row[col]) for col in vcf_columns) + '\\n'
f.write(vcf_line)
# Create summary CSV
print(f"Writing summary CSV", file=sys.stderr)
summary = df_filtered[['CHROM', 'POS', 'REF', 'ALT', 'QUAL_numeric']].copy()
summary.columns = ['CHROM', 'POS', 'REF', 'ALT', 'QUAL']
summary.to_csv(f"{patient_name}_filtered_variants_summary.csv", index=False)
print(f"Done!", file=sys.stderr)
"""
}
// ==================== FILTER TRANSCRIPTOME ====================
process FILTER_TRANSCRIPTOME {
memory 2.GB
container "${params.container_borzoi}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path tpm_file
output:
path "*_filtered_TPM.csv", emit: filtered_tpm
script:
"""
#!/opt/conda/envs/borzoi/bin/python
import pandas as pd
import numpy as np
patient_name = "${tpm_file}".replace('_TPM.csv', '')
# Read TPM data
df = pd.read_csv("${tpm_file}", index_col=0)
# Calculate mean expression across tissues
df['mean_expression'] = df.mean(axis=1)
# Calculate log2 fold change from median (as reference)
median_expr = df.drop('mean_expression', axis=1).median(axis=1)
df['log2FC'] = np.log2((df['mean_expression'] + 1) / (median_expr + 1))
# Filter: |log2FC| > 1.5
# Note: In production, you'd need proper control samples for statistical testing
df['abs_log2FC'] = abs(df['log2FC'])
df_filtered = df[df['abs_log2FC'] > ${params.transcriptome_log2fc_threshold}]
# Sort by absolute fold change and take top N
df_filtered = df_filtered.sort_values('abs_log2FC', ascending=False)
df_filtered = df_filtered.head(${params.top_n_genes})
# Remove helper columns
df_output = df_filtered.drop(['mean_expression', 'log2FC', 'abs_log2FC'], axis=1)
# Save filtered results
df_output.to_csv(f"{patient_name}_filtered_TPM.csv")
"""
}
// ==================== FILTER PROTEOME ====================
process FILTER_PROTEOME {
memory 2.GB
container "${params.container_rna2protexpression}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path protein_file
output:
path "*_filtered_Protein_Expression.csv", emit: filtered_proteins
script:
"""
#!/opt/conda/envs/rna2protexpresson/bin/python3
import pandas as pd
import numpy as np
patient_name = "${protein_file}".replace('_Protein_Expression_log2.csv', '')
# Read protein expression data
df = pd.read_csv("${protein_file}", index_col=0)
# Calculate mean expression across tissues
df['mean_expression'] = df.mean(axis=1)
# Calculate 75th percentile threshold
threshold_75 = df['mean_expression'].quantile(0.75)
# Filter: Expression > 75th percentile
df_filtered = df[df['mean_expression'] > threshold_75]
# Sort by expression level and take top N
df_filtered = df_filtered.sort_values('mean_expression', ascending=False)
df_filtered = df_filtered.head(${params.top_n_proteins})
# Remove helper column
df_output = df_filtered.drop('mean_expression', axis=1)
# Save filtered results
df_output.to_csv(f"{patient_name}_filtered_Protein_Expression.csv")
"""
}
// ==================== FILTER IMMUNE CELLS ====================
process FILTER_IMMUNE_CELLS {
memory 1.GB
container "${params.container_ecotyper}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path immune_file
output:
path "*_filtered_immune_cells.csv", emit: filtered_immune
script:
"""
#!/opt/conda/envs/ecotyper/bin/python3
import pandas as pd
patient_name = "${immune_file}".replace('_immune_cells.csv', '')
# Read immune cell data
df = pd.read_csv("${immune_file}", index_col=0)
df.to_csv(f"{patient_name}_filtered_immune_cells.csv")
"""
}
// ==================== FILTER METABOLOME ====================
process FILTER_METABOLOME {
memory 1.GB
container "${params.container_corto}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path metabolome_file
output:
path "*_filtered_metabolome.csv", emit: filtered_metabolome
script:
"""
#!/usr/bin/Rscript
library(data.table)
patient_name <- gsub("_metabolome.csv", "", "${metabolome_file}")
# Read metabolome data
df <- fread("${metabolome_file}")
# Assuming the data has columns: pathway, activity_score, p_value
# Adjust based on actual CORTO output format
# Filter: p-value < 0.05 (if p-value column exists)
if ("P_value" %in% colnames(df)) {
df_filtered <- df[df\$P_value < ${params.metabolome_pvalue_threshold}, ]
} else if ("p_value" %in% colnames(df)) {
df_filtered <- df[df\$p_value < ${params.metabolome_pvalue_threshold}, ]
} else {
df_filtered <- df
}
# Sort by activity score (absolute value)
if ("Activity_Score" %in% colnames(df_filtered)) {
df_filtered <- df_filtered[order(-abs(df_filtered\$Activity_Score)), ]
} else if (ncol(df_filtered) > 1) {
# If column names are different, sort by second column (assuming it's the score)
df_filtered <- df_filtered[order(-abs(df_filtered[[2]])), ]
}
# Take top N pathways
df_filtered <- head(df_filtered, ${params.top_n_metabolites})
# Save filtered results
fwrite(df_filtered, paste0(patient_name, "_filtered_metabolome.csv"))
"""
}
// ==================== FILTER MUTATED PROTEINS ====================
process FILTER_MUTATED_PROTEINS {
memory 2.GB
container "${params.container_vcf2prot}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path fasta_file
path filtered_vcf
output:
path "*_filtered_mutations.fasta", emit: filtered_fasta
script:
"""
#!/opt/conda/envs/vcf2prot/bin/python3
import re
patient_name = "${fasta_file}".replace('_transcript_id_mutations.fasta', '')
# Read filtered VCF to get list of positions to keep
filtered_positions = set()
with open("${filtered_vcf}") as f:
for line in f:
if not line.startswith('#'):
parts = line.strip().split('\\t')
if len(parts) >= 2:
filtered_positions.add(f"{parts[0]}:{parts[1]}")
# Read FASTA and filter based on mutations in filtered VCF
sequences = {}
current_header = None
current_seq = []
with open("${fasta_file}") as f:
for line in f:
if line.startswith('>'):
if current_header:
sequences[current_header] = ''.join(current_seq)
current_header = line.strip()
current_seq = []
else:
current_seq.append(line.strip())
if current_header:
sequences[current_header] = ''.join(current_seq)
# Write filtered FASTA (keep top N based on filtered variants)
with open(f"{patient_name}_filtered_mutations.fasta", 'w') as f:
count = 0
for header, seq in sequences.items():
if count >= ${params.top_n_variants}:
break
f.write(header + '\\n')
# Write sequence in 60 character lines
for i in range(0, len(seq), 60):
f.write(seq[i:i+60] + '\\n')
count += 1
"""
}
// ==================== CREATE SUMMARY REPORT ====================
process CREATE_SUMMARY_REPORT {
memory 1.GB
container "${params.container_synthea}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/filtered", mode: 'copy'
input:
path filtered_tpm
path filtered_proteins
path filtered_immune
path filtered_metabolome
path filtered_vcf
output:
path "*_summary_report.json"
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import pandas as pd
import json
patient_name = "${filtered_tpm}".replace('_filtered_TPM.csv', '')
summary = {
'patient_id': patient_name,
'filtering_params': {
'top_n_genes': ${params.top_n_genes},
'top_n_proteins': ${params.top_n_proteins},
'top_n_immune_cells': ${params.top_n_immune_cells},
'top_n_metabolites': ${params.top_n_metabolites},
'top_n_variants': ${params.top_n_variants}
},
'filtered_counts': {}
}
# Count filtered entries
try:
df = pd.read_csv("${filtered_tpm}", index_col=0)
summary['filtered_counts']['genes'] = len(df)
except:
summary['filtered_counts']['genes'] = 0
try:
df = pd.read_csv("${filtered_proteins}", index_col=0)
summary['filtered_counts']['proteins'] = len(df)
except:
summary['filtered_counts']['proteins'] = 0
try:
df = pd.read_csv("${filtered_immune}", index_col=0)
summary['filtered_counts']['immune_cell_types'] = len(df.columns)
except:
summary['filtered_counts']['immune_cell_types'] = 0
try:
df = pd.read_csv("${filtered_metabolome}")
summary['filtered_counts']['metabolic_pathways'] = len(df)
except:
summary['filtered_counts']['metabolic_pathways'] = 0
try:
with open("${filtered_vcf}") as f:
count = sum(1 for line in f if not line.startswith('#'))
summary['filtered_counts']['variants'] = count
except:
summary['filtered_counts']['variants'] = 0
# Save summary
with open(f"{patient_name}_summary_report.json", 'w') as f:
json.dump(summary, f, indent=2)
"""
}

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nextflow.enable.dsl=2
process PREDICT_EXPRESSION_NO_MUTATIONS {
container "${params.container_borzoi}"
containerOptions "${params.containerOptions}"
debug true
maxForks 1
input:
path MANE
output:
path "TPM_NO_MUTATIONS.csv", emit: expression_output
script:
"""
#!/opt/conda/envs/borzoi/bin/python
#Predict expression of reference genom
import json
import os
import time
import warnings
import pickle
from itertools import compress
import h5py
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import numpy as np
import pandas as pd
import pysam
import pyfaidx
import tensorflow as tf
from baskerville import seqnn
from baskerville import gene as bgene
from baskerville import dna
import sys
sys.path.append( '/home/omic/borzoi' )
from examples.borzoi_helpers import *
#Reference protein dna sequence from MANE dataset
prot_bigger = pd.read_csv("/home/omic/borzoi/prot_bigger.csv")
with open("/home/omic/borzoi/prot_subset.pickle", "rb") as fp:
prot_subset = pickle.load(fp)
MANE_data = pd.read_csv("${MANE}", sep = '\t')
batch_size = 4
#Model configuration
params_file = '/home/omic/borzoi/examples/params_pred.json'
targets_file = '/home/omic/borzoi/examples/targets_gtex.txt' #Subset of targets_human.txt
n_folds = 1 #4 #To use only one model fold, set to 'n_folds = 1'. To use all four folds, set 'n_folds = 4'.
rc = True #Average across reverse-complement prediction
#Read model parameters
with open(params_file) as params_open :
params = json.load(params_open)
params_model = params['model']
params_train = params['train']
#Read targets
targets_df = pd.read_csv(targets_file, index_col=0, sep='\t')
target_index = targets_df.index
#Create local index of strand_pair (relative to sliced targets)
if rc :
strand_pair = targets_df.strand_pair
target_slice_dict = {ix : i for i, ix in enumerate(target_index.values.tolist())}
slice_pair = np.array([
target_slice_dict[ix] if ix in target_slice_dict else ix for ix in strand_pair.values.tolist()
], dtype='int32')
#Initialize model ensemble
models = []
for fold_ix in range(n_folds) :
model_file = "/home/omic/borzoi/saved_models/f" + str(fold_ix) + "/model0_best.h5"
seqnn_model = seqnn.SeqNN(params_model)
seqnn_model.restore(model_file, 0)
seqnn_model.build_slice(target_index)
if rc :
seqnn_model.strand_pair.append(slice_pair)
seqnn_model.build_ensemble(rc, [0]) #changed '0' to [0]
models.append(seqnn_model)
fasta_open = pysam.Fastafile('/home/omic/borzoi/hg38.fa')
#Make predictions/ run model
def predict_tracks(models, sequence_one_hot):
predicted_tracks = []
for fold_ix in range(len(models)):
yh = models[fold_ix](sequence_one_hot)[:, None, ...].astype("float16")
predicted_tracks.append(yh)
predicted_tracks = np.concatenate(predicted_tracks, axis=1)
return predicted_tracks
#calculate TPM from borzoi
def CalTPM(borzoi_data, start, cluster, prot_data, targets_df, plot = False):
TPM_list = []
#loop over all protrin in cluster
for i in range(len(cluster)):
#get exon start and end
ex_st = [(int(i)-(start + (32*16)))//32 for i in np.array(prot_data[prot_data['symbol'] == cluster[i]]['exonStarts'])[0].split(',')]
ex_en = [(int(i)-(start + (32*16)))//32 for i in np.array(prot_data[prot_data['symbol'] == cluster[i]]['exonEnds'])[0].split(',')]
#exon bool mask
exon_mask = np.zeros(borzoi_data.shape[-2])
for s,n in zip(ex_st,ex_en):
exon_mask = exon_mask + ((np.arange(borzoi_data.shape[-2]) >= s) & (np.arange(borzoi_data.shape[-2]) <= n))
#protrin TPM per person per tissue
TPM_per_tissue_replicates = np.sum(borzoi_data[:,exon_mask== 1], axis = 1)
#Plot proteins with exon marks if needed
if plot == True:
#Will plot only first adipose_tissue borzoi_data[0,:,x] change x for different tissue
plt.plot(borzoi_data[0,:,0])
plt.vlines(x = ex_st, ymin=0, ymax=3.5, colors='red', ls='--', lw=2, label='vline_multiple - full height')
plt.vlines(x = ex_en, ymin=0, ymax=3.5, colors='blue', ls='--', lw=2, label='vline_multiple - full height')
plt.xlim(ex_st[0]-100, ex_en[-1]+100)
plt.show()
#Get average for tissue replicates
TPM_per_tissue = [np.mean(i) for i in np.split(TPM_per_tissue_replicates[0], np.unique(targets_df['description'], return_index=True)[1][1:])]
TPM_list.append(TPM_per_tissue)
#cretae Datafreame
TPM_dataframe = pd.DataFrame(TPM_list,cluster,np.unique(targets_df['description'], return_index=True)[0])
return(TPM_dataframe)
#Protrin cluster list of list
protein_clusters = [np.array(i[2]) for i in prot_subset]
#all proroteins present in dataset
all_reference_proteins = list(pd.concat([pd.concat([i[-1] for i in prot_subset]), prot_bigger['symbol']]))
#use variable names from mutation
proteins_with_mutations = all_reference_proteins
proteins_with_mutations_working = proteins_with_mutations
TPM = []
#run until the expression of all proteins is predicted
while len(proteins_with_mutations_working) > 0:
TPM_dfs = []
sequences_one_hot_muts = []
st = []
cl = []
#append proteins to a list until equal to batch size if protein is smaller, if it's big just run borzoi for it (don't append)
while len(sequences_one_hot_muts) < batch_size and len(proteins_with_mutations_working) > 0:
#get work protein
protein = proteins_with_mutations_working[0]
#print(protein)
#get cluster
mask = [protein in i for i in protein_clusters]
cluster = list(compress(protein_clusters, mask))
#run borzoi for big proteins
if protein in np.array(prot_bigger['symbol']):
sequences_one_hot_muts_big = []
proteins_with_mutations_working = proteins_with_mutations_working[1:]
protein_data = prot_bigger[prot_bigger['symbol'] == protein]
prot_start = np.array(protein_data['chr_start']).astype('int')[0] - (16*32) - np.array(protein_data['chr_strand'] == '+')[0] * 1000
prot_end = np.array(protein_data['chr_end']).astype('int')[0] + (16*32) + np.array(protein_data['chr_strand'] == '-')[0] * 1000
chrom = protein_data.iloc[0]['chrom'].split('_')[0]
star = prot_start
st_big = star
while star < prot_end:
end = star + 524288
sequence_one_hot_wt = process_sequence(fasta_open, chrom, star, end, seq_len = 524288)
sequences_one_hot_muts_big.append(sequence_one_hot_wt)
star = end - (32*32)
sequences_one_hot_muts_big = np.array(sequences_one_hot_muts_big)
#if number of protein splits is begger than batch size
#print(sequences_one_hot_muts_big.shape)
if sequences_one_hot_muts_big.shape[0] > batch_size:
borzoi_pred_list = []
for seq_slice in np.array_split(sequences_one_hot_muts_big, np.ceil(sequences_one_hot_muts_big.shape[0]/batch_size)):
borzoi_pred_list.append(predict_tracks(models, seq_slice))
y_mut = np.concatenate(borzoi_pred_list)
else:
y_mut = predict_tracks(models, sequences_one_hot_muts_big)
y_mut = np.reshape(y_mut, [1,1,-1,89])
TPM.append(CalTPM(y_mut[0], st_big, [protein], MANE_data, targets_df))
#np.save('expression_predictions_%s.npy' %protein, y_mut)
else:
#append to a list of proteins to run
#get star and end of the cluste
star, end = (list(compress(prot_subset, mask))[0][:2])
#get mutated proteins in the cluster
mask = [i in cluster[0] for i in proteins_with_mutations_working]
proteins_in_cluster = list(compress(proteins_with_mutations_working, mask))
#remove cluster proteins from the ptoein list
proteins_with_mutations_working = list(compress(proteins_with_mutations_working, ~np.array(mask)))
chrom = MANE_data[MANE_data['symbol'] == proteins_in_cluster[0]].iloc[0]['chrom'].split('_')[0]
sequence_one_hot_wt = process_sequence(fasta_open, chrom, star, end, seq_len = 524288)
sequences_one_hot_muts.append(sequence_one_hot_wt)
st.append(star)
cl.append(cluster)
### Test wt
#sequences_one_hot_muts.append(sequence_one_hot_wt)
###
sequences_one_hot_muts = np.array(sequences_one_hot_muts)
#run borzoi for smaller proteins, if list is empty isn't empty(can be empty for last step)
if sequences_one_hot_muts.shape != (0,):
y_mut = predict_tracks(models, sequences_one_hot_muts)
for i in range(len(y_mut)):
TPM_dfs.append(CalTPM(y_mut[i], st[i], cl[i][0], MANE_data, targets_df))
TPM_dfs = pd.concat(TPM_dfs)
TPM.append(TPM_dfs)
#np.save('expression_predictions_%s.npy' %protein, y_mut)
TPM = pd.concat(TPM)
TPM.to_csv('TPM_NO_MUTATIONS.csv')
"""
}

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nextflow.enable.dsl=2
process RNA2PROTEXPRESSION {
memory 2.GB
accelerator 1
container "${params.container_rna2protexpression}"
label 'gpu_process'
//publishDir "${params.outdir_rna2protexpression}", mode: 'copy'
// debug true
// maxForks 1
input:
path borzoi_tpm
output:
path "*Protein_Expression_log2.csv", emit: protrin_expression_scores
script:
"""
. activate rna2protexpresson
python3 /home/omic/rna2protexpression/rna2protexpression.py --borzoi_ouput ${borzoi_tpm}
"""
}

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nextflow.enable.dsl=2
process generate_patients {
container "${params.container_synthea}"
containerOptions "$params.containerOptions_synthea"
//publishDir "${params.outdir}/patients", mode: 'copy'
// echo true
// errorStrategy 'ignore'
output:
tuple path('*/patients.csv'), path('*/conditions.csv'), emit: patient_tuple
path "*"
script:
"""
workdir=`pwd`
cd /synthea
./run_synthea -p ${params.n_pat} -a ${params.age} --exporter.csv.export true
cd /synthea/output
cp -r * \$workdir
"""
}
process get_disease_stats_no_patients {
memory 1.GB
accelerator 1
label 'gpu_process'
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
// echo true
input:
path pheno_store
path imputed_store
output:
tuple path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import pandas as pd
import subprocess
import os.path
from pathlib import Path
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
from os import system
system("ls -alh")
system("ls ${imputed_store} | head")
system("ls -alh /mnt/Avatar")
df_meta = pd.read_csv('${pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'], engine='python')
imputed_dir = Path('${imputed_store}')
for target in '${params.disease}'.replace("[", "").replace("]", "").replace(" ", "").split(','):
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne(target , df_meta['phenotype_description'], score_cutoff=80)
#print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz').is_file():
ukbb_var_m = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_m), "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.male.tsv', f'{ukbb_id}_male.tsv'])
elif (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz').is_file():
ukbb_var_m = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_m), "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv', f'{ukbb_id}_male.tsv'])
elif (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz').is_file():
ukbb_var_m = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_m), "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.female.tsv', f'{ukbb_id}_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz').is_file():
ukbb_var_f = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = f'{ukbb_id}.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_f), "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.female.tsv', f'{ukbb_id}_female.tsv'])
elif (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz').is_file():
ukbb_var_f = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_f), "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.both_sexes.tsv', f'{ukbb_id}_female.tsv'])
elif (imputed_dir / f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz').is_file():
ukbb_var_f = imputed_dir / f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = f'{ukbb_id}.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", str(ukbb_var_f), "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", f'{ukbb_id}.gwas.imputed_v3.male.tsv', f'{ukbb_id}_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process get_disease_stats_cudf {
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
echo true
input:
tuple path(pat_csv), path(cond_csv)
path pheno_store
output:
tuple path(pat_csv), path(cond_csv), path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
#import pandas as pd
import cudf as pd
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
import numpy as np
import subprocess
import os.path
################## IMPORT SYNTHETIC PATIENTS ##############################################
## conditions, used to find the right imputed variant file
df_cond = pd.read_csv('${cond_csv}', delim_whitespace=False)
## patients
df_pat = pd.read_csv('${pat_csv}', delim_whitespace=False)
try:
df_pat_m = df_pat.loc[df_pat['GENDER'] == 'M']
except:
'No men in dataset'
try:
df_pat_f = df_pat.loc[df_pat['GENDER'] == 'F']
except:
'No women in dataset'
try:
df_pat_bs = df_pat.loc[df_pat['GENDER'] == '']
except:
'No intersex/undefined sex in dataset'
df_meta = pd.read_csv('${pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'])
print(df_meta)
## find variant file associated with condition - need the patient's sex m/f/other or unknown = both_sexes - add sex to condition table based on patient id
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne('${params.disease}', df_meta['phenotype_description'].to_pandas(), score_cutoff=80)
if not ukbb_cond:
raise ValueError(f"No match found for disease '${params.disease}' with score >= 80")
print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process generate_m_variants_cudf {
accelerator 1
memory 6.GB
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
// echo true
maxForks 1
input:
tuple path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: m_var
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
def process_variants(target_file):
# Create gzip directory if it doesn't exist
os.makedirs('gzip', exist_ok=True)
# Copy and compress file
subprocess.run(['cp', target_file, 'gzip/'], check=True)
subprocess.run(['gzip', 'gzip/' + target_file], check=True)
print(f"Processing {target_file}.gz")
# Read the compressed file
df_var_m = pd.read_csv('gzip/' + target_file + '.gz', sep='\\t', header=0)
################## GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
##read variants
df_var = df_var_m
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr'] = df_var['chr'].astype('str')
df_var['pos'] = df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
# Perform the operation on host memory
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = df_var_all[['minor_allele','major_allele']].to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] = arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
output_file = f"{target_file.split('.')[0]}_patient_{p}_variants.csv"
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['chr','pos']).sort_index()
df_var_final.to_csv(output_file, index=False)
# Main execution
for target in '${dis_var_m}'.split():
try:
if not os.path.exists(target):
raise FileNotFoundError(f"Input file {target} does not exist")
process_variants(target)
except FileNotFoundError as e:
print(f"Error: {e}")
raise
except Exception as e:
print(f"Error processing {target}: {str(e)}")
raise
"""
}
process generate_f_variants_cudf {
memory 6.GB
accelerator 1
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
maxForks 1
echo true
input:
tuple path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: f_var
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
def process_variants(target_file):
# Create gzip directory if it doesn't exist
os.makedirs('gzip', exist_ok=True)
# Copy and compress file
subprocess.run(['cp', target_file, 'gzip/'], check=True)
subprocess.run(['gzip', 'gzip/' + target_file], check=True)
print(f"Processing {target_file}.gz")
# Read the compressed file
df_var_f = pd.read_csv('gzip/' + target_file + '.gz', sep='\\t', header=0)
##################### GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
## read variant data
df_var = df_var_f
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr'] = df_var['chr'].astype('str')
df_var['pos'] = df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = pd.DataFrame(data=df_var_all, columns=['minor_allele','major_allele']).to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] = arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['chr','pos']).sort_index()
output_file = f"{target_file.split('.')[0]}_patient_{p}_variants.csv"
df_var_final.to_csv(output_file, index=False)
# Main execution
for target in '${dis_var_f}'.split():
try:
if not os.path.exists(target):
raise FileNotFoundError(f"Input file {target} does not exist")
process_variants(target)
except FileNotFoundError as e:
print(f"Error: {e}")
raise
except Exception as e:
print(f"Error processing {target}: {str(e)}")
raise
"""
}
process generate_m_healthy_cudf {
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: m_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.male.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XY'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final['chr'] = [i.split('chr')[-1] for i in df_var_final.to_pandas()['chr']]
df_var_final.to_csv('healthy_male_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process generate_f_healthy_cudf {
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: f_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.female.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XX'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final['chr'] = [i.split('chr')[-1] for i in df_var_final.to_pandas()['chr']]
df_var_final.to_csv('healthy_female_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process make_vcfs {
memory 15.GB
container "$params.container_synthea"
containerOptions "$params.containerOptions_synthea"
//publishDir "${params.outdir}/variants_vcfs", mode: 'copy'
// echo true
maxForks 1
input:
path patient_vars
path support_dir
output:
path "${patient_vars.baseName}.vcf", emit: patient_vcfs
//path "${patient_vars.baseName}.vcf.gz", emit: patient_gz
//path "${patient_vars.baseName}.vcf.gz.tbi", emit: patient_index
//path "${patient_vars.baseName}_filt.csv", emit: filtered_csv
script:
"""
## only print disease-associated variants not found in the ref/major allele position as they will already be covered by the ref genome
#I don't think this is correct \$16 == \$18 cuz we changed csv file format
#it only removes first line from csv
awk '\$16 == \$18 { print \$0 }' ${patient_vars} | tail -n +2 > ${patient_vars.baseName}_filt.csv
## copy the variant template to the workdir
cp ${support_dir}/vcf/vcf_template.vcf .
## print the filtered variants to vcf format
printf "#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\tNA00001" >> vcf_template.vcf
printf "\\n" >> vcf_template.vcf
awk -F',' '{print "chr"\$1,\$2,".",\$3,\$4,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print "chr"\$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print \$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
# sort the genome karyotypically (in chromosomal order) and index
#files are sorted already just for security
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar SortVcf -I vcf_template.vcf -O ${patient_vars.baseName}_sorted.vcf
#Liftover form 19 to 38 standard
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar LiftoverVcf -I ${patient_vars.baseName}_sorted.vcf -O ${patient_vars.baseName}.vcf -C ${support_dir}/ucsc-liftover/hg19ToHg38.over.chain.gz -REJECT rejected_variants.vcf -R ${support_dir}/genome/hg38.fa
#change this part to save on memory usage
#bgzip < ${patient_vars.baseName}.vcf > ${patient_vars.baseName}.vcf.gz
#gatk IndexFeatureFile -I ${patient_vars.baseName}.vcf.gz
#delete unnecessary files
rm vcf_template.vcf
rm ${patient_vars.baseName}_filt.csv
rm ${patient_vars.baseName}_sorted.vcf
rm rejected_variants.vcf
rm *vcf.idx
"""
}

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main_synthea.nf.bk Normal file
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nextflow.enable.dsl=2
process generate_patients {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/patients", mode: 'copy'
echo true
// errorStrategy 'ignore'
output:
tuple path('*/patients.csv'), path('*/conditions.csv'), emit: patient_tuple
path "*"
script:
"""
workdir=`pwd`
cd /synthea
./run_synthea -p ${params.n_pat} -a ${params.age} ${params.state} ${params.city} --exporter.csv.export true
cd /synthea/output
cp -r * \$workdir
"""
}
process get_disease_stats_no_patients {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
echo true
output:
tuple path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import pandas as pd
import subprocess
import os.path
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
df_meta = pd.read_csv('${params.pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'], engine='python')
for target in '${params.disease}'.replace("[", "").replace("]", "").replace(" ", "").split(','):
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne(target , df_meta['phenotype_description'], score_cutoff=80)
#print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process get_disease_stats_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
echo true
input:
tuple path(pat_csv), path(cond_csv)
output:
tuple path(pat_csv), path(cond_csv), path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
#import pandas as pd
import cudf as pd
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
import numpy as np
import subprocess
import os.path
################## IMPORT SYNTHETIC PATIENTS ##############################################
## conditions, used to find the right imputed variant file
df_cond = pd.read_csv('${cond_csv}', delim_whitespace=False)
## patients
df_pat = pd.read_csv('${pat_csv}', delim_whitespace=False)
try:
df_pat_m = df_pat.loc[df_pat['GENDER'] == 'M']
except:
'No men in dataset'
try:
df_pat_f = df_pat.loc[df_pat['GENDER'] == 'F']
except:
'No women in dataset'
try:
df_pat_bs = df_pat.loc[df_pat['GENDER'] == '']
except:
'No intersex/undefined sex in dataset'
df_meta = pd.read_csv('${params.pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'])
print(df_meta)
## find variant file associated with condition - need the patient's sex m/f/other or unknown = both_sexes - add sex to condition table based on patient id
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne('${params.disease}', df_meta['phenotype_description'].to_pandas(), score_cutoff=80)
print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process generate_m_variants_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/variants", mode: 'copy'
//errorStrategy 'ignore'
echo true
// memory '15.0 GB'
maxForks 1
input:
tuple path(dis_var_f), path(dis_var_m)
//tuple path(pat_csv), path(cond_csv), path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: m_var
//path "selected_proteins.txt", emit: proteins
//path "selected_proteins_liftover_m.bed", emit: m_bed
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
for target in '${dis_var_m}'.split(" "):
try:
subprocess.run(['mkdir', 'gzip'])
subprocess.run(['cp', target, 'gzip/'])
subprocess.run(['gzip', 'gzip/' + target])
print(target,'.gz')
df_var_m = pd.read_csv('gzip/' + target + '.gz', sep='\\t', header=0)
except:
print("the male variant file does not exist")
################## GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
##read variantes
df_var = df_var_m
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr']=df_var['chr'].astype('str')
df_var['pos']=df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
# Perform the operation on host memory
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = df_var_all[['minor_allele','major_allele']].to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
df_var_final.to_csv(target.split('.')[0] + '_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process generate_f_variants_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/variants", mode: 'copy'
maxForks 1
//errorStrategy 'ignore'
echo true
input:
tuple path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: f_var
//path "selected_proteins.txt", emit: proteins
//path "selected_proteins_liftover_f.bed", emit: f_bed
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
for target in '${dis_var_f}'.split(" "):
try:
subprocess.run(['mkdir', 'gzip'])
subprocess.run(['cp', target, 'gzip/'])
subprocess.run(['gzip', 'gzip/' + target])
print(target,'.gz')
df_var_f = pd.read_csv('gzip/' + target + '.gz', sep='\\t', header=0)
except:
print("the female variant file does not exist")
##################### GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
## read variant data
df_var = df_var_f
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr']=df_var['chr'].astype('str')
df_var['pos']=df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = pd.DataFrame(data=df_var_all, columns=['minor_allele','major_allele']).to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
df_var_final.to_csv(target.split('.')[0] + '_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process generate_m_healthy_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: m_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.male.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XY'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final.to_csv('healthy_male_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process generate_f_healthy_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: f_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.female.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XX'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final.to_csv('healthy_female_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process make_vcfs {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/variants_vcfs", mode: 'copy'
echo true
maxForks 1
input:
path patient_vars
output:
path "${patient_vars.baseName}.vcf", emit: patient_vcfs
//path "${patient_vars.baseName}.vcf.gz", emit: patient_gz
//path "${patient_vars.baseName}.vcf.gz.tbi", emit: patient_index
//path "${patient_vars.baseName}_filt.csv", emit: filtered_csv
script:
"""
## only print disease-associated variants not found in the ref/major allele position as they will already be covered by the ref genome
#I don't think this is correct \$16 == \$18 cuz we changed csv file format
#it only removes first line from csv
awk '\$16 == \$18 { print \$0 }' ${patient_vars} | tail -n +2 > ${patient_vars.baseName}_filt.csv
## copy the variant template to the workdir
cp /mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf .
## print the filtered variants to vcf format
printf "#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\tNA00001" >> vcf_template.vcf
printf "\\n" >> vcf_template.vcf
awk -F',' '{print "chr"\$1,\$2,".",\$3,\$4,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print "chr"\$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print \$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
# sort the genome karyotypically (in chromosomal order) and index
#files are sorted already just for security
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar SortVcf -I vcf_template.vcf -O ${patient_vars.baseName}_sorted.vcf
#Liftover form 19 to 38 standard
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar LiftoverVcf -I ${patient_vars.baseName}_sorted.vcf -O ${patient_vars.baseName}.vcf -C /mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz -REJECT rejected_variants.vcf -R /mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa
#change this part to save on memory usage
#bgzip < ${patient_vars.baseName}.vcf > ${patient_vars.baseName}.vcf.gz
#gatk IndexFeatureFile -I ${patient_vars.baseName}.vcf.gz
#delete unnecessary files
rm vcf_template.vcf
rm ${patient_vars.baseName}_filt.csv
rm ${patient_vars.baseName}_sorted.vcf
rm rejected_variants.vcf
rm *vcf.idx
"""
}

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nextflow.enable.dsl=2
process generate_patients {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/patients", mode: 'copy'
// echo true
// errorStrategy 'ignore'
output:
tuple path('*/patients.csv'), path('*/conditions.csv'), emit: patient_tuple
path "*"
script:
"""
workdir=`pwd`
cd /synthea
./run_synthea -p ${params.n_pat} -a ${params.age} ${params.state} ${params.city} --exporter.csv.export true
cd /synthea/output
cp -r * \$workdir
"""
}
process get_disease_stats_no_patients {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
echo true
output:
tuple path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import pandas as pd
import subprocess
import os.path
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
df_meta = pd.read_csv('${params.pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'], engine='python')
for target in '${params.disease}'.replace("[", "").replace("]", "").replace(" ", "").split(','):
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne(target , df_meta['phenotype_description'], score_cutoff=80)
#print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process get_disease_stats_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
echo true
input:
tuple path(pat_csv), path(cond_csv)
output:
tuple path(pat_csv), path(cond_csv), path("*_female.tsv"), path("*_male.tsv")
script:
"""
#!/opt/conda/envs/synthea/bin/python3
#import pandas as pd
import cudf as pd
from fuzzywuzzy import fuzz
from fuzzywuzzy import process
import numpy as np
import subprocess
import os.path
################## IMPORT SYNTHETIC PATIENTS ##############################################
## conditions, used to find the right imputed variant file
df_cond = pd.read_csv('${cond_csv}', delim_whitespace=False)
## patients
df_pat = pd.read_csv('${pat_csv}', delim_whitespace=False)
try:
df_pat_m = df_pat.loc[df_pat['GENDER'] == 'M']
except:
'No men in dataset'
try:
df_pat_f = df_pat.loc[df_pat['GENDER'] == 'F']
except:
'No women in dataset'
try:
df_pat_bs = df_pat.loc[df_pat['GENDER'] == '']
except:
'No intersex/undefined sex in dataset'
df_meta = pd.read_csv('${params.pheno_store}', sep=',', delim_whitespace=False, header=None, names=['phenotype_code', 'phenotype_description', 'sex', 'file'])
print(df_meta)
## find variant file associated with condition - need the patient's sex m/f/other or unknown = both_sexes - add sex to condition table based on patient id
# lookup ukbb condition from metadata using fuzzy matching
ukbb_cond = process.extractOne('${params.disease}', df_meta['phenotype_description'].to_pandas(), score_cutoff=80)
if not ukbb_cond:
raise ValueError(f"No match found for disease '${params.disease}' with score >= 80")
print(ukbb_cond)
ukbb_id = df_meta.at[ukbb_cond[2],'phenotype_code']
## get male imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_male.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_m = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_m = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_m, "."])
subprocess.run(["bgzip", "-d", ukbb_file_m, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_male.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
## get female imputed variants, replace if not found
try:
if os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.female.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.female.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.both_sexes.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.both_sexes.tsv', ukbb_id + '_female.tsv'])
elif os.path.isfile('${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'):
ukbb_var_f = '${params.imputed_store}/' + ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
ukbb_file_f = ukbb_id + '.gwas.imputed_v3.male.tsv.bgz'
subprocess.run(["cp", ukbb_var_f, "."])
subprocess.run(["bgzip", "-d", ukbb_file_f, "."])
subprocess.run(["mv", ukbb_id + '.gwas.imputed_v3.male.tsv', ukbb_id + '_female.tsv'])
else:
print('imputed variants not present')
except:
print('no files exist')
"""
}
process generate_m_variants_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
echo true
maxForks 1
input:
tuple path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: m_var
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
def process_variants(target_file):
# Create gzip directory if it doesn't exist
os.makedirs('gzip', exist_ok=True)
# Copy and compress file
subprocess.run(['cp', target_file, 'gzip/'], check=True)
subprocess.run(['gzip', 'gzip/' + target_file], check=True)
print(f"Processing {target_file}.gz")
# Read the compressed file
df_var_m = pd.read_csv('gzip/' + target_file + '.gz', sep='\\t', header=0)
################## GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
##read variants
df_var = df_var_m
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr'] = df_var['chr'].astype('str')
df_var['pos'] = df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
# Perform the operation on host memory
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = df_var_all[['minor_allele','major_allele']].to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] = arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
output_file = f"{target_file.split('.')[0]}_patient_{p}_variants.csv"
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['chr','pos']).sort_index()
df_var_final.to_csv(output_file, index=False)
# Main execution
for target in '${dis_var_m}'.split():
try:
if not os.path.exists(target):
raise FileNotFoundError(f"Input file {target} does not exist")
process_variants(target)
except FileNotFoundError as e:
print(f"Error: {e}")
raise
except Exception as e:
print(f"Error processing {target}: {str(e)}")
raise
"""
}
process generate_f_variants_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
maxForks 1
echo true
input:
tuple path(dis_var_f), path(dis_var_m)
output:
path "*_variants.csv", emit: f_var
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
import os
import subprocess
import io
import requests
import itertools
import re
import json
def process_variants(target_file):
# Create gzip directory if it doesn't exist
os.makedirs('gzip', exist_ok=True)
# Copy and compress file
subprocess.run(['cp', target_file, 'gzip/'], check=True)
subprocess.run(['gzip', 'gzip/' + target_file], check=True)
print(f"Processing {target_file}.gz")
# Read the compressed file
df_var_f = pd.read_csv('gzip/' + target_file + '.gz', sep='\\t', header=0)
##################### GENERATE VARIANTS USING UKBB IMPUTED DATA ##############################
## read variant data
df_var = df_var_f
## calculate major and minor alleles and frequencies
df_var['minor_AF'] = pd.to_numeric(df_var['minor_AF'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
## split variant into parts
df_var[['chr', 'pos', 'ref', 'alt']] = df_var['variant'].str.split(':', expand=True)
df_var['chr'] = df_var['chr'].astype('str')
df_var['pos'] = df_var['pos'].astype('int')
## filter out low confidence variants
df_var_hc = df_var.loc[df_var['low_confidence_variant'] == False]
df_var_all = df_var_hc.drop(['low_confidence_variant'], axis=1)
## determine which is the minor allele
# Convert to pandas DataFrame in host memory
df_var_all_host = df_var_all.to_pandas()
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['alt'], 'major_allele'] = df_var_all_host['ref']
df_var_all_host.loc[df_var_all_host['minor_allele'] == df_var_all_host['ref'], 'major_allele'] = df_var_all_host['alt']
# Convert back to cuDF DataFrame in device memory
df_var_all = pd.from_pandas(df_var_all_host)
## define variant array and probabilities, patient array
arr_var = pd.DataFrame(data=df_var_all, columns=['minor_allele','major_allele']).to_numpy()
arr_prob = df_var_all[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
## loop through rows, using weighted random choice by variant probability to assign predicted allele
for p in range(n_patients):
df_var_all['prediction'] = arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var_all.loc[df_var_all['prediction'] != df_var_all['ref']]
df_var_final = df_var_final[['chr', 'pos', 'ref', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['chr','pos']).sort_index()
output_file = f"{target_file.split('.')[0]}_patient_{p}_variants.csv"
df_var_final.to_csv(output_file, index=False)
# Main execution
for target in '${dis_var_f}'.split():
try:
if not os.path.exists(target):
raise FileNotFoundError(f"Input file {target} does not exist")
process_variants(target)
except FileNotFoundError as e:
print(f"Error: {e}")
raise
except Exception as e:
print(f"Error processing {target}: {str(e)}")
raise
"""
}
process generate_m_healthy_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: m_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.male.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XY'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final['chr'] = [i.split('chr')[-1] for i in df_var_final.to_pandas()['chr']]
df_var_final.to_csv('healthy_male_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process generate_f_healthy_cudf {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
maxForks 1
echo true
input:
tuple path(healthy_dir)
output:
path "*_variants.csv", emit: f_healthy
script:
"""
#!/opt/conda/envs/synthea/bin/python3
import cudf as pd
import numpy as np
df_var = pd.read_csv('${healthy_dir}/gnomad.genomes.v4.1.sites.female.txt')
df_var['minor_AF'] = pd.to_numeric(df_var['AF_XX'])
major_af = 1 - df_var[['minor_AF']]
df_var['major_AF'] = major_af
arr_var = pd.DataFrame(data=df_var, columns=['ALT','REF']).to_numpy()
arr_prob = df_var[['minor_AF', 'major_AF']].to_numpy()
n_patients = ${params.n_pat} - int(${params.n_pat} * ${params.percent_male})
for p in range(n_patients):
df_var['prediction'] =arr_var[np.arange(arr_var.shape[0]), (np.random.rand(arr_var.shape[0], 1) < arr_prob.cumsum(axis=1)).argmax(axis=1)]
df_var_final = df_var.loc[df_var['prediction'] != df_var['REF']]
df_var_final = df_var_final[['#CHROM', 'POS', 'REF', 'prediction']]
#randomly select mutation if more than one mutation is passed for a position
df_var_final = df_var_final.sample(frac=1).drop_duplicates(['#CHROM','POS']).sort_index()
df_var_final.rename(columns={"#CHROM": "chr", "POS": "pos", "REF": "ref"}, inplace = True)
df_var_final['chr'] = [i.split('chr')[-1] for i in df_var_final.to_pandas()['chr']]
df_var_final.to_csv('healthy_female_patient_' + str(p) + '_variants.csv', index=False)
"""
}
process make_vcfs {
container 'synthea:cudf'
containerOptions "--rm --privileged --gpus all -v /mnt:/mnt"
//publishDir "${params.outdir}/variants_vcfs", mode: 'copy'
echo true
maxForks 1
input:
path patient_vars
output:
path "${patient_vars.baseName}.vcf", emit: patient_vcfs
//path "${patient_vars.baseName}.vcf.gz", emit: patient_gz
//path "${patient_vars.baseName}.vcf.gz.tbi", emit: patient_index
//path "${patient_vars.baseName}_filt.csv", emit: filtered_csv
script:
"""
## only print disease-associated variants not found in the ref/major allele position as they will already be covered by the ref genome
#I don't think this is correct \$16 == \$18 cuz we changed csv file format
#it only removes first line from csv
awk '\$16 == \$18 { print \$0 }' ${patient_vars} | tail -n +2 > ${patient_vars.baseName}_filt.csv
## copy the variant template to the workdir
cp /mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf .
## print the filtered variants to vcf format
printf "#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\tNA00001" >> vcf_template.vcf
printf "\\n" >> vcf_template.vcf
awk -F',' '{print "chr"\$1,\$2,".",\$3,\$4,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print "chr"\$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
#awk -F',' '{print \$13,\$14,".",\$15,\$16,"100","PASS","NS=1","GT","0/1"}' OFS='\\t' ${patient_vars.baseName}_filt.csv >> vcf_template.vcf
# sort the genome karyotypically (in chromosomal order) and index
#files are sorted already just for security
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar SortVcf -I vcf_template.vcf -O ${patient_vars.baseName}_sorted.vcf
#Liftover form 19 to 38 standard
java -jar /synthea/synthea/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar LiftoverVcf -I ${patient_vars.baseName}_sorted.vcf -O ${patient_vars.baseName}.vcf -C /mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz -REJECT rejected_variants.vcf -R /mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa
#change this part to save on memory usage
#bgzip < ${patient_vars.baseName}.vcf > ${patient_vars.baseName}.vcf.gz
#gatk IndexFeatureFile -I ${patient_vars.baseName}.vcf.gz
#delete unnecessary files
rm vcf_template.vcf
rm ${patient_vars.baseName}_filt.csv
rm ${patient_vars.baseName}_sorted.vcf
rm rejected_variants.vcf
rm *vcf.idx
"""
}

65
main_vcf2prot.nf Normal file
View File

@@ -0,0 +1,65 @@
nextflow.enable.dsl=2
process VCF2PROT {
memory 2.GB
container "${params.container_vcf2prot}"
containerOptions "${params.containerOptions}"
// echo true
publishDir "${params.outdir}/vcf2prot", mode: 'copy'
stageInMode 'copy'
maxForks 1
input:
path vcf
path vcf_filtered
output:
path "*.fasta"
script:
"""
#!/bin/bash
workdir=`pwd`
patient_name=\$(basename $vcf .vcf)
grep '^#' $vcf > work1.vcf
/opt/conda/envs/vcf2prot/bin/python3 -c "
import pickle
import numpy as np
import pandas as pd
with open('$vcf_filtered', 'rb') as fp:
vcf_file = pickle.load(fp)
vcf_filtered=[]
for i in vcf_file:
vcf_filtered.extend(i[1])
vcf_filtered = pd.DataFrame(vcf_filtered)
#drop duplicates, it returns error, consequence of overlapping genes on genome
vcf_filtered = vcf_filtered.drop_duplicates()
vcf_filtered = vcf_filtered.replace({'chr':''}, regex=True)
vcf_filtered = vcf_filtered.sort_values(by=[0,1])
with open('work1.vcf', 'a') as f:
for line in np.array(vcf_filtered):
li = str(line).replace('[', '').replace(']', '').replace('\\'', '').replace(' ', '\\t').replace('\\n', '')
f.write(f'{li}\\n')
"
awk '{gsub(/^##contig=<ID=chr/,"##contig=<ID="); print}' work1.vcf > \$workdir/work_2.vcf
###remove non canonical chromososms
grep -v '[0-9]_\\|Y_\\|X_\\|Un_' \$workdir/work_2.vcf > \$workdir/work.vcf
###
bcftools csq -f /home/omic/Homo_sapiens.GRCh38.dna.toplevel.fa -g /home/omic/Homo_sapiens.GRCh38.112.gff3 \$workdir/work.vcf --phase a --ncsq 120 -O v -o \$workdir/annotated.vcf
/home/omic/vcf2prot/bins/Linux/vcf2prot -f \$workdir/annotated.vcf -r /home/omic/vcf2prot/MANE_transcipts_reference.fasta -v -g st -o \$workdir
mv *.fasta \${patient_name}_transcript_id_mutations.fasta
"""
}

289
ncbiRefSeq_bigger.csv Normal file
View File

@@ -0,0 +1,289 @@
,Unnamed: 0,bin,name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,score,name2,cdsStartStat,cdsEndStat,exonFrames
2378,2378,9,XM_047416024.1,chr1,+,6785453,7769706,6785550,7766522,20,"6785453,6825091,7091303,7249490,7640399,7661725,7663352,7670910,7677598,7732447,7736343,7736930,7737254,7738297,7744834,7745844,7747709,7751198,7752458,7766458,","6785575,6825210,7091371,7249626,7640553,7661866,7665199,7671037,7677733,7732599,7736540,7737009,7737570,7738482,7745022,7746091,7747781,7751392,7752533,7769706,",0,CAMTA1,cmpl,cmpl,"0,1,0,2,0,1,1,0,1,1,0,2,0,1,0,2,0,0,2,2,"
9028,9028,10,XM_005245795.6,chr1,+,13892823,15118043,13893635,15114635,17,"13892823,14180434,14598982,14960683,15034748,15043988,15056090,15060171,15063571,15065629,15094179,15094814,15101542,15103358,15104022,15112426,15114470,","13893756,14180592,14599223,14960875,15034885,15044159,15056280,15060302,15063622,15065753,15094385,15094933,15101774,15103460,15104189,15112541,15118043,",0,KAZN,cmpl,cmpl,"0,1,0,1,1,0,0,1,0,0,1,0,2,0,0,2,0,"
4079,4079,1,NM_052896.5,chr1,-,33513997,34165842,33519517,34165813,70,"33513997,33519464,33519811,33521462,33523306,33524881,33527195,33533049,33533795,33537021,33537435,33540524,33541129,33542719,33546036,33550176,33567592,33569373,33571531,33572505,33577295,33580752,33583641,33586503,33587087,33600864,33602368,33605281,33605862,33611040,33614503,33616905,33617498,33622166,33623369,33624518,33625050,33626485,33633421,33635213,33636359,33646647,33652322,33657945,33662889,33692929,33698752,33700516,33709088,33714586,33716285,33724196,33724515,33725348,33726546,33739139,33743279,33772568,33788599,33792422,33810742,33819712,33820468,33825696,33846883,33918093,33935759,34032593,34088976,34165746,","33516570,33519677,33519950,33521550,33523419,33525043,33527258,33533229,33533907,33537095,33537609,33540698,33541309,33542896,33546219,33550350,33567766,33569547,33571726,33572691,33577484,33580899,33583830,33586617,33587168,33601010,33602546,33605470,33605988,33611250,33614620,33616975,33617617,33622271,33623466,33624643,33625254,33626581,33633535,33635330,33636554,33646835,33652461,33658137,33663092,33693056,33698944,33700673,33709258,33714775,33716501,33724313,33724704,33725536,33726685,33739334,33743606,33772751,33788712,33792526,33810864,33819837,33820556,33825774,33846996,33918301,33935954,34032706,34089193,34165842,",0,CSMD2,cmpl,cmpl,"-1,2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,2,1,1,2,1,0,"
469,469,14,XM_017002595.3,chr1,-,48522510,50023954,48522580,50023796,13,"48522510,48539641,48587003,48590832,48634492,48653336,48663151,48867190,49045583,49245769,49697312,49851395,50023762,","48522692,48539738,48587166,48590985,48634604,48653451,48663241,48867230,49045800,49245864,49697437,49851518,50023954,",0,AGBL4,cmpl,cmpl,"2,1,0,0,2,1,1,0,2,0,1,1,0,"
5886,5886,121,XM_047442743.1,chr1,-,50437027,50960267,50441439,50788105,20,"50437027,50475463,50490587,50491720,50535368,50539591,50567076,50582617,50583651,50584684,50596120,50655441,50705785,50738862,50744683,50787999,50801630,50857928,50959014,50959766,","50441523,50475679,50490665,50491801,50535457,50539728,50567231,50582699,50583715,50584811,50596216,50655528,50705891,50738954,50744775,50788205,50801677,50857997,50959111,50960267,",0,FAF1,cmpl,cmpl,"0,0,0,0,1,2,0,2,1,0,0,0,2,0,1,0,-1,-1,-1,-1,"
4417,4417,15,NM_001379461.1,chr1,-,56994777,58546726,57010694,57291030,21,"56994777,57010679,57011144,57014882,57023530,57025980,57062889,57069359,57071022,57071521,57072282,57136542,57145289,57290963,57649591,57883998,58150510,58343351,58506059,58527260,58546702,","56998128,57010790,57011272,57015431,57023639,57026043,57062943,57069425,57071061,57071641,57072414,57136641,57145429,57291166,57649665,57884162,58150588,58343403,58506209,58527335,58546726,",0,DAB1,cmpl,cmpl,"-1,0,1,1,0,0,0,0,0,0,0,0,1,0,-1,-1,-1,-1,-1,-1,-1,"
14956,14956,16,NM_001297440.2,chr1,+,65792509,66374579,65913351,66372678,16,"65792509,65913244,66247459,66257646,66257792,66266037,66332507,66355526,66361614,66363167,66363406,66365666,66367695,66367942,66368786,66372312,","65792630,65913356,66247654,66257683,66257863,66266087,66332620,66355620,66361793,66363266,66363571,66365766,66367850,66368065,66368969,66374574,",0,PDE4B,cmpl,cmpl,"-1,0,2,2,0,2,1,0,1,0,0,0,1,0,0,0,"
11282,11282,139,NM_001366838.3,chr1,+,69567921,70144364,69568639,70121887,26,"69567921,69678380,69760190,69792042,69825747,69834779,69838226,69931506,69980378,69986241,69994560,70011796,70012973,70016464,70018718,70021004,70023125,70028170,70036120,70036443,70038112,70053025,70076076,70089726,70107751,70121779,","69568641,69678478,69760393,69792160,69825826,69834869,69838283,69931570,69980453,69986386,69994633,70011926,70013089,70016534,70018818,70021129,70023374,70028371,70036232,70036624,70039793,70053145,70076298,70089819,70107826,70144364,",0,LRRC7,cmpl,cmpl,"0,2,1,0,1,2,2,2,0,0,1,2,0,2,0,1,0,0,0,1,2,0,0,0,0,0,"
13105,13105,141,NM_173808.3,chr1,-,71395942,72282539,71407445,72282494,7,"71395942,71592816,71611025,71698007,71776171,71935078,72282318,","71407570,71592968,71611146,71698139,71776297,71935311,72282539,",0,NEGR1,cmpl,cmpl,"1,2,1,1,1,2,0,"
19473,19473,18,NM_001349109.3,chr1,+,76074745,76637339,76074866,76634191,4,"76074745,76313804,76412007,76634127,","76074884,76313999,76412417,76637339,",0,ST6GALNAC3,cmpl,cmpl,"0,0,0,2,"
387,387,18,NM_001393349.1,chr1,+,81306131,81993932,81836984,81991145,26,"81306131,81445020,81580875,81761810,81836884,81907016,81936727,81942033,81942968,81950188,81951017,81951956,81952986,81955876,81966057,81966403,81968025,81969177,81970313,81971851,81979868,81981807,81984582,81985258,81986900,81990390,","81306509,81445089,81580980,81761852,81837057,81907230,81936837,81942045,81943769,81950482,81951121,81952142,81953025,81956060,81966183,81966609,81968199,81969387,81970534,81971918,81979960,81981976,81984711,81985355,81987029,81993932,",0,ADGRL2,cmpl,cmpl,"-1,-1,-1,-1,0,1,2,1,1,1,1,0,0,0,1,1,0,0,0,2,0,2,0,0,1,1,"
5084,5084,20,XM_005270562.3,chr1,-,97077742,97921059,97078975,97920922,22,"97077742,97082329,97098488,97193068,97234851,97305258,97306176,97373560,97382392,97450058,97549559,97573759,97593217,97595058,97679094,97691716,97699350,97721509,97740391,97828113,97883263,97920883,","97079146,97082470,97098632,97193248,97234994,97305378,97306297,97373644,97382461,97450223,97549744,97573970,97593387,97595166,97679182,97691798,97699547,97721671,97740479,97828196,97883374,97921059,",0,DPYD,cmpl,cmpl,"0,0,0,0,1,1,0,0,0,0,1,0,1,1,0,2,0,0,2,0,0,0,"
5008,5008,29,XM_017000984.2,chr1,+,171841497,172418466,171841656,172418317,20,"171841497,171921747,171987655,171988944,172032401,172033104,172038318,172042008,172044384,172048611,172068818,172081831,172092823,172131174,172253572,172308727,172379017,172387132,172388572,172418280,","171841817,171921821,171987805,171989148,172032500,172033265,172038461,172042144,172044452,172048750,172068905,172081902,172092875,172131288,172253682,172308839,172379182,172387359,172388809,172418466,",0,DNM3,cmpl,cmpl,"0,2,1,1,1,1,0,2,0,2,0,0,2,0,0,2,0,0,2,2,"
16657,16657,239,XM_047436039.1,chr1,+,174159519,174995308,174219157,174990001,25,"174159519,174219124,174220971,174231144,174241482,174250474,174252479,174272413,174275832,174278612,174304985,174370978,174393994,174637374,174683521,174699524,174702112,174752312,174811831,174957456,174969276,174976077,174978806,174982833,174989848,","174159657,174219184,174221164,174231355,174241657,174250632,174252590,174272480,174275935,174278779,174305127,174371072,174394145,174637488,174683596,174699650,174702256,174752354,174811960,174957549,174969387,174976182,174978890,174982905,174995308,",0,RABGAP1L,cmpl,cmpl,"-1,0,0,1,2,0,2,2,0,1,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0,"
21862,21862,34,NM_206933.4,chr1,-,215622890,216423448,215625780,216422336,72,"215622890,215628813,215634458,215639154,215640557,215647521,215648527,215650591,215670971,215674099,215680148,215728029,215741374,215743176,215758594,215759659,215766680,215779842,215782041,215782737,215786669,215790058,215798906,215813735,215816996,215837990,215844293,215845823,215867006,215877757,215878763,215888425,215900074,215900754,215934615,215965316,215970624,215993019,215998886,216000402,216046430,216048533,216070100,216072888,216073096,216078088,216083455,216084697,216086718,216089012,216097082,216175251,216190222,216196552,216198314,216199626,216207272,216217386,216231952,216246584,216250902,216289279,216292174,216321882,216323473,216324167,216325304,216327590,216364952,216418513,216421851,216423213,","215625870,215629035,215634703,215639238,215640734,215647730,215648766,215650801,215671293,215675616,215680376,215728384,215741537,215743335,215758752,215759843,215766788,215780041,215782196,215782935,215786874,215790282,215799125,215813904,215817195,215838103,215844496,215846033,215867170,215877880,215879098,215889054,215900217,215900905,215934795,215965479,215970776,215993167,215999058,216000562,216046592,216048647,216070292,216072969,216073300,216078362,216083586,216084877,216086820,216089139,216097213,216175482,216190367,216196722,216198584,216200121,216207431,216217550,216232136,216247226,216251098,216289410,216292370,216321976,216323695,216324352,216325599,216327654,216365085,216418679,216422540,216423448,",0,USH2A,cmpl,cmpl,"0,0,1,1,1,2,0,0,2,0,0,2,1,1,2,1,1,0,1,1,0,1,1,0,2,0,1,1,2,2,0,1,2,1,1,0,1,0,2,1,1,1,1,1,1,0,1,1,1,0,1,1,0,1,1,1,1,2,1,1,0,1,0,2,2,0,2,1,0,2,0,-1,"
5754,5754,34,XM_017000625.2,chr1,-,216503245,217137702,216506938,216905339,9,"216503245,216519151,216564218,216567987,216650972,216677075,216905247,216939581,217137666,","216507183,216519421,216564401,216568098,216651089,216677491,216905683,216939673,217137702,",0,ESRRG,cmpl,cmpl,"1,1,1,1,1,2,0,-1,-1,"
17643,17643,299,XM_017002028.2,chr1,+,237042183,237833988,237042521,237832647,106,"237042183,237270496,237330877,237364357,237369533,237374716,237377322,237387280,237388086,237417048,237423091,237441318,237445400,237454390,237456599,237469091,237491805,237492953,237496510,237500710,237503288,237506709,237511687,237530426,237548430,237550543,237566566,237569144,237589792,237590639,237591738,237593475,237594099,237595497,237602024,237610761,237614038,237617285,237623764,237625660,237627806,237631426,237633577,237634888,237638356,237639014,237640896,237643326,237648443,237649876,237651410,237654273,237655820,237657943,237659984,237660809,237666511,237667882,237674095,237674730,237678047,237680455,237687454,237698964,237700228,237701977,237705212,237706948,237708857,237709479,237711744,237717197,237718461,237723127,237726272,237727086,237730259,237732045,237733704,237742295,237743599,237756287,237757696,237759775,237760954,237770806,237772011,237773519,237778665,237781564,237783674,237785968,237787987,237791428,237792104,237793866,237795288,237798036,237801855,237806136,237808900,237819035,237828380,237830529,237831513,237832551,","237042569,237270616,237330982,237364372,237369608,237374795,237377435,237387380,237388183,237417123,237423248,237441483,237445522,237454574,237456735,237469187,237491924,237493087,237496752,237500903,237503505,237506814,237511791,237530510,237548590,237550691,237566775,237569319,237590001,237590992,237591853,237593636,237594129,237595657,237602111,237610988,237614843,237617486,237623870,237625804,237628080,237631541,237633710,237634992,237638492,237639201,237641002,237643447,237648613,237650097,237651501,237654414,237655984,237658022,237660074,237660947,237666589,237667958,237674219,237674846,237678112,237680577,237687504,237699025,237700467,237702059,237705343,237707269,237709098,237709567,237711837,237717368,237718521,237723262,237726308,237727199,237730356,237732149,237733756,237742349,237743623,237756387,237757776,237759852,237761028,237770887,237772100,237773648,237778770,237781646,237784972,237786036,237788135,237791515,237792323,237793997,237795331,237798170,237801916,237806283,237809035,237819192,237828445,237830630,237831565,237833988,",0,RYR2,cmpl,cmpl,"0,0,0,0,0,0,1,0,1,2,2,0,0,2,0,1,1,0,2,1,2,0,0,2,2,0,1,0,1,0,2,0,2,2,0,0,2,0,0,1,1,2,0,1,0,1,2,0,1,0,2,0,0,2,0,0,0,0,1,2,1,0,2,1,2,1,2,1,1,2,0,0,0,0,0,0,2,0,2,0,0,0,1,0,2,1,1,0,0,0,1,0,2,0,0,0,2,0,2,0,0,0,1,0,2,0,"
3358,3358,301,XM_047443244.1,chr1,+,239386567,239915450,239907451,239909224,4,"239386567,239545640,239678185,239907432,","239387227,239545749,239678288,239915450,",0,CHRM3,cmpl,cmpl,"-1,-1,-1,0,"
17061,17061,37,NM_001374808.1,chr1,-,240774741,241357230,240800646,241098762,19,"240774741,240800640,240802903,240806139,240811917,240813617,240814715,240816316,240827097,240868586,240868775,240870054,240930716,240936599,240983078,241098665,241101832,241355698,241356898,","240776213,240800721,240802993,240806326,240812043,240813728,240814777,240816415,240827172,240868668,240868852,240870119,240930768,240936706,240983129,241098762,241101978,241355826,241357205,",0,RGS7,cmpl,cmpl,"-1,0,0,2,2,2,0,0,0,2,0,1,0,1,1,0,-1,-1,-1,"
9259,9259,38,NM_018012.4,chr1,+,245154984,245709432,245155424,245702606,15,"245154984,245156281,245366833,245419578,245540766,245602576,245607650,245609265,245611792,245646120,245684232,245685404,245698105,245698886,245702457,","245155487,245156683,245367367,245419745,245540950,245602783,245607744,245609528,245611976,245646280,245684395,245688807,245698308,245699037,245709432,",0,KIF26B,cmpl,cmpl,"0,0,0,0,2,0,0,1,0,1,2,0,1,0,1,"
18940,18940,38,NM_001167740.2,chr1,-,245749346,246507279,245749562,246507217,12,"245749346,245764040,245858495,245863798,245915529,245927930,245929869,246327200,246330479,246335366,246355030,246507053,","245749664,245764149,245858670,245863886,245915640,245928033,245929937,246327337,246330537,246335474,246355094,246507279,",0,SMYD3,cmpl,cmpl,"0,2,1,0,0,2,0,1,0,0,2,0,"
337,337,74,NM_018702.4,chr10,-,1177312,1737525,1183192,1737150,10,"1177312,1184860,1199965,1216950,1233693,1242130,1270954,1363027,1379073,1737050,","1183369,1185039,1200147,1217119,1233845,1242299,1271069,1363917,1379160,1737525,",0,ADARB2,cmpl,cmpl,"0,1,2,1,2,1,0,1,1,0,"
3080,3080,10,NM_001326317.2,chr10,+,10462549,11336675,11165504,11329053,15,"10462549,10682455,10919963,11165485,11217424,11249152,11257737,11266597,11270665,11275056,11288417,11314138,11321206,11325835,11328925,","10462586,10682494,10919999,11165682,11217507,11249201,11257872,11266677,11270824,11275120,11288552,11314258,11321386,11325979,11336675,",0,CELF2,cmpl,cmpl,"-1,-1,-1,0,1,0,1,1,0,0,1,1,1,1,1,"
6571,6571,86,NM_018027.5,chr10,-,13643705,14330924,13651904,14330102,25,"13643705,13651902,13654415,13656635,13659322,13660315,13663452,13666096,13670405,13674910,13693897,13701339,13707036,13737843,13740193,13740511,13747735,13761646,13762623,13782921,13796495,13810813,13858846,14330057,14330596,","13647035,13651974,13654512,13657522,13659490,13660553,13663509,13666325,13670528,13675044,13694039,13701478,13707113,13737930,13740251,13740577,13747819,13761669,13762680,13783006,13796588,13810908,13858912,14330183,14330924,",0,FRMD4A,cmpl,cmpl,"-1,2,1,2,2,1,1,0,0,1,0,2,0,0,2,2,2,0,0,2,2,0,0,0,-1,"
11589,11589,91,XM_011519454.2,chr10,+,19046926,19734478,19048959,19734237,41,"19046926,19048958,19066718,19087839,19088023,19103978,19123491,19124523,19128220,19133855,19136573,19146197,19155074,19165636,19175207,19203727,19204307,19204897,19209267,19257683,19280046,19283018,19323948,19327562,19331368,19347770,19352005,19387527,19389451,19450306,19491516,19498484,19531193,19567501,19595193,19607776,19615856,19692281,19692457,19730705,19734156,","19046982,19049137,19066859,19087934,19088185,19104075,19123593,19124670,19128387,19133948,19136781,19146344,19155172,19165810,19175328,19203880,19204413,19205265,19209680,19257771,19280223,19283181,19324105,19327673,19331582,19348018,19352297,19387773,19389609,19450490,19491645,19498646,19531351,19567703,19595457,19607902,19615923,19692361,19692554,19730781,19734478,",0,MALRD1,cmpl,cmpl,"-1,0,1,1,0,0,1,1,1,0,0,1,1,0,0,1,1,2,1,0,1,1,2,0,0,1,0,1,1,0,1,1,1,0,1,1,1,2,1,2,0,"
9222,9222,11,NM_001098500.3,chr10,+,23694726,24547843,24219795,24546324,19,"23694726,24007224,24219625,24380868,24432994,24438385,24473227,24494499,24495146,24501378,24513258,24520122,24521781,24524322,24527935,24531829,24533069,24544980,24545826,","23695234,24007374,24219909,24381067,24433193,24438479,24474060,24494604,24495196,24501545,24513434,24520253,24521929,24524764,24528119,24531993,24533237,24545103,24547843,",0,KIAA1217,cmpl,cmpl,"-1,-1,0,0,1,2,0,2,2,1,0,2,1,2,0,1,0,0,0,"
14702,14702,13,NM_019619.4,chr10,-,34109560,34815296,34111168,34814995,25,"34109560,34119612,34131462,34269656,34284134,34317106,34331116,34336198,34337274,34341626,34347955,34359146,34360070,34372497,34374873,34377966,34382539,34384128,34399329,34401825,34450316,34470084,34516978,34696317,34814875,","34111562,34119740,34131583,34269899,34284245,34317338,34331344,34336243,34337426,34341816,34348115,34359317,34360259,34372536,34375002,34378106,34382922,34384254,34399413,34401917,34450448,34470263,34517159,34696419,34815296,",0,PARD3,cmpl,cmpl,"2,0,2,2,2,1,1,1,2,1,0,0,0,0,0,1,2,2,2,0,0,1,0,0,0,"
860,860,118,XM_006717951.4,chr10,-,47467992,47991796,47468846,47991772,12,"47467992,47471261,47472132,47473969,47474304,47474944,47475492,47476231,47477080,47478532,47479797,47991679,","47468906,47471384,47472191,47474065,47474398,47475004,47475572,47476322,47477194,47478627,47479888,47991796,",0,ANXA8,cmpl,cmpl,"0,0,1,1,0,0,1,0,0,1,0,0,"
16070,16070,15,NM_001098512.3,chr10,+,50990887,52298350,50991378,52293900,18,"50990887,51153163,51467722,51804584,51907506,52054483,52062536,52133839,52161888,52251569,52271349,52272391,52280788,52282152,52288725,52288930,52290223,52293801,","50991644,51153330,51467836,51804690,51907570,52054561,52062631,52133905,52161963,52251666,52271489,52272481,52280930,52282316,52288848,52288993,52290290,52298350,",0,PRKG1,cmpl,cmpl,"0,2,1,1,2,0,0,2,2,2,0,2,2,0,2,2,2,0,"
14788,14788,15,NM_001354404.2,chr10,-,53802770,55627942,53821857,54664262,35,"53821098,53827392,53828564,53831314,53840319,53857174,53866641,53903242,53938814,53940865,53959731,53961751,53995648,54020191,54022891,54066756,54079330,54089983,54132874,54153099,54183443,54185133,54195682,54213935,54236822,54317270,54329595,54346364,54369119,54378781,54664171,54897449,55166575,55627624,55627864,","53823358,53827548,53828573,53831533,53840496,53857263,53866857,53903370,53938955,53940975,53959844,53961892,53995765,54020416,54023197,54066885,54079424,54090063,54133007,54153293,54183593,54185268,54195889,54214048,54236931,54317441,54329706,54346484,54369275,54378942,54664290,54897500,55166651,55627753,55627942,",0,PCDH15,cmpl,cmpl,"2,2,2,2,2,0,0,1,1,2,0,0,0,0,0,0,2,0,2,0,0,0,0,1,0,0,0,0,0,1,0,-1,-1,-1,-1,"
743,743,130,NM_001204403.2,chr10,-,60026297,60733528,60042690,60733319,44,"60026297,60042671,60055657,60059339,60059697,60063110,60064156,60067934,60080536,60082614,60083491,60084601,60085156,60086676,60088146,60105904,60108829,60114224,60134270,60138963,60166590,60166823,60172307,60172899,60173087,60181328,60186714,60196144,60196526,60198339,60200128,60203001,60205791,60208035,60213411,60234687,60261858,60263834,60270130,60278773,60279049,60279537,60615185,60733262,","60029826,60042759,60056036,60059430,60060006,60063254,60064288,60068009,60080618,60082737,60083617,60084830,60085253,60086884,60088358,60106059,60109054,60114331,60134373,60139087,60166653,60166896,60172403,60172998,60173186,60181427,60186912,60196243,60196625,60198537,60200227,60203100,60205890,60208233,60213510,60234786,60261957,60264020,60270229,60278872,60279148,60279639,60615224,60733528,",0,ANK3,cmpl,cmpl,"-1,0,2,1,1,1,1,1,0,0,0,2,1,0,1,2,2,0,2,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"
4199,4199,0,XM_047425124.1,chr10,-,65912522,67763594,65920329,67648770,19,"65912522,65966611,65988691,66069307,66103156,66280469,66379151,66520616,66621691,66766263,66775443,67180316,67219606,67521841,67539502,67606856,67647414,67648739,67763433,","65920617,65966746,65988797,66069489,66103249,66280621,66379352,66520773,66621784,66766416,66775524,67180520,67219870,67521961,67539669,67607049,67647518,67648816,67763594,",0,CTNNA3,cmpl,cmpl,"0,0,2,0,0,1,1,0,0,0,0,0,0,0,1,0,1,0,-1,"
408,408,17,XM_017015705.2,chr10,+,74151220,74709290,74151278,74708356,9,"74151220,74200763,74224537,74314666,74394140,74398470,74589281,74670182,74708320,","74151343,74200838,74224591,74314745,74394313,74398579,74589317,74670269,74709290,",0,ADK,cmpl,cmpl,"0,2,2,2,0,2,0,0,0,"
11205,11205,2,NM_001305581.2,chr10,+,75431623,76560168,75431724,76557288,7,"75431623,75438393,76036007,76047163,76058665,76324400,76557208,","75431754,75438494,76036134,76047303,76058783,76324485,76560168,",0,LRMDA,cmpl,cmpl,"0,0,2,0,2,0,1,"
9117,9117,18,XM_017016207.3,chr10,-,76869601,77637808,76877868,77637642,32,"76869601,76887290,76889450,76891524,76909965,76914056,76914935,76944772,76949141,76953800,76969973,77001406,77011966,77019012,77025445,77027822,77039527,77073096,77079480,77084636,77086487,77090399,77108480,77110172,77112366,77120972,77183420,77184822,77251194,77403861,77493797,77637264,","76877893,76887515,76889569,76891719,76910096,76914137,76915049,76944965,76949366,76953924,76970067,77001580,77012043,77019099,77025457,77027891,77039637,77073252,77079550,77084719,77086593,77090510,77108572,77110343,77112442,77121048,77183532,77184916,77251256,77404023,77493929,77637808,",0,KCNMA1,cmpl,cmpl,"2,2,0,0,1,1,1,0,0,2,1,1,2,2,2,2,0,0,2,0,2,2,0,0,2,1,0,2,0,0,0,0,"
13578,13578,18,XM_047424512.1,chr10,+,81875193,82987179,81875340,82985605,9,"81875193,82358738,82738576,82951468,82958948,82973787,82978949,82984782,82985097,","81876163,82358868,82738650,82951571,82959075,82973915,82979120,82984854,82987179,",0,NRG3,cmpl,cmpl,"0,1,2,1,2,0,2,2,2,"
7470,7470,19,NM_017551.3,chr10,-,85599551,86366795,85602272,86366392,16,"85599551,85613406,85619866,85647201,85723002,85724351,85727854,85729512,85854495,85856028,85869009,85916185,86138818,86206363,86363940,86366313,","85602701,85613647,85620033,85647397,85723141,85724676,85728052,85729614,85854615,85856190,85869180,85916239,86139024,86206648,86364096,86366795,",0,GRID1,cmpl,cmpl,"0,2,0,2,1,0,0,0,0,0,0,0,1,1,1,0,"
8254,8254,20,XM_047425614.1,chr10,-,98457076,99315951,98459573,99144331,12,"98457076,98482635,98490050,98614903,98620601,98641846,98693899,98721656,98743882,99144237,99232347,99315928,","98459739,98482782,98490196,98615018,98620708,98641940,98693947,98721828,98744056,99144399,99232505,99315951,",0,HPSE2,cmpl,cmpl,"2,2,0,2,0,2,2,1,1,0,-1,-1,"
19053,19053,21,NM_014978.3,chr10,+,104641289,105265242,104641327,105263374,27,"104641289,104842791,104915832,104977334,105043054,105089774,105105396,105139396,105147616,105157137,105158891,105164302,105167257,105178065,105199998,105201119,105211136,105214441,105216935,105223115,105245541,105247218,105252774,105255701,105256818,105262330,105263309,","104641954,104842859,104915932,104977493,105043128,105089839,105105515,105139486,105147796,105157284,105158994,105164379,105167349,105178173,105200116,105201253,105211250,105214613,105217122,105223249,105245665,105247331,105252906,105255801,105256924,105262491,105265242,",0,SORCS3,cmpl,cmpl,"0,0,2,0,0,2,1,0,0,0,0,1,0,2,2,0,2,2,0,1,0,1,0,0,1,2,1,"
19051,19051,21,XM_017015617.1,chr10,-,106573662,107181138,106574101,107181066,27,"106573662,106579090,106579368,106597350,106607165,106611910,106618148,106620427,106629201,106652381,106667688,106671236,106672867,106675048,106677312,106679255,106679631,106688191,106699213,106706544,106709222,106730049,106761587,106776533,106829573,106956512,107181063,","106574181,106579251,106579474,106597450,106607297,106612023,106618272,106620561,106629388,106652553,106667802,106671367,106672985,106675156,106677404,106679332,106679734,106688338,106699393,106706634,106709341,106730114,106761661,106776692,106829673,106956580,107181138,",0,SORCS1,cmpl,cmpl,"1,2,1,0,0,1,0,1,0,2,2,0,2,2,0,1,0,0,0,0,1,2,0,0,2,0,0,"
1465,1465,22,XM_011539588.3,chr10,+,115093364,115948999,115093544,115944779,29,"115093364,115120184,115121698,115127592,115129326,115160039,115165557,115171036,115215696,115241570,115265192,115266796,115268325,115281354,115286215,115300033,115301854,115315517,115334281,115394658,115426249,115461940,115467173,115469171,115519262,115549457,115727247,115847876,115944657,","115093636,115120268,115121812,115127721,115129535,115160214,115165645,115171292,115215880,115241725,115265277,115267005,115268444,115281487,115286397,115300247,115302043,115315736,115334419,115394752,115426302,115462035,115467252,115469329,115519324,115549536,115727355,115847991,115948999,",0,ATRNL1,cmpl,cmpl,"0,2,2,2,2,1,2,0,1,2,1,2,1,0,1,0,1,1,1,1,2,1,0,1,0,2,0,0,1,"
5022,5022,194,NM_001377548.1,chr10,+,126905427,127452516,126905517,127451427,51,"126905427,126977947,126981917,126987520,126990454,126996747,126998091,126999353,127000171,127008731,127012294,127018709,127023199,127024684,127026351,127031649,127032136,127037718,127042624,127043063,127052680,127061667,127106230,127110247,127125473,127127668,127248007,127257334,127339005,127343645,127354668,127362063,127373780,127374057,127380081,127381277,127384789,127403054,127404324,127409036,127409312,127410839,127415151,127418364,127419665,127425873,127433282,127439026,127444125,127447393,127451331,","126905563,126977988,126981973,126987617,126990603,126996883,126998249,126999435,127000307,127008804,127012374,127018835,127023324,127024783,127026424,127031753,127032320,127037816,127042714,127043164,127052815,127061776,127106301,127110354,127125601,127127764,127248109,127257429,127339084,127343746,127354727,127362212,127373866,127374214,127380122,127381368,127384909,127403144,127404429,127409178,127409391,127410924,127415238,127418541,127419749,127426011,127433428,127439225,127444279,127447545,127452516,",0,DOCK1,cmpl,cmpl,"0,1,0,2,0,2,0,2,0,1,2,1,1,0,0,1,0,1,0,0,2,2,0,2,1,0,0,0,2,0,2,1,0,2,0,2,0,0,0,0,1,2,0,0,0,0,0,2,0,1,0,"
17755,17755,82,NM_001424318.1,chr11,-,9778667,10303837,9780417,10300496,41,"9778667,9781506,9784350,9785124,9787633,9789108,9790555,9795830,9807999,9808900,9812531,9816839,9829355,9832223,9839497,9842624,9845564,9846955,9850022,9852675,9853539,9856457,9858225,9895942,9961956,9963772,9968340,9989496,9992414,9992989,9993920,9998265,10000913,10002556,10028451,10029764,10031047,10042843,10193901,10300405,10303295,","9780516,9781638,9784438,9785318,9787738,9789342,9790683,9795957,9808185,9809002,9812708,9817024,9829496,9832420,9839696,9842770,9845740,9847083,9850218,9852749,9853712,9856720,9858396,9896011,9962106,9963882,9968545,9989595,9992543,9993103,9993998,9998379,10001022,10002689,10028557,10029875,10031170,10042981,10193987,10300498,10303837,",0,SBF2,cmpl,cmpl,"0,0,2,0,0,0,1,0,0,0,0,1,1,2,1,2,0,1,0,1,2,0,0,0,0,1,0,0,0,0,0,0,2,1,0,0,0,0,1,0,-1,"
19080,19080,88,NM_001367872.1,chr11,-,15966448,16738477,15972808,16341248,17,"15966448,15986203,15988996,16014941,16046513,16049754,16055751,16097608,16111802,16183885,16186782,16234581,16318445,16341011,16612080,16714829,16738424,","15973112,15986420,15989230,16015050,16046701,16049938,16055901,16097688,16111923,16183954,16186955,16234671,16318653,16341252,16612260,16714905,16738477,",0,SOX6,cmpl,cmpl,"2,1,1,0,1,0,0,1,0,0,1,1,0,0,-1,-1,-1,"
12885,12885,11,XM_047427831.1,chr11,+,19345235,20121601,19350952,20118258,37,"19345235,19350372,19832483,19842870,19868924,19879868,19892433,19933175,19939660,19946400,19948690,19984124,20035958,20043980,20044967,20048727,20054079,20055768,20062306,20068185,20068323,20077551,20077992,20080063,20083006,20090864,20092205,20093098,20095671,20097576,20100936,20103254,20103652,20105530,20107663,20114591,20118132,","19345311,19351027,19832601,19842923,19868997,19880127,19892594,19934277,19939773,19946509,19949080,19984247,20036097,20044272,20045670,20049195,20054240,20055957,20062359,20068209,20068398,20077635,20078104,20080209,20083179,20091018,20092368,20093199,20095767,20097745,20101172,20103409,20103724,20105727,20107782,20114795,20121601,",0,NAV2,cmpl,cmpl,"-1,0,0,1,0,1,2,1,2,1,2,2,2,0,1,2,2,1,1,0,0,0,0,1,0,2,0,1,0,0,1,0,2,2,1,0,0,"
13130,13130,11,NM_001288714.1,chr11,+,20669550,21575686,20669723,21575022,19,"20669550,20677931,20783679,20885443,20918181,20919251,20927307,20928376,20937785,20947335,20960431,21113588,21229331,21370852,21534373,21560188,21570763,21573184,21574971,","20669778,20678060,20783830,20885540,20918254,20919334,20927442,20928479,20937859,20947435,20960560,21113714,21229454,21370948,21534514,21560382,21570940,21573409,21575686,",0,NELL1,cmpl,cmpl,"0,1,1,2,0,1,0,0,1,0,1,1,1,1,1,1,0,0,0,"
11397,11397,96,NM_001252008.2,chr11,+,24497052,25082638,24738227,25078658,12,"24497052,24729172,24732117,24738220,24763245,24905990,24914475,24976590,24983125,25050037,25077328,25078553,","24497305,24729286,24732188,24738302,24763308,24906053,24914538,24976665,24983293,25050130,25077406,25082638,",0,LUZP2,cmpl,cmpl,"-1,-1,-1,0,0,0,0,0,0,0,0,0,"
11268,11268,13,XM_047427350.1,chr11,-,40114198,41459652,40114369,40116292,10,"40114198,40140800,40241518,40319627,40648141,40933634,41222796,41330938,41346263,41459430,","40116334,40140853,40241598,40319721,40648278,40933723,41223008,41345575,41346346,41459652,",0,LRRC4C,cmpl,cmpl,"0,-1,-1,-1,-1,-1,-1,-1,-1,-1,"
18207,18207,140,XM_047426616.1,chr11,-,70467853,71253228,70472868,71147326,23,"70467853,70485313,70490275,70492334,70502205,70502795,70659827,70661595,70698687,70798442,70807001,70820363,70896500,71056480,71075158,71092421,71094536,71109940,71113292,71118828,71147119,71224696,71253034,","70473439,70487720,70490387,70492465,70502286,70502931,70659952,70661678,70698763,70798556,70807171,70820682,70896567,71056558,71075275,71092589,71094688,71110049,71113364,71119032,71147338,71224796,71253228,",0,SHANK2,cmpl,cmpl,"2,1,0,1,1,0,1,2,1,1,2,1,0,0,0,0,1,0,0,0,0,-1,-1,"
20214,20214,148,NM_001098816.3,chr11,-,78652828,79441030,78658057,79069944,34,"78652828,78661448,78668936,78672032,78676151,78688053,78701525,78708360,78712481,78720369,78722667,78726078,78729375,78732315,78738450,78756804,78770991,78778601,78786897,78805291,78812121,78814293,78854103,78855963,78862961,78889784,78891237,78903267,79064737,79069721,79148709,79215807,79297487,79440508,","78658816,78661591,78670551,78672329,78676387,78688226,78702403,78708515,78712714,78720390,78722917,78726222,78729643,78732577,78738570,78757021,78771138,78778628,78787083,78805492,78812316,78814395,78854314,78856178,78863132,78890020,78891336,78903523,79065007,79070009,79148806,79215909,79297543,79441030,",0,TENM4,cmpl,cmpl,"0,1,0,0,1,2,0,1,2,2,1,1,0,2,2,1,1,1,1,1,1,1,0,1,1,2,2,1,1,0,-1,-1,-1,-1,"
4861,4861,2,XM_047426495.1,chr11,-,83455011,85628373,83459817,85626617,28,"83455011,83462001,83466707,83469200,83471625,83472726,83484128,83532707,83541681,83633210,83786689,83833613,83874419,83930327,83962884,83965323,83980505,84059314,84098922,84163460,84251237,84534569,85111660,85154555,85285219,85308984,85598656,85626598,","83459924,83462093,83466817,83469373,83471727,83472777,83484228,83532783,83541858,83633325,83786792,83833770,83874488,83930483,83963023,83965468,83980642,84059484,84099047,84163511,84251291,84534731,85111735,85154651,85285365,85309023,85598788,85628373,",0,DLG2,cmpl,cmpl,"1,2,0,1,1,1,0,2,2,1,0,2,2,2,1,0,1,2,0,0,0,0,0,0,1,1,1,0,"
7504,7504,157,NM_001143831.3,chr11,-,88504641,89065982,88508591,89047872,10,"88504641,88525308,88567052,88590600,88597183,88604717,88653167,88849905,89047211,89065775,","88509504,88525404,88567992,88590727,88597352,88604964,88653403,88850155,89048072,89065982,",0,GRM5,cmpl,cmpl,"2,2,1,0,2,1,2,1,0,-1,"
6146,6146,2,XM_017017186.2,chr11,+,92224817,92896473,92524671,92891113,28,"92224817,92524633,92697383,92761855,92764878,92765506,92774040,92789942,92792766,92797835,92805152,92806361,92809842,92831621,92834869,92836565,92837662,92840561,92843933,92857213,92859164,92866740,92880730,92882737,92886999,92889188,92889855,92890490,","92225174,92524948,92697445,92762170,92765089,92765575,92774180,92790218,92792977,92801909,92805349,92806515,92810076,92832011,92835084,92836703,92837806,92840759,92844732,92857348,92859322,92867209,92880884,92883393,92887113,92889248,92889891,92896473,",0,FAT3,cmpl,cmpl,"-1,0,1,0,0,1,1,0,0,1,1,0,1,1,1,0,0,0,0,1,1,0,1,2,1,1,1,1,"
3704,3704,20,XM_047427130.1,chr11,+,99020948,100358885,99556214,100356220,23,"99020948,99556144,99844851,99845086,99916053,99956805,100002033,100061211,100070423,100071704,100074143,100191125,100193487,100224691,100255759,100271091,100297624,100299161,100308358,100340462,100341092,100350701,100356116,","99021270,99556269,99844975,99845262,99916149,99957009,100002136,100061393,100070560,100071834,100074294,100191253,100193663,100224812,100255918,100271241,100297695,100299396,100308468,100340649,100341205,100350870,100358885,",0,CNTN5,cmpl,cmpl,"-1,0,1,2,1,1,1,2,1,0,1,2,1,0,1,1,1,0,1,0,1,0,1,"
9625,9625,24,XM_011543027.3,chr11,-,126423357,127000870,126424579,127000509,17,"126423357,126425637,126429178,126431343,126435267,126436810,126440448,126444978,126446758,126449008,126456348,126463156,126473308,126521314,126526537,126562834,127000454,","126425023,126425724,126429288,126431526,126435303,126437009,126440549,126445105,126446886,126449157,126456454,126463307,126473466,126521464,126526687,126562912,127000870,",0,KIRREL3,cmpl,cmpl,"0,0,1,1,1,0,1,0,1,2,1,0,1,1,1,1,0,"
13653,13653,24,NM_001048209.2,chr11,+,131370614,132336822,131370806,132335146,8,"131370614,131911563,132146281,132212021,132307688,132310111,132314551,132335045,","131370888,131911648,132146514,132212147,132307823,132310232,132314703,132336822,",0,NTM,cmpl,cmpl,"0,1,2,1,1,1,2,1,"
13870,13870,24,NM_001012393.5,chr11,-,132414980,133532501,132420192,133532324,8,"132414980,132436085,132436658,132437221,132529060,132657086,132942925,133532263,","132420293,132436237,132436779,132437359,132529186,132657319,132943010,133532501,",0,OPCML,cmpl,cmpl,"1,2,1,1,1,2,1,0,"
2293,2293,9,XM_017019953.2,chr12,+,1970779,2697950,1971062,2691199,47,"1970779,2115223,2120324,2448975,2457566,2486103,2493189,2504435,2512811,2549942,2556950,2566421,2567568,2581589,2582821,2584502,2585375,2585834,2593212,2595873,2597436,2601853,2605080,2605678,2606610,2606983,2608510,2610540,2611902,2633628,2648474,2651639,2653834,2655146,2664824,2665580,2666685,2668932,2674540,2677093,2677732,2679443,2682549,2685735,2686165,2688446,2690899,","1971201,2115545,2120430,2449115,2457706,2486262,2493386,2504539,2512984,2550033,2556977,2566582,2567794,2581797,2582942,2584617,2585496,2585904,2593345,2596003,2597496,2601960,2605168,2605786,2606663,2607130,2608712,2610699,2612013,2633712,2648507,2651768,2653900,2655238,2664990,2665708,2666782,2669035,2674642,2677221,2677867,2679796,2682678,2685842,2686269,2688779,2697950,",0,CACNA1C,cmpl,cmpl,"0,1,2,0,2,1,1,0,2,1,2,2,1,2,0,1,2,0,1,2,0,0,2,0,0,2,2,0,0,0,0,0,0,0,2,0,2,0,1,1,0,0,2,2,1,0,0,"
19079,19079,11,XM_047429457.1,chr12,-,23529503,24562650,23534218,23896023,21,"23529503,23536452,23543210,23546315,23563257,23575660,23604386,23640811,23665443,23734683,23740866,23755637,23845982,23895792,24213342,24277215,24331276,24368562,24407484,24460595,24562337,","23534522,23536669,23543384,23546424,23563403,23575838,23604533,23640897,23665567,23734752,23741039,23755724,23846193,23896024,24213417,24277312,24331396,24368639,24407566,24460776,24562650,",0,SOX5,cmpl,cmpl,"2,1,1,0,1,0,0,1,0,0,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,"
20573,20573,14,XM_047429662.1,chr12,+,43795801,44399108,43844651,44388672,9,"43795801,43795974,43844623,43944209,44143524,44211289,44299579,44376594,44388025,","43795820,43796150,43844928,43944342,44143624,44211387,44299739,44376724,44389758,",0,TMEM117,cmpl,cmpl,"-1,-1,0,1,2,0,2,0,1,"
19861,19861,16,XM_024448962.2,chr12,-,61708272,62260034,61710405,62259544,6,"61708272,61753621,61754871,61867319,62258762,62259478,","61710417,61753746,61755024,61867426,62258842,62260034,",0,TAFA2,cmpl,cmpl,"0,1,1,2,0,0,"
7487,7487,136,XM_005268754.5,chr12,-,66347430,67069338,66349018,67069107,25,"66347430,66353416,66371693,66377016,66377173,66379279,66392307,66392676,66394207,66406282,66420719,66432547,66444583,66445321,66455408,66456186,66462923,66465274,66515618,66517900,66529830,66539077,66541814,66596846,67069049,","66349246,66353563,66371927,66377061,66377285,66379436,66392502,66392816,66394352,66406428,66420789,66432628,66444729,66445508,66455564,66456342,66463093,66465422,66515764,66517976,66529914,66539223,66541950,66596927,67069338,",0,GRIP1,cmpl,cmpl,"0,0,0,0,2,1,1,2,1,2,1,1,2,1,1,1,2,1,2,1,1,2,1,1,0,"
21121,21121,17,XM_017019244.2,chr12,+,72087265,72670758,72286810,72663195,20,"72087265,72105647,72286680,72377994,72469757,72473066,72499497,72542290,72562164,72562852,72568567,72575254,72575486,72618890,72621107,72621643,72652321,72653015,72656926,72663051,","72087439,72105752,72286954,72378121,72469912,72473180,72499635,72542356,72562230,72563040,72568656,72575388,72575542,72619038,72621205,72621751,72652489,72653156,72657008,72670758,",0,TRHDE,cmpl,cmpl,"-1,-1,0,0,1,0,0,0,0,0,2,1,0,2,0,2,2,2,2,0,"
12886,12886,18,XM_047429826.1,chr12,+,77571861,78213010,77572194,78210517,35,"77571861,77940318,77941080,77966228,77968518,77998336,78006418,78021746,78049992,78050763,78058995,78116771,78118026,78119236,78128705,78137176,78140281,78146368,78148841,78159202,78168754,78175305,78177140,78179528,78180870,78185600,78188247,78188608,78189983,78197246,78198604,78199334,78200472,78204934,78210397,","77572266,77940436,77941133,77966301,77968702,77998476,78007445,78021862,78050101,78051147,78059115,78116904,78118297,78119945,78128866,78137365,78140334,78146392,78148919,78159286,78168866,78175427,78177313,78179682,78181045,78185698,78188343,78188777,78190219,78197401,78198676,78199531,78200591,78205138,78213010,",0,NAV3,cmpl,cmpl,"0,0,1,0,1,2,1,2,1,2,2,2,0,1,2,1,1,0,0,0,0,1,0,2,0,1,0,0,1,0,2,2,1,0,0,"
19765,19765,148,NM_001135805.2,chr12,+,78863981,79452008,79217519,79449124,12,"78863981,78864997,78977798,79047296,79217502,79285786,79292007,79296068,79299383,79353501,79444072,79448917,","78864335,78865109,78977931,79047362,79217685,79285971,79292130,79296236,79299551,79353619,79444206,79452008,",0,SYT1,cmpl,cmpl,"-1,-1,-1,-1,0,1,0,0,0,0,1,0,"
12048,12048,19,NM_001351285.2,chr12,-,85955666,86839000,85979288,85989546,9,"85955666,85983522,85989399,86049673,86334064,86435156,86495250,86727208,86838665,","85980430,85983670,85989552,86049723,86334127,86435265,86495315,86727241,86839000,",0,MGAT4C,cmpl,cmpl,"1,0,0,-1,-1,-1,-1,-1,-1,"
820,820,20,XM_006719507.5,chr12,-,98734785,99984936,98735559,99984237,27,"98734785,98751354,98773041,98781116,98782125,98798933,98800996,98807843,98829173,98832028,99053156,99084924,99154288,99244341,99246274,99399630,99443672,99504475,99655066,99772921,99775547,99779870,99782021,99806403,99812154,99825308,99984103,","98735634,98751522,98773179,98781203,98782137,98799005,98801125,98807918,98829353,98832136,99053309,99085023,99154395,99244414,99246864,99399811,99443809,99504641,99655210,99773088,99775661,99779972,99782097,99806700,99812311,99825389,99984936,",0,ANKS1B,cmpl,cmpl,"0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,0,2,2,0,"
20593,20593,196,NM_133448.3,chr12,-,129071725,129904025,129073874,129903339,9,"129071725,129078533,129081758,129084496,129209519,129337633,129531058,129699809,129903260,","129075059,129078725,129082032,129084702,129209663,129337817,129531205,129700698,129904025,",0,TMEM132D,cmpl,cmpl,"0,0,2,0,0,2,2,1,0,"
2294,2294,73,XM_054332314.1,chr12_KZ208916v1_fix,+,311695,1046066,313206,1039315,47,"311695,457367,462468,797091,805682,834219,841305,852551,860927,898058,905066,914537,915684,929705,930937,932618,933491,933950,941328,943989,945552,949969,953196,953794,954726,955099,956626,958656,960018,981744,996590,999755,1001950,1003262,1012940,1013696,1014801,1017048,1022656,1025209,1025848,1027559,1030665,1033851,1034281,1036562,1039015,","313345,457689,462574,797231,805822,834378,841502,852655,861100,898149,905093,914698,915910,929913,931058,932733,933612,934020,941461,944119,945612,950076,953284,953902,954779,955246,956828,958815,960129,981828,996623,999884,1002016,1003354,1013106,1013824,1014898,1017151,1022758,1025337,1025983,1027912,1030794,1033958,1034385,1036895,1046066,",0,CACNA1C,cmpl,cmpl,"0,1,2,0,2,1,1,0,2,1,2,2,1,2,0,1,2,0,1,2,0,0,2,0,0,2,2,0,0,0,0,0,0,0,2,0,2,0,1,1,0,0,2,2,1,0,0,"
1450,1450,97,NM_001411005.1,chr13,+,25371973,26025851,25372212,26019985,36,"25371973,25468976,25529998,25530561,25532271,25533272,25537987,25540318,25541918,25543290,25551337,25553792,25554990,25558972,25559720,25563955,25570766,25571609,25574807,25577068,25578814,25579807,25581818,25589634,25699172,25769045,25774848,25837162,25839545,25860194,25860803,25862300,25961574,25968574,26012530,26019887,","25372288,25469121,25530098,25530660,25532317,25533313,25538061,25540388,25542046,25543402,25551503,25553920,25555068,25559061,25559765,25564031,25570872,25571692,25574857,25577138,25578899,25579947,25581957,25589699,25699345,25769229,25774959,25837285,25839624,25860256,25860860,25862408,25961663,25968679,26012622,26025851,",0,ATP8A2,cmpl,cmpl,"0,1,2,0,0,1,0,2,0,2,0,1,0,0,2,2,0,1,0,2,0,1,0,1,0,2,0,0,0,1,0,0,0,2,2,1,"
12591,12591,12,NM_001384605.1,chr13,+,28819962,29505947,29024698,29503206,16,"28819962,28839777,29024456,29033884,29100772,29281703,29324612,29359261,29439982,29480149,29487899,29492645,29497237,29498417,29501096,29502992,","28820285,28839850,29026903,29034125,29100970,29281865,29324711,29359473,29440049,29480364,29488005,29492719,29497336,29498537,29501194,29505947,",0,MTUS2,cmpl,cmpl,"-1,-1,0,0,1,1,1,1,0,1,0,1,0,0,0,2,"
19501,19501,1,NM_001243476.3,chr13,-,33103136,33676794,33105592,33524267,18,"33103136,33106757,33109872,33110685,33111777,33112720,33118064,33126080,33127372,33128928,33142309,33165336,33167550,33439690,33524237,33661276,33663889,33676677,","33105710,33106934,33110090,33110907,33111892,33112931,33118263,33126240,33127546,33130289,33142373,33165418,33167622,33439724,33524372,33661343,33664137,33676794,",0,STARD13,cmpl,cmpl,"2,2,0,0,2,1,0,2,2,0,2,1,1,0,0,-1,-1,-1,"
12892,12892,13,XM_047430269.1,chr13,+,34942269,35672736,34942820,35670991,58,"34942269,35040932,35044946,35045305,35048562,35050268,35056009,35058716,35069907,35070718,35098296,35109289,35110809,35117413,35118227,35118376,35123481,35142268,35155773,35156082,35157077,35159015,35161749,35164355,35171271,35173463,35176995,35182359,35183975,35195863,35208699,35211052,35232491,35290388,35309527,35349107,35352156,35432268,35452091,35472399,35550476,35550929,35554986,35566904,35583897,35593327,35606425,35628080,35645868,35646258,35649654,35651804,35654854,35655578,35665084,35667373,35668367,35670900,","34943114,35041164,35045047,35045401,35048684,35050395,35056129,35058863,35070105,35070852,35098405,35109442,35110978,35117493,35118290,35118474,35123574,35142377,35155855,35156206,35157270,35160032,35161967,35164509,35171452,35173594,35177103,35182528,35184071,35196302,35208836,35211179,35232619,35290450,35309592,35349216,35352323,35432393,35452235,35472536,35550594,35551032,35555102,35567017,35584038,35593447,35606578,35628248,35645931,35646348,35649847,35651876,35655010,35655749,35665186,35667570,35668519,35672736,",0,NBEA,cmpl,cmpl,"0,0,1,0,0,2,0,0,0,0,2,0,0,1,0,0,2,2,0,1,2,0,0,2,0,1,0,0,1,1,2,1,2,1,0,2,0,2,1,1,0,1,2,1,0,0,0,0,0,0,0,1,1,1,1,1,0,2,"
5570,5570,114,NM_001347966.2,chr13,-,43213129,43786972,43213989,43412914,18,"43213129,43224052,43236635,43265397,43269469,43298345,43322383,43326418,43344537,43355918,43359850,43361278,43411915,43412844,43484008,43667478,43761728,43786651,","43214121,43224138,43236738,43265454,43269577,43298530,43322501,43326525,43344750,43356152,43360057,43361452,43412053,43412988,43484152,43667544,43761837,43786972,",0,ENOX1,cmpl,cmpl,"0,1,0,0,0,1,0,1,1,1,1,1,1,0,-1,-1,-1,-1,"
14795,14795,0,NM_203487.3,chr13,-,66302833,67230336,66304654,67228440,5,"66302833,66631209,66903503,67225404,67229779,","66305028,66631411,66903605,67228575,67230336,",0,PCDH9,cmpl,cmpl,"1,0,0,0,-1,"
9640,9640,143,NM_001400139.1,chr13,-,73686088,74306045,73695489,73995022,8,"73686088,73715367,73764937,73813151,73845826,73943980,73994989,74305995,","73695671,73715525,73765000,73813287,73846373,73944070,73995053,74306045,",0,KLF12,cmpl,cmpl,"1,2,2,1,0,0,0,-1,"
7298,7298,2,NM_004466.6,chr13,+,91398620,92867237,91399046,92866439,8,"91398620,91448760,91693186,91728531,91756294,91907936,92144829,92866281,","91399209,91448922,91693881,91728665,91756420,91908057,92144989,92867237,",0,GPC5,cmpl,cmpl,"0,1,1,0,2,2,0,1,"
7299,7299,20,XM_047429990.1,chr13,+,93216528,94408020,93545312,94403217,9,"93216528,93545262,93830153,94027728,94286348,94305979,94382413,94398465,94403014,","93226682,93545421,93830545,94027894,94286479,94306123,94382550,94398641,94408020,",0,GPC6,cmpl,cmpl,"-1,0,1,0,1,0,0,2,1,"
8282,8282,20,NM_153456.4,chr13,+,96090106,96839562,96090862,96833198,2,"96090106,96832489,","96091569,96839562,",0,HS6ST3,cmpl,cmpl,"0,2,"
6324,6324,21,NM_001321938.2,chr13,-,101710803,102402443,101722830,102220709,7,"101710803,101726611,101868724,101875185,102220696,102401470,102401953,","101722967,101726810,101868828,101875296,102220933,102401598,102402443,",0,FGF14,cmpl,cmpl,"1,0,1,1,0,-1,-1,"
12844,12844,175,NM_001080396.3,chr13,-,107163509,107867496,107170496,107866596,3,"107163509,107210583,107865681,","107170786,107210755,107867496,",0,NALF1,cmpl,cmpl,"1,0,0,"
12739,12739,2,XM_047430183.1,chr13,+,108495715,109208005,108665923,109206836,35,"108495715,108665885,108712660,108727439,108785634,108793515,108806678,108820336,108823124,108844345,108855442,108866176,108883058,108888371,108898015,108910002,108957687,108961538,108962423,108964760,108992375,109008896,109019710,109046915,109052299,109055045,109055389,109100784,109120369,109125111,109127281,109140263,109164900,109179541,109206608,","108495924,108666149,108712731,108727583,108785743,108793640,108806804,108820412,108823278,108844493,108855553,108866242,108883186,108888477,108898133,108910150,108957799,108961656,108962495,108964902,108992448,109009049,109019911,109046991,109052475,109055126,109055595,109100887,109120466,109125358,109127550,109141376,109165059,109179633,109208005,",0,MYO16,cmpl,cmpl,"-1,0,1,0,0,1,0,0,1,2,0,0,0,2,0,1,2,0,1,1,2,0,0,0,1,0,0,2,0,1,2,1,1,1,0,"
13458,13458,1,XM_017021585.2,chr14,+,32934784,33804173,32934845,33801109,11,"32934784,33215181,33367185,33560120,33676210,33735213,33774336,33778465,33793896,33797456,33799733,","32935003,33215426,33367268,33560210,33676385,33735332,33774530,33778572,33794044,33797581,33804173,",0,NPAS3,cmpl,cmpl,"0,2,1,0,0,1,0,2,1,2,1,"
11874,11874,14,NM_001113498.3,chr14,-,46839622,47675605,46841930,47674796,17,"46840091,46845765,46855023,46873432,46874044,46877488,46882043,46920011,46957373,47035010,47061248,47096853,47131713,47144077,47218020,47301410,47674516,","46842019,46845871,46855154,46873591,46874200,46877509,46882221,46920160,46957643,47035304,47061578,47097123,47131846,47144274,47218195,47301550,47675605,",0,MDGA2,cmpl,cmpl,"1,0,1,1,1,1,0,1,1,1,1,1,0,1,0,1,0,"
7307,7307,0,XM_047430879.1,chr14,+,66508146,67735355,66508527,67735340,15,"66508146,66681106,66776463,66824473,66842677,66879938,66916002,66922665,66924193,66965190,66985681,66987935,67023632,67058648,67735194,","66508591,66681185,66776521,66824566,66842716,66880033,66916069,66922938,66924292,66965325,66985738,66988007,67023675,67058786,67735355,",0,GPHN,cmpl,cmpl,"0,1,2,0,0,0,2,0,0,0,0,0,0,1,1,"
16685,16685,17,NM_001321818.2,chr14,+,67819778,68683096,67823543,68682944,11,"67819778,67823541,67825463,67835079,67865002,67885868,67887020,68291883,68411423,68468171,68682936,","67819853,67823627,67825577,67835196,67865139,67885988,67887204,68291980,68411527,68468250,68683096,",0,RAD51B,cmpl,cmpl,"-1,0,0,0,0,2,2,0,1,0,1,"
17060,17060,17,XM_024449761.2,chr14,+,71867334,72630029,71964791,72563027,22,"71867334,71869925,71908164,71964771,72352094,72454527,72458270,72459631,72465757,72470006,72472871,72474624,72476741,72478267,72495151,72510153,72518350,72536185,72540040,72541469,72562416,72562714,","71867623,71869984,71908434,71964875,72352194,72454578,72458377,72459683,72465822,72470083,72472953,72474699,72476840,72478329,72495262,72510279,72518537,72536275,72540094,72541620,72562585,72566530,",0,RGS6,cmpl,cmpl,"-1,-1,-1,0,0,1,1,0,1,0,2,0,0,0,2,2,2,0,0,0,1,2,"
13605,13605,18,XM_024449753.2,chr14,+,78170372,79868291,78243093,79861964,19,"78170372,78242390,78278644,78297830,78645119,78651164,78709216,78714755,78803619,78957241,78966024,78967207,78968172,78988021,79467220,79663777,79697629,79805111,79861662,","78170674,78243802,78278662,78297860,78645421,78651326,78709655,78715139,78803823,78957361,78966406,78967398,78968346,78988141,79467402,79663949,79697937,79805190,79868291,",0,NRXN3,cmpl,cmpl,"-1,0,1,1,1,0,0,1,1,1,1,2,1,1,1,0,1,0,1,"
6709,6709,12,NM_033223.5,chr15,+,26971180,27541984,26971535,27532881,10,"26971180,26977001,27026753,27326808,27328805,27480649,27519971,27527432,27527932,27532599,","26971588,26977150,27026821,27327029,27328888,27480787,27520124,27527629,27527992,27541984,",0,GABRG3,cmpl,cmpl,"0,2,1,0,2,1,1,1,0,0,"
5592,5592,12,NM_001387215.1,chr15,-,29117711,29675409,29118994,29252466,12,"29117711,29123344,29124686,29126266,29128788,29136365,29137033,29151733,29196429,29252367,29381774,29675098,","29119018,29123655,29124761,29126491,29128864,29136501,29137194,29151841,29196564,29252478,29381831,29675409,",0,ENTREP2,cmpl,cmpl,"0,1,1,1,0,2,0,0,0,0,-1,-1,"
17644,17644,1,XM_017022476.2,chr15,+,33310966,33866102,33311045,33865226,102,"33310966,33473418,33530591,33533310,33539349,33540790,33543621,33548129,33550159,33562836,33566677,33579975,33581507,33584394,33585997,33601418,33603122,33613182,33623806,33628470,33629939,33631209,33632948,33634585,33635613,33636375,33644310,33646350,33647423,33649071,33652717,33659719,33660196,33662152,33663536,33669353,33670418,33696217,33697881,33699703,33700976,33706918,33722714,33724064,33726385,33728856,33731473,33736234,33738449,33739831,33742365,33746067,33748113,33748467,33749978,33750162,33755064,33756305,33757474,33768657,33769111,33771919,33773533,33780210,33785661,33788217,33800769,33801868,33810478,33810977,33812862,33813466,33815833,33818577,33819755,33820755,33821269,33821522,33822995,33825602,33826251,33826671,33827198,33830962,33834967,33836905,33837630,33840824,33841863,33843487,33844861,33848290,33853044,33853554,33854388,33854765,33857779,33859574,33860594,33861077,33864137,33865130,","33311096,33473538,33530666,33533389,33539462,33540890,33543715,33548204,33550316,33563010,33566799,33580144,33581643,33584490,33586116,33601552,33603364,33613375,33624023,33628575,33630043,33631293,33633108,33634733,33635819,33636550,33644519,33646526,33647460,33649235,33652883,33659806,33660423,33662948,33663737,33669456,33670556,33696491,33697996,33699833,33701080,33707054,33722895,33724176,33726506,33729026,33731694,33736325,33738590,33739995,33742444,33746157,33748260,33748530,33750054,33750286,33755180,33756373,33757596,33768707,33769172,33772158,33773615,33780341,33785982,33788458,33800857,33801961,33810649,33811037,33812994,33813579,33815933,33818684,33819807,33820812,33821369,33821602,33823072,33825676,33826269,33826752,33827287,33831091,33835072,33836987,33838958,33840883,33842035,33843574,33845062,33848421,33853087,33853682,33854449,33854912,33857914,33859731,33860659,33861178,33864189,33866102,",0,RYR3,cmpl,cmpl,"0,0,0,0,1,0,1,2,2,0,0,2,0,1,1,0,2,1,2,0,0,2,2,0,1,0,1,0,2,0,2,0,0,2,0,0,1,1,2,0,1,0,1,2,0,1,0,2,0,0,2,0,0,0,0,1,2,1,0,2,1,2,1,2,1,1,2,0,0,0,0,0,2,0,2,0,0,1,0,2,1,1,1,0,0,0,1,0,2,0,0,0,2,0,2,0,0,0,1,0,2,0,"
17982,17982,14,NM_001198999.2,chr15,+,47184088,47774228,47759798,47771785,20,"47184088,47412392,47470473,47600864,47759744,47760303,47760977,47761157,47761329,47761660,47762199,47763015,47763849,47764173,47764637,47764882,47765868,47766104,47766576,47770496,","47184418,47412472,47470545,47600896,47759907,47760415,47761038,47761220,47761431,47761751,47762319,47763104,47764067,47764305,47764793,47765056,47766009,47766182,47766677,47774221,",0,SEMA6D,cmpl,cmpl,"-1,-1,-1,-1,0,1,2,0,0,0,1,1,0,2,2,2,2,2,2,1,"
21794,21794,15,XM_017022222.2,chr15,+,53837601,54633440,54012903,54627113,35,"53837601,53876877,53878173,54012647,54143017,54143619,54235029,54236429,54237618,54250224,54264167,54265354,54293894,54297810,54300209,54321938,54332042,54333766,54338360,54393047,54414981,54494607,54500078,54500834,54507116,54511752,54525548,54532916,54546721,54549634,54555431,54567799,54622326,54623794,54626827,","53837659,53877058,53878298,54015886,54143040,54143684,54235108,54236435,54237690,54250444,54264395,54265496,54294064,54297926,54300373,54322095,54332111,54333856,54338489,54393181,54415067,54494734,54500175,54500978,54507194,54511830,54525637,54533066,54546845,54549691,54555512,54567947,54622419,54623954,54633440,",0,UNC13C,cmpl,cmpl,"-1,-1,-1,0,1,0,2,0,0,0,1,1,2,1,0,2,0,0,0,0,2,1,2,0,0,0,0,2,2,0,0,0,1,1,2,"
17333,17333,16,XM_047432928.1,chr15,-,60488283,61229302,60497454,60514628,11,"60488283,60499891,60500958,60502759,60503534,60505507,60511225,60514615,60531765,60677150,61229052,","60497619,60500004,60501069,60502867,60503667,60505629,60511621,60514757,60531851,60678686,61229302,",0,RORA,cmpl,cmpl,"0,1,1,1,0,1,1,0,-1,-1,-1,"
20382,20382,17,NM_001394532.1,chr15,+,71096893,71783383,71141527,71777374,18,"71096893,71141448,71154862,71215034,71242648,71256612,71411686,71660529,71728548,71731120,71737731,71745105,71746837,71748420,71757901,71765019,71771063,71777231,","71097006,71141556,71154932,71215399,71243096,71256715,71411823,71660734,71728724,71731217,71738007,71745235,71747042,71748594,71758075,71765199,71771208,71783383,",0,THSD4,cmpl,cmpl,"-1,0,2,0,2,0,1,0,1,0,1,1,2,0,0,0,0,1,"
17780,17780,18,NM_001353010.2,chr15,-,76347903,76905340,76348632,76804624,33,"76347903,76351236,76353948,76376161,76381377,76404523,76434077,76471211,76504858,76574157,76621763,76665652,76701757,76702849,76705902,76728594,76733228,76753807,76764960,76765336,76765562,76766917,76771741,76774854,76795279,76800247,76804532,76841733,76851167,76857808,76862415,76883811,76905192,","76348736,76351288,76354140,76376311,76381615,76404679,76434310,76471335,76504974,76574284,76621829,76665789,76701865,76703002,76705984,76728737,76733384,76753948,76765072,76765454,76765638,76767088,76771954,76775117,76795440,76800364,76804633,76841931,76851222,76857879,76862533,76883876,76905340,",0,SCAPER,cmpl,cmpl,"1,0,0,0,2,2,0,2,0,2,2,0,0,0,2,0,0,0,2,1,0,0,0,1,2,2,0,-1,-1,-1,-1,-1,-1,"
465,465,155,XM_011521227.4,chr15,+,86079619,87031476,86079972,87028840,23,"86079619,86142003,86143698,86154429,86158932,86224913,86247670,86256852,86257963,86262777,86264257,86266373,86266989,86269918,86271618,86279638,86295254,86397365,86522809,86546001,86554360,86674272,87028824,","86080023,86142067,86143845,86154561,86159026,86224951,86247879,86257018,86258031,86262894,86264838,86266457,86267076,86270067,86271706,86279783,86295408,86397546,86522939,86546133,86554537,86674436,87031476,",0,AGBL1,cmpl,cmpl,"0,0,1,1,1,2,1,0,1,0,0,2,2,2,1,2,0,1,2,0,0,0,2,"
5593,5593,74,NM_001387215.1,chr15_KI270905v1_alt,-,1392758,1959533,1394045,1528000,12,"1392758,1397973,1399315,1400895,1403417,1411936,1412604,1427301,1471992,1527901,1657276,1959222,","1394069,1398284,1399390,1401120,1403493,1412072,1412765,1427409,1472127,1528012,1657333,1959533,",0,ENTREP2,cmpl,cmpl,"0,1,1,1,0,2,0,0,0,0,-1,-1,"
5594,5594,74,NM_001387215.1,chr15_KN538374v1_fix,-,1280274,1847049,1281561,1415516,12,"1280274,1285489,1286831,1288411,1290933,1299452,1300120,1314817,1359508,1415417,1544792,1846738,","1281585,1285800,1286906,1288636,1291009,1299588,1300281,1314925,1359643,1415528,1544849,1847049,",0,ENTREP2,cmpl,cmpl,"0,1,1,1,0,2,0,0,0,0,-1,-1,"
16812,16812,9,NM_001415888.1,chr16,+,5239720,7713340,5239766,7710745,18,"5239720,5467215,5598901,5867302,6316994,6654602,7052056,7518146,7579776,7587246,7595548,7597370,7607284,7653814,7664928,7676773,7709055,7710622,","5240105,5467254,5598961,5867335,6317057,6654650,7052098,7518389,7579920,7587300,7595641,7597431,7607338,7653947,7664968,7676838,7709131,7713340,",0,RBFOX1,cmpl,cmpl,"0,0,0,0,0,0,0,0,0,0,0,0,1,1,2,0,2,0,"
19019,19019,84,NM_032167.5,chr16,+,11976733,12574287,11976806,12568629,21,"11976733,11999296,12002990,12027319,12042896,12046383,12048371,12051846,12061527,12069056,12078832,12126632,12129629,12199600,12277932,12356162,12398445,12403447,12477718,12524701,12568505,","11976813,11999358,12003043,12027444,12043077,12046454,12048620,12052222,12061646,12069132,12078915,12126696,12129758,12199683,12278036,12356279,12398501,12403529,12477859,12524841,12574287,",0,SNX29,cmpl,cmpl,"0,1,0,2,1,2,1,1,2,1,2,1,2,2,1,0,0,2,0,0,2,"
18231,18231,85,XM_011522642.3,chr16,+,12901597,13474651,12901941,13474248,5,"12901597,12916687,13203393,13350179,13474209,","12902627,12916815,13203549,13350421,13474651,",0,SHISA9,cmpl,cmpl,"0,2,1,1,0,"
22592,22592,17,NM_001386735.1,chr16,-,72782884,73891930,72787163,72960145,17,"72782884,72793254,72800026,72811576,72811904,72829778,72889730,72950468,72957426,73093234,73130967,73143751,73257046,73318239,73456002,73680179,73891650,","72788848,72798714,72800129,72811777,72812038,72829859,72889962,72950965,72960194,73093598,73131094,73143831,73257136,73318336,73456258,73680240,73891930,",0,ZFHX3,cmpl,cmpl,"1,1,0,0,1,1,0,1,0,-1,-1,-1,-1,-1,-1,-1,-1,"
22333,22333,18,NM_001291997.2,chr16,+,78099653,79212667,78115084,79211796,8,"78099653,78109777,78114975,78164182,78386859,78424869,78432487,79211607,","78099885,78109835,78115154,78164289,78386948,78425055,78432752,79212667,",0,WWOX,cmpl,cmpl,"-1,-1,0,1,0,2,2,0,"
2945,2945,18,NM_001220490.2,chr16,+,82626968,83800640,83344987,83795030,13,"82626968,82858361,83125384,83217344,83344861,83486476,83602453,83670789,83678207,83748107,83779967,83783253,83795022,","82627137,82858473,83125501,83217497,83345006,83486655,83602594,83670972,83678461,83748250,83780201,83783472,83800640,",0,CDH13,cmpl,cmpl,"-1,-1,-1,-1,0,1,0,0,0,2,1,1,1,"
1260,1260,1,NM_001094.5,chr17,-,33013086,34156768,33013964,34156532,10,"33013086,33015970,33017604,33021218,33023860,33025925,33028241,33088862,33111916,34155977,","33014066,33016039,33017684,33021310,33024014,33025982,33028392,33088990,33112067,34156768,",0,ASIC2,cmpl,cmpl,"0,0,1,2,1,1,0,1,0,0,"
11247,11247,117,XM_024450773.2,chr17,+,46372791,47049128,46512712,47049061,11,"46512467,46517361,46520211,46523083,46523803,46540175,46540806,46546254,46548311,46550414,47049055,","46515321,46517433,46520283,46523155,46523884,46540247,46540881,46546373,46549843,46550519,47049128,",0,LRRC37A2,cmpl,cmpl,"0,2,2,2,2,2,2,2,1,0,0,"
2260,2260,122,NM_001082534.2,chr17,-,51630312,52160023,51631583,52157786,10,"51630319,51633475,51635854,51649181,51653640,51747632,51930989,52072318,52157725,52159923,","51631606,51633650,51636009,51649254,51653736,51747818,51931132,52072393,52158369,52160023,",0,CA10,cmpl,cmpl,"1,0,1,0,0,0,1,1,0,-1,"
1627,1627,16,NM_017679.5,chr17,+,60677850,61392831,60679457,61392125,24,"60677850,60679452,60683981,60689685,60709218,60747197,60808003,60868575,60874661,60889694,60902619,60910531,60924406,60947218,60989970,61015750,61034665,61037888,61040791,61074919,61078332,61084466,61368326,61391976,","60677914,60679540,60684036,60689761,60709325,60747279,60808076,60868683,60874738,60889771,60902703,60910702,60924500,60947352,60990235,61015901,61034790,61038054,61040892,61075020,61078529,61084564,61368494,61392831,",0,BCAS3,cmpl,cmpl,"-1,0,2,0,1,0,1,2,2,1,0,0,0,1,0,1,2,1,2,1,0,2,1,1,"
3122,3122,16,NM_001353129.2,chr17,-,65635536,66192133,65635970,66183299,27,"65635536,65637123,65640963,65689128,65743067,65750661,65851803,65902151,65927581,65961462,66005689,66027500,66028312,66029122,66029868,66053735,66062962,66066777,66069914,66096250,66096584,66129745,66132669,66175043,66176829,66183193,66191996,","65635974,65637188,65641065,65689218,65743217,65750724,65852034,65902334,65927689,65961598,66005769,66027560,66028405,66029252,66030023,66053879,66063081,66066877,66070001,66096331,66096632,66129823,66132763,66175216,66177020,66183307,66192133,",0,CEP112,cmpl,cmpl,"2,0,0,0,0,0,0,0,0,2,0,0,0,2,0,0,1,0,0,0,0,0,2,0,1,0,-1,"
16815,16815,148,XM_024450593.2,chr17,-,79089344,79665571,79092596,79115715,17,"79091946,79094450,79095512,79096652,79097291,79097691,79101583,79103161,79104072,79106650,79115493,79235765,79307723,79482453,79644136,79646195,79665370,","79092641,79094529,79095574,79096833,79097424,79097745,79101644,79103254,79104126,79106788,79115748,79235805,79307824,79482598,79644242,79646334,79665571,",0,RBFOX3,cmpl,cmpl,"0,2,0,2,1,1,0,0,0,0,0,-1,-1,-1,-1,-1,-1,"
4865,4865,9,XM_024451288.2,chr18,-,3496031,4455307,3499184,3880068,15,"3496031,3502492,3508569,3534193,3567489,3581874,3656083,3729134,3742334,3814058,3879111,4005115,4106580,4151179,4455005,","3499394,3502645,3508661,3534615,3567581,3582248,3656113,3729375,3742512,3814273,3880140,4005201,4107046,4151287,4455307,",0,DLGAP1,cmpl,cmpl,"0,0,1,2,0,1,1,0,2,0,0,-1,-1,-1,-1,"
16475,16475,1,NM_002845.4,chr18,+,7567315,8406856,7567818,8406162,31,"7567315,7774148,7888105,7906504,7926567,7949180,7955120,8069685,8076454,8085670,8088748,8113485,8114790,8143646,8244057,8247844,8253226,8296367,8314780,8319177,8343422,8370889,8376045,8376461,8378264,8379166,8380295,8384560,8387071,8394475,8406108,","7567891,7774271,7888377,7906583,7926683,7949355,7955414,8069994,8076564,8085872,8088851,8113759,8114827,8143779,8244209,8247919,8253414,8296455,8314857,8319214,8343520,8371006,8376200,8376597,8378414,8379340,8380427,8384686,8387235,8394611,8406856,",0,PTPRM,cmpl,cmpl,"0,1,1,0,1,0,1,1,1,0,1,2,0,1,2,1,1,0,1,0,1,0,0,2,0,0,0,0,0,2,0,"
4493,4493,15,XM_047437311.1,chr18,+,52340196,53535899,52340787,53530653,29,"52340196,52752053,52906043,52923706,52925233,53063304,53066045,53157355,53178961,53205215,53207678,53215547,53305577,53322046,53339712,53386042,53391714,53397307,53402785,53410451,53416123,53435143,53450499,53459231,53467893,53486796,53499297,53526616,53530563,","52340878,52752374,52906328,52923857,52925370,53063459,53066166,53157512,53179116,53205364,53207817,53215597,53305719,53322157,53339907,53386138,53391887,53397446,53402893,53410646,53416156,53435209,53450662,53459458,53468010,53486952,53499510,53526759,53535899,",0,DCC,cmpl,cmpl,"0,1,1,1,2,1,0,1,2,1,0,1,0,1,1,1,1,0,1,1,1,1,1,2,1,1,1,1,0,"
12786,12786,9,XM_017003604.2,chr2,-,1789112,2331275,1791866,1979777,27,"1789112,1792320,1801689,1809075,1839148,1840759,1851640,1886538,1887058,1887487,1889240,1892036,1903079,1910239,1912019,1917204,1922285,1942981,1979164,1979520,1979722,1997190,2053977,2172871,2284403,2326035,2330966,","1792007,1792464,1801799,1809167,1839370,1840843,1851703,1886607,1887121,1887609,1889477,1892287,1903294,1910347,1912110,1917339,1923263,1943334,1979227,1979554,1979777,1997347,2054123,2172988,2284503,2326111,2331275,",0,MYT1L,cmpl,cmpl,"0,0,1,2,2,2,2,2,2,0,0,1,2,2,1,1,1,2,2,1,0,-1,-1,-1,-1,-1,-1,"
12890,12890,87,XM_017004317.2,chr2,-,14998066,15561334,15137403,15561304,53,"14998066,15137355,15178987,15186741,15190263,15218772,15232421,15234544,15238467,15275483,15276850,15287072,15292536,15308215,15309170,15327749,15328198,15330597,15351991,15353552,15356302,15366579,15374607,15379601,15383214,15394226,15396412,15402167,15415545,15417526,15424314,15427710,15461200,15461686,15467328,15467663,15468381,15473221,15474066,15475686,15478225,15488893,15504144,15511211,15534542,15536417,15539222,15551492,15553425,15554060,15556782,15558579,15561187,","14998224,15137445,15179116,15186880,15190403,15218968,15232511,15234747,15238686,15275818,15277101,15287183,15292766,15308353,15309247,15327870,15328312,15330765,15352081,15353710,15356416,15366693,15374720,15379831,15383317,15394349,15396475,15402301,15415719,15417712,15424468,15427794,15461337,15461791,15467407,15467804,15468533,15473347,15474324,15475880,15478289,15489022,15504213,15511350,15534641,15536551,15539356,15551536,15553473,15554138,15556819,15558634,15561334,",0,NBAS,cmpl,cmpl,"-1,0,0,2,0,2,2,0,0,1,2,2,0,0,1,0,0,0,0,1,1,1,2,0,2,2,2,0,0,0,2,2,0,0,2,2,0,0,0,1,0,0,0,2,2,0,1,2,2,2,1,0,0,"
643,643,12,NM_004304.5,chr2,-,29192773,29921586,29193223,29920659,29,"29192773,29196769,29197541,29207170,29209785,29213983,29220705,29222343,29222516,29223341,29225460,29226921,29227573,29228883,29232303,29233564,29239679,29251104,29275098,29275401,29296887,29318303,29320750,29328349,29383731,29531914,29694849,29717577,29919992,","29193922,29196860,29197676,29207272,29209878,29214081,29220835,29222408,29222607,29223528,29225565,29227074,29227672,29229066,29232448,29233696,29239830,29251267,29275227,29275496,29297057,29318404,29320882,29328481,29383859,29532116,29695014,29717697,29921586,",0,ALK,cmpl,cmpl,"0,2,2,2,2,0,2,0,2,1,1,1,1,1,0,0,2,1,1,2,0,1,1,1,2,1,1,1,0,"
16059,16059,14,XM_005264428.2,chr2,+,45651278,46187990,45652100,46184881,16,"45651278,45651903,45842999,45976428,45978975,45980295,45984550,46001403,46004541,46007461,46010343,46086207,46145092,46151040,46159605,46184734,","45651703,45652448,45843063,45976588,45979010,45980381,45984680,46001546,46004638,46007661,46010517,46086362,46145231,46151229,46159752,46187990,",0,PRKCE,cmpl,cmpl,"-1,0,0,1,2,1,0,1,0,1,0,0,2,0,0,0,"
13603,13603,1,NM_001135659.3,chr2,-,49918502,51032132,49921943,51028273,24,"49918502,49943703,50053270,50054954,50091322,50236788,50465441,50472297,50495904,50497332,50506494,50528624,50531226,50538252,50552586,50620021,50621204,50623313,50921868,50922657,50925937,51026370,51027501,51031980,","49922251,49943791,50053590,50055044,50091494,50236970,50465561,50472471,50496095,50497714,50506617,50528651,50531430,50538636,50553025,50620183,50621249,50623615,50921880,50922687,50925955,51026469,51029194,51032132,",0,NRXN1,cmpl,cmpl,"1,0,1,1,0,1,1,1,2,1,1,1,1,1,0,0,0,1,1,1,1,1,0,-1,"
22196,22196,133,XM_047444626.1,chr2,-,63119558,63840826,63121820,63571377,21,"63119558,63152913,63174669,63259306,63313247,63378385,63381905,63404047,63433744,63437420,63439756,63484603,63484916,63486541,63487446,63492855,63571374,63650658,63673866,63813621,63840042,","63122056,63152945,63174832,63259409,63313311,63378509,63382094,63404657,63433936,63437554,63439871,63484663,63484987,63486586,63487494,63492940,63571626,63650838,63678253,63813707,63840826,",0,WDPCP,cmpl,cmpl,"1,2,1,0,2,1,1,0,0,1,0,0,1,1,1,0,0,-1,-1,-1,-1,"
5817,5817,17,NM_001321731.2,chr2,-,72175983,72826033,72182889,72825910,23,"72175983,72182852,72184074,72334946,72379728,72465159,72480615,72492317,72495429,72496453,72498453,72499900,72513131,72514633,72515042,72559452,72575491,72718102,72731006,72731154,72733070,72741303,72825797,","72179461,72182905,72184187,72335020,72379870,72465339,72480750,72492429,72495539,72496559,72498551,72499972,72513252,72514680,72515126,72559521,72575668,72718307,72731052,72731245,72733118,72741469,72826033,",0,EXOC6B,cmpl,cmpl,"-1,2,0,1,0,0,0,2,0,2,0,0,2,0,0,0,0,2,1,0,0,2,0,"
11314,11314,146,NM_001134745.3,chr2,-,76747684,77522376,76748694,77521671,4,"76747684,77518317,77521667,77522108,","76748916,77519864,77521818,77522376,",0,LRRTM4,cmpl,cmpl,"0,1,0,-1,"
4198,4198,18,NM_001399737.1,chr2,+,79185376,80648780,79651556,80647872,22,"79185376,79197958,79312708,79373830,79505053,79651551,79744386,79858012,79869815,79874075,79909593,80393210,80419448,80544981,80545906,80555692,80574162,80581705,80589303,80604073,80608183,80647584,","79185431,79198076,79312796,79374013,79505182,79651658,79744582,79858179,79869935,79874342,79909797,80393291,80419601,80545074,80546063,80555893,80574314,80581819,80589485,80604179,80608318,80648780,",0,CTNNA2,cmpl,cmpl,"-1,-1,-1,-1,-1,0,0,1,0,0,0,0,0,0,0,1,1,0,0,2,0,0,"
447,447,20,XM_047444279.1,chr2,-,99545418,100142590,99551473,100110104,28,"99545418,99554310,99554682,99558874,99560364,99565486,99568851,99578326,99582797,99587153,99593194,99601434,99649625,99672537,99727076,99744103,99752220,99837476,100006631,100007147,100008811,100011496,100104401,100105503,100110053,100112385,100129223,100142483,","99551595,99554534,99554732,99558968,99560436,99565623,99568915,99578451,99582999,99587278,99594289,99601621,99649666,99672589,99727128,99744140,99752301,99837524,100007017,100007460,100008932,100011571,100104518,100105583,100110333,100112524,100129306,100142590,",0,AFF3,cmpl,cmpl,"1,2,0,2,2,0,2,0,2,0,0,2,0,2,1,0,0,0,1,0,2,2,2,0,0,-1,-1,-1,"
16726,16726,2,XM_047445367.1,chr2,+,108719481,109842301,108719606,109841457,25,"108719481,108729131,108730773,108731321,108735531,108736103,108740488,108746710,108748919,108751263,108751527,108751870,108752997,108753425,108753824,108754904,108755175,108758412,108762100,108763236,108769259,108771700,108772488,108772867,109841403,","108719678,108729199,108730885,108731474,108735762,108736249,108740681,108746798,108749129,108751445,108751703,108751994,108753159,108753563,108753971,108755084,108755259,108758548,108762195,108768388,108769337,108771871,108772581,108773046,109842301,",0,RANBP2,cmpl,cmpl,"0,0,2,0,0,0,2,0,1,1,0,2,0,0,0,0,0,0,1,0,1,1,1,1,0,"
5065,5065,22,NM_001321913.3,chr2,+,114442640,115845780,115739803,115842345,25,"114442640,115343816,115499509,115525897,115689686,115689839,115727815,115739738,115746085,115753173,115762571,115768296,115777207,115777786,115780873,115782351,115791080,115791286,115814792,115815674,115836156,115836506,115836673,115840749,115842210,","114442838,115343912,115499604,115525972,115689739,115689921,115727936,115739893,115746183,115753297,115762610,115768404,115777299,115777834,115780995,115782399,115791179,115791356,115814987,115815729,115836256,115836565,115836746,115840823,115845780,",0,DPP10,cmpl,cmpl,"-1,-1,-1,-1,-1,-1,-1,0,0,2,0,0,0,2,2,1,1,1,2,2,0,1,0,1,0,"
3714,3714,23,NM_130773.4,chr2,+,124025286,124921219,124025650,124914288,24,"124025286,124221704,124242199,124417442,124434483,124446752,124474738,124504291,124524302,124527284,124563216,124609800,124647757,124747228,124763671,124763976,124772798,124789901,124798095,124865305,124869674,124902881,124911466,124914091,","124025732,124221809,124242393,124417590,124434687,124446937,124474879,124504556,124524452,124527456,124563323,124609920,124647958,124747385,124763799,124764147,124773017,124790141,124798320,124865436,124869762,124903100,124911538,124921219,",0,CNTNAP5,cmpl,cmpl,"0,1,1,0,1,1,0,0,1,1,2,1,1,1,2,1,1,1,1,1,0,1,1,1,"
12943,12943,24,XM_011511100.4,chr2,-,132671787,133674836,132673023,133517526,19,"132671787,132728815,132731736,132773815,132781051,132781939,132790022,132796627,132860491,132868935,132878847,132963719,132994151,133129977,133213715,133303036,133517457,133559049,133674673,","132673305,132728952,132732051,132773894,132781229,132785718,132790205,132796729,132860611,132868974,132878916,132963869,132994239,133130111,133213779,133303110,133517587,133559117,133674836,",0,NCKAP5,cmpl,cmpl,"0,1,1,0,2,0,0,0,0,0,0,0,2,0,2,0,0,-1,-1,"
20384,20384,25,NM_001316349.2,chr2,+,136765544,137677718,136882178,137676605,28,"136765544,136882143,137056419,137094872,137115123,137160212,137170740,137231043,137232898,137242456,137272532,137275922,137405612,137411608,137450844,137563220,137572405,137616174,137618391,137620608,137642487,137655500,137656795,137657064,137659663,137663382,137667773,137676523,","136765687,136882317,137057230,137095121,137115293,137160368,137170938,137231235,137233133,137242572,137272662,137276026,137405807,137411872,137451023,137563354,137572556,137616316,137618507,137620726,137642633,137655660,137656969,137657160,137659746,137663575,137667861,137677718,",0,THSD7B,cmpl,cmpl,"-1,0,1,2,2,1,1,1,1,2,1,2,1,1,1,0,2,0,1,0,1,0,1,1,1,0,1,2,"
11210,11210,25,NM_018557.3,chr2,-,140231422,142131016,140233185,142130729,91,"140231422,140234785,140238151,140239441,140247085,140270241,140274423,140297807,140314934,140321962,140323892,140325761,140334452,140335614,140350796,140352952,140356341,140357978,140358820,140364660,140370709,140371178,140373007,140378179,140385892,140442503,140444329,140444562,140450567,140456454,140457462,140475137,140485342,140487616,140492607,140495564,140501686,140502962,140506795,140509927,140514652,140516888,140525843,140526236,140534020,140536580,140540972,140541778,140598630,140601449,140700249,140701720,140702140,140702426,140715972,140716681,140769212,140770880,140776097,140813656,140839990,140840917,140850101,140851651,140867589,140868098,140883816,140886137,140902919,140907876,140922964,140950234,140951859,140982159,140989531,140993994,141005334,141013555,141015695,141019921,141048985,141055115,141058882,141062050,141188420,141229182,141247225,141254521,141480395,141810278,142130647,","140233326,140234884,140238296,140239532,140247162,140270346,140274598,140297969,140315099,140322088,140324066,140325878,140334559,140335838,140351038,140353072,140356476,140358116,140358946,140364783,140370842,140371285,140373137,140378286,140386009,140442623,140444449,140444679,140450661,140456603,140457651,140475337,140485524,140487739,140492693,140495748,140501874,140503103,140506918,140510056,140514772,140517011,140525993,140526350,140534140,140536709,140541098,140541971,140598835,140601639,140700621,140701845,140702292,140702553,140716102,140716816,140769344,140771006,140776238,140813806,140840085,140841092,140850329,140851783,140867834,140868263,140884021,140886335,140903165,140908077,140923147,140950402,140951940,140982276,140989657,140994135,141005457,141013745,141015915,141020102,141049222,141055259,141059054,141062273,141188583,141229440,141247354,141254641,141480533,141810401,142131016,",0,LRP1B,cmpl,cmpl,"0,0,2,1,2,2,1,1,1,1,1,1,2,0,1,1,1,1,1,1,0,1,0,1,1,1,1,1,0,1,1,2,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,0,2,1,1,2,0,2,1,1,1,1,1,1,2,1,1,1,2,2,1,1,1,1,1,1,1,1,1,1,1,0,2,1,1,1,0,2,1,1,1,1,1,1,0,"
1039,1039,26,XM_017004500.3,chr2,+,143129418,143768352,143129430,143768172,13,"143129418,143202133,143216383,143228580,143250510,143435600,143436912,143487372,143519265,143556407,143624132,143703418,143767988,","143129466,143202202,143216445,143228668,143250600,143435699,143437042,143487495,143519364,143556485,143624267,143703524,143768352,",0,ARHGAP15,cmpl,cmpl,"0,0,0,2,0,0,0,1,1,1,1,1,2,"
6752,6752,27,NM_001422883.1,chr2,+,153068292,154456574,154242762,154450551,17,"153068292,153078339,153311474,153332573,153333236,153732768,153900935,153944393,154242029,154242697,154245811,154259020,154301408,154395990,154408983,154438591,154450410,","153068361,153078454,153311933,153332640,153333327,153732830,153901007,153944639,154242196,154242905,154245982,154259138,154301589,154396130,154409082,154438726,154456574,",0,GALNT13,cmpl,cmpl,"-1,-1,-1,-1,-1,-1,-1,-1,-1,0,2,2,0,1,0,0,0,"
1512,1512,3,NM_020981.4,chr2,+,167293000,167874045,167869039,167870020,5,"167293000,167490176,167646908,167818671,167868810,","167293334,167490277,167646966,167818793,167874045,",0,B3GALT1,cmpl,cmpl,"-1,-1,-1,-1,0,"
14949,14949,30,XM_047444688.1,chr2,-,182140040,182716797,182147078,182716764,16,"182140040,182147035,182185891,182186467,182188978,182201438,182201687,182205939,182223863,182230005,182231014,182234431,182240109,182264300,182522275,182716690,","182143038,182147152,182186079,182186588,182189060,182201559,182201789,182206065,182223964,182230146,182231131,182234498,182240292,182264414,182522386,182716797,",0,PDE1A,cmpl,cmpl,"-1,1,2,1,0,2,2,2,0,0,0,2,2,2,2,0,"
14703,14703,33,NM_152526.6,chr2,+,204545474,205620162,204545999,205615813,22,"204545474,204686180,204965151,205047580,205104425,205113490,205118920,205121590,205124326,205125608,205172210,205176444,205185763,205193204,205245777,205300529,205301463,205401012,205440369,205499895,205553323,205615455,","204546119,204686282,204965323,205047690,205104514,205113577,205119046,205121949,205124466,205125737,205172381,205176577,205185863,205193320,205245822,205300736,205301701,205401123,205440672,205500031,205553403,205620162,",0,PARD3B,cmpl,cmpl,"0,0,0,1,0,2,2,2,1,0,0,0,1,2,1,1,1,2,2,2,0,2,"
5677,5677,34,XM_017003577.3,chr2,-,211375716,212538802,211383614,212538530,30,"211375716,211386852,211387944,211420440,211422006,211424154,211428407,211430944,211561902,211619176,211623921,211630461,211657753,211657949,211665322,211673163,211679051,211701966,211704103,211705317,211712049,211713534,211722392,211725075,211750638,211781457,211788024,211947429,212124751,212538448,","211384060,211387150,211387992,211420611,211422104,211424301,211428483,211431100,211562088,211619275,211624044,211630594,211657828,211657994,211665477,211673257,211679184,211702166,211704194,211705391,211712176,211713648,211722534,211725194,211750704,211781535,211788159,211947616,212124903,212538802,",0,ERBB4,cmpl,cmpl,"1,0,0,0,1,1,0,0,0,0,0,2,2,2,0,2,1,2,1,2,1,1,0,1,1,1,1,0,1,0,"
19118,19118,34,XM_011511820.3,chr2,+,213284463,214410501,213284483,214410315,15,"213284463,213296063,213297261,213310058,213317218,213340162,213350527,213364075,213375009,213489962,213862484,214013950,214108195,214149139,214410139,","213284619,213296110,213297357,213310177,213317356,213340270,213350645,213364145,213375119,213490090,213862628,214014077,214108261,214149266,214410501,",0,SPAG16,cmpl,cmpl,"0,1,0,0,2,2,2,0,1,0,2,2,0,0,1,"
458,458,37,NM_014914.5,chr2,+,235494042,236131793,235494686,236124122,17,"235494042,235709178,235717556,235740962,235744697,235750353,235797758,235799366,235807238,235883344,235908737,235968461,236036560,236040750,236049058,236120191,236123918,","235494849,235709237,235717644,235741048,235744839,235750488,235797886,235799522,235807331,235883449,235908906,235968623,236036715,236040841,236049281,236120447,236131793,",0,AGAP1,cmpl,cmpl,"0,1,0,1,0,1,1,0,0,0,0,1,1,0,1,2,0,"
15393,15393,1,NM_015192.4,chr20,+,8132265,8884900,8132651,8881849,32,"8132265,8150293,8371381,8628293,8646101,8647899,8649373,8657183,8658537,8684931,8697625,8708669,8716263,8717670,8722353,8724655,8727308,8729049,8733237,8737027,8739260,8740343,8741463,8757045,8760406,8765138,8774538,8788448,8788632,8789517,8790174,8881621,","8132750,8150371,8371450,8628431,8646181,8647953,8649449,8657284,8658704,8685078,8697783,8708752,8716348,8717848,8722421,8724752,8727393,8729174,8733392,8737192,8739360,8740448,8741573,8757178,8760460,8765358,8774719,8788525,8788722,8789575,8790261,8884900,",0,PLCB1,cmpl,cmpl,"0,0,0,0,0,2,2,0,2,1,1,0,2,0,1,0,1,2,1,0,0,1,1,0,1,1,2,0,2,2,0,0,"
11512,11512,10,NM_080676.6,chr20,+,13995515,16053197,13995763,16049876,17,"13995515,14002287,14085620,14493478,14684842,15229939,15431404,15499773,15862744,15885763,15933275,15937475,15967552,15986726,15987065,16041200,16049829,","13995809,14002404,14085728,14493508,14684959,15230061,15431435,15499847,15862826,15885811,15933338,15937544,15967630,15986801,15987158,16041278,16053197,",0,MACROD2,cmpl,cmpl,"0,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,"
16482,16482,14,XM_047439848.1,chr20,-,42031889,43189906,42043543,43189733,32,"42031889,42043521,42081881,42084681,42085727,42098420,42102123,42104568,42106785,42110332,42115198,42118402,42119934,42128753,42141914,42161351,42199239,42236228,42248686,42282488,42315722,42350627,42352083,42448219,42472265,42677865,42756461,42771434,42780217,42791194,42885806,43189645,","42032336,42043639,42082017,42084845,42085853,42098552,42102297,42104718,42106921,42110487,42115315,42118500,42119971,42128830,42142002,42161539,42199388,42236258,42248822,42282525,42315996,42350730,42352285,42448329,42472562,42678159,42756636,42771550,42780299,42791466,42885932,43189906,",0,PTPRT,cmpl,cmpl,"-1,0,2,0,0,0,0,0,2,0,0,1,0,1,0,1,2,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,"
21370,21370,15,XM_047439879.1,chr20,+,52972357,53495330,52973293,53487145,5,"52972357,53253498,53487143,53490865,53494873,","52973333,53256444,53487332,53490947,53495330,",0,TSHZ2,cmpl,cmpl,"0,1,1,-1,-1,"
2958,2958,16,NM_001794.5,chr20,+,61252260,61940617,61252513,61936943,16,"61252260,61254825,61743562,61773002,61844667,61852753,61873727,61894909,61910421,61923450,61924333,61928189,61929608,61932984,61934055,61936736,","61252570,61254937,61743789,61773182,61844823,61852898,61873900,61895047,61910607,61923704,61924476,61928423,61929842,61933124,61934220,61940617,",0,CDH4,cmpl,cmpl,"0,0,1,0,0,0,1,0,0,0,2,1,1,1,0,0,"
12919,12919,93,NM_001352595.2,chr21,+,20998408,21543329,20998563,21537957,15,"20998408,21292103,21324382,21335504,21338388,21373862,21410273,21418472,21432107,21466605,21468661,21477290,21508850,21534536,21537845,","20998618,21292241,21324500,21335665,21338534,21374013,21410461,21418569,21432281,21466725,21468783,21477471,21509055,21534656,21543329,",0,NCAM2,cmpl,cmpl,"0,1,1,2,1,0,1,0,1,1,1,0,1,2,2,"
5114,5114,111,NM_001389.5,chr21,-,40010998,40847158,40013033,40846661,33,"40010998,40042370,40044077,40051957,40055724,40062868,40075036,40078686,40080151,40083907,40085601,40087169,40093720,40124194,40133853,40142557,40144490,40167217,40178926,40187130,40187890,40189041,40276096,40296054,40312080,40338100,40339118,40347669,40353464,40369098,40692809,40708453,40846618,","40013386,40042673,40044275,40052107,40055840,40062899,40075213,40078977,40080340,40084006,40085765,40087287,40093874,40124328,40134009,40142704,40144731,40167288,40179094,40187259,40187987,40189238,40276270,40296174,40312359,40338376,40339415,40347945,40353743,40369245,40692956,40708771,40847158,",0,DSCAM,cmpl,cmpl,"1,1,1,1,2,1,1,1,1,1,2,1,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,"
5115,5115,73,NM_001389.5,chr21_MU273391v1_fix,-,150306,986812,152341,986315,33,"150306,181704,183411,191296,195063,202213,214361,218011,219810,223565,225261,226829,233380,263864,273523,282211,284144,306871,318580,326784,327544,328695,415750,435708,451734,477754,478772,487323,493118,508752,832463,848107,986272,","152694,182007,183609,191446,195179,202244,214538,218302,219999,223664,225425,226947,233534,263998,273679,282358,284385,306942,318748,326913,327641,328892,415924,435828,452013,478030,479069,487599,493397,508899,832610,848425,986812,",0,DSCAM,cmpl,cmpl,"1,1,1,1,2,1,1,1,1,1,2,1,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,"
21455,21455,12,NM_001145418.2,chr22,-,27978013,28679840,27982220,28679723,23,"27978013,27985248,27989877,27990788,27992586,27993286,27996134,27998539,28001373,28014247,28030225,28094079,28096189,28098914,28101170,28105278,28107061,28163091,28296197,28297579,28306495,28629551,28679621,","27983851,27985356,27990007,27990812,27992663,27993518,27996259,27999260,28001553,28014392,28030366,28094245,28096408,28099044,28101280,28105802,28108403,28163599,28296328,28297852,28306643,28629830,28679840,",0,TTC28,cmpl,cmpl,"1,1,0,0,1,0,1,0,0,2,2,1,1,0,1,2,1,0,1,1,0,0,0,"
19734,19734,104,XM_017028962.3,chr22,-,32507819,33058381,32513691,33006662,14,"32507819,32518042,32527917,32528873,32533792,32538035,32541570,32596673,32864914,32868965,32931389,32980644,33006351,33057160,","32513824,32518334,32528005,32529008,32533895,32538110,32541713,32596736,32865004,32869125,32931481,32980702,33006824,33058381,",0,SYN3,cmpl,cmpl,"2,1,0,0,2,2,0,0,0,2,0,2,0,-1,"
10078,10078,1,XM_024452302.2,chr22,-,33162227,33922824,33166762,33761476,15,"33162227,33283201,33304228,33316084,33337645,33381918,33384191,33432160,33564847,33604434,33626243,33650366,33761370,33856739,33919994,","33166832,33283348,33304507,33316248,33337801,33382044,33384304,33432265,33565019,33604558,33626326,33650668,33761558,33856802,33920476,",0,LARGE1,cmpl,cmpl,"2,2,2,0,0,0,1,1,0,2,0,1,0,-1,-1,"
3703,3703,75,XM_006713004.5,chr3,+,2098865,3057959,2571503,3056220,24,"2098865,2339177,2571415,2736214,2745521,2819485,2866751,2883144,2887039,2900684,2902875,2925628,2988344,3026101,3030857,3034631,3037178,3038932,3040036,3042309,3042976,3043591,3053806,3056119,","2098978,2339233,2571558,2736341,2745697,2819581,2866949,2883247,2887224,2900821,2903005,2925779,2988472,3026277,3030975,3034790,3037328,3039003,3040271,3042422,3043163,3043704,3053975,3057959,",0,CNTN4,cmpl,cmpl,"-1,-1,0,1,2,1,1,1,2,1,0,1,2,1,0,1,1,1,0,1,0,1,0,1,"
7506,7506,9,NM_000844.4,chr3,+,6861114,7741533,6861388,7740406,10,"6861114,7146451,7298683,7306497,7415022,7452606,7461582,7578421,7680048,7740356,","6861907,7146668,7298825,7306652,7415163,7452807,7461722,7579357,7680295,7741533,",0,GRM7,cmpl,cmpl,"0,0,1,2,1,1,1,0,0,1,"
20041,20041,89,XM_047449300.1,chr3,-,17157161,17742631,17160962,17508570,26,"17157161,17166766,17167748,17185108,17214206,17238162,17258505,17291894,17307991,17372074,17374470,17374628,17376524,17383912,17403180,17404693,17404871,17406417,17428449,17508473,17562018,17586352,17622647,17623848,17672544,17742480,","17161256,17166928,17167828,17185208,17214370,17238419,17258591,17292001,17308134,17372247,17374540,17374679,17376613,17384015,17403248,17404768,17404961,17406526,17428519,17508605,17562142,17586557,17622765,17623913,17672705,17742631,",0,TBC1D5,cmpl,cmpl,"0,0,1,0,1,2,0,1,2,0,2,2,0,2,0,0,0,2,1,0,-1,-1,-1,-1,-1,-1,"
22860,22860,11,XM_017007191.2,chr3,-,21412217,22372763,21421213,22372555,10,"21416334,21423962,21425491,21436969,21441685,21510860,21564573,21664885,22168816,22372449,","21421447,21424064,21425670,21437203,21441742,21511023,21564684,21665028,22169035,22372763,",0,ZNF385D,cmpl,cmpl,"0,0,1,1,1,0,0,1,1,0,"
16751,16751,1,NM_001290216.3,chr3,+,24829320,25597932,25174397,25596616,11,"24829320,24858673,25060124,25174118,25461192,25501181,25569757,25580545,25593502,25594519,25596419,","24829403,24858752,25060176,25174575,25461341,25501323,25569918,25580722,25593707,25594678,25597932,",0,RARB,cmpl,cmpl,"-1,-1,-1,0,1,0,1,0,0,1,1,"
16860,16860,12,XM_017006181.2,chr3,+,29281070,30010395,29281681,30003862,13,"29281070,29434745,29488440,29587113,29739719,29762909,29868857,29884161,29897378,29936085,29988142,29991081,30003855,","29281756,29434915,29488499,29587205,29739877,29762989,29868964,29884208,29897475,29936196,29988223,29991209,30010395,",0,RBMS3,cmpl,cmpl,"0,0,2,1,0,2,1,0,2,0,0,0,2,"
21785,21785,1,NM_017886.4,chr3,-,41246598,41962103,41246928,41954759,37,"41246598,41249488,41398078,41455496,41463086,41566024,41615668,41663606,41681507,41681752,41705056,41705253,41715236,41715446,41717727,41754360,41789660,41800131,41819422,41835863,41883873,41895517,41896821,41898431,41900724,41907844,41911316,41911540,41912806,41915976,41918456,41919716,41931843,41935800,41938097,41954621,41962015,","41246992,41249574,41398264,41455595,41463253,41566130,41615717,41663699,41681652,41681804,41705151,41705305,41715293,41715568,41717861,41754488,41789843,41800293,41819506,41835971,41883952,41895564,41897003,41898492,41900829,41907941,41911386,41911659,41912899,41916052,41918540,41919818,41932006,41935940,41938197,41954807,41962103,",0,ULK4,cmpl,cmpl,"2,0,0,0,1,0,2,2,1,0,1,0,0,1,2,0,0,0,0,0,2,0,1,0,0,2,1,2,2,1,1,1,0,1,0,0,-1,"
5026,5026,15,XM_047447599.1,chr3,+,50674926,51384198,50675263,51381559,52,"50674926,50778674,50841674,50890025,50933980,51064447,51075355,51089242,51090229,51146548,51159243,51160554,51208773,51214121,51225648,51227282,51227981,51228660,51229511,51236344,51237489,51246725,51260155,51270814,51275078,51280105,51310231,51312003,51312475,51312843,51314979,51330137,51333157,51338358,51338934,51341236,51348851,51350287,51354881,51356088,51356406,51356961,51357757,51357960,51360510,51361858,51362526,51374468,51375747,51379448,51380124,51381049,","50675300,50778758,50841715,50890081,50934077,51064596,51075440,51089284,51090384,51146630,51159304,51160702,51208862,51214247,51225773,51227445,51228088,51228832,51229609,51236428,51237590,51246807,51260326,51271007,51275206,51280204,51310326,51312079,51312576,51312902,51315128,51330223,51333253,51338419,51339028,51341385,51348938,51350392,51355023,51356255,51356493,51357141,51357841,51358077,51360632,51361997,51362674,51374587,51375835,51379571,51380207,51384198,",0,DOCK3,cmpl,cmpl,"0,1,1,0,2,0,2,0,0,2,0,1,2,1,1,0,1,0,1,0,0,2,0,0,1,0,0,2,0,2,1,0,2,2,0,1,0,0,0,1,0,0,0,0,0,2,0,1,0,1,1,0,"
2304,2304,15,NM_018398.3,chr3,+,54122551,55074557,54122713,55074206,38,"54122551,54123512,54320441,54386714,54503491,54562799,54569794,54569953,54581802,54627786,54642127,54752598,54764217,54816852,54837158,54838567,54846392,54871538,54879017,54879349,54880795,54885280,54885488,54887958,54891354,54896748,54899787,54968449,54969799,54984607,54987682,55004762,55007789,55009387,55018205,55073444,55073776,55074113,","54122835,54123594,54320558,54386774,54503654,54562931,54569855,54570104,54581877,54627876,54642241,54752677,54764351,54816870,54837230,54838648,54846467,54871622,54879089,54879411,54880863,54885326,54885586,54888052,54891450,54896870,54899868,54968511,54969844,54984670,54987753,55004838,55007842,55009443,55018317,55073557,55073859,55074557,",0,CACNA2D3,cmpl,cmpl,"0,2,0,0,0,1,1,2,0,0,0,0,1,0,0,0,0,0,0,0,2,1,2,1,2,2,1,1,0,0,0,2,0,2,1,2,1,0,"
5681,5681,15,XM_047447942.1,chr3,-,55508310,56468467,55606909,56435007,18,"55508310,55606779,55699377,55734749,55888388,55950424,55992056,56007180,56010448,56018893,56080816,56139508,56148976,56170128,56173445,56296018,56434350,56468247,","55511276,55606966,55699512,55734918,55888549,55950560,55992250,56007321,56010589,56019031,56080984,56139676,56149132,56170170,56173520,56296435,56435147,56468467,",0,ERC2,cmpl,cmpl,"-1,0,0,2,0,2,0,0,0,0,0,0,0,0,0,0,0,-1,"
6362,6362,16,NM_001320900.2,chr3,-,59747276,61251452,59752225,60536962,10,"59747276,59922345,60011370,60014006,60536859,60821918,61042046,61196749,61200616,61251300,","59752321,59922414,60011400,60014152,60536979,60822011,61042099,61196843,61200665,61251452,",0,FHIT,cmpl,cmpl,"0,0,0,1,0,-1,-1,-1,-1,-1,"
16470,16470,16,NM_001375471.1,chr3,+,61561570,62297609,61562287,62293307,29,"61561570,61748877,61989624,62003348,62078162,62132601,62157066,62167970,62191468,62195061,62201504,62203172,62218850,62243806,62255123,62262797,62267409,62267684,62269034,62271382,62272945,62273697,62275872,62276971,62277550,62281562,62282726,62292420,62293160,","61562372,61748982,61989804,62003497,62078258,62132668,62157224,62168163,62191653,62195170,62201554,62203950,62218983,62243898,62255215,62262894,62267492,62267819,62269169,62271555,62273081,62273844,62275966,62277048,62277679,62281709,62282869,62292556,62297609,",0,PTPRG,cmpl,cmpl,"0,1,1,1,0,0,1,0,1,0,1,0,1,2,1,0,1,0,0,0,2,0,0,1,0,0,0,2,0,"
11573,11573,135,NM_001365903.2,chr3,-,65353525,66038918,65357075,66038308,25,"65353525,65359063,65361198,65363464,65364664,65364852,65375744,65379260,65381876,65383531,65387142,65391141,65401438,65429519,65430698,65437154,65439878,65442791,65448021,65453257,65470282,65478591,65493511,65621971,66037995,","65357132,65359152,65361337,65363608,65364725,65364946,65375948,65379554,65382069,65383623,65387226,65391358,65401470,65430140,65430881,65437247,65440012,65442849,65448057,65453340,65470487,65478798,65493631,65622088,66038918,",0,MAGI1,cmpl,cmpl,"0,1,0,0,2,1,1,1,0,1,1,0,1,1,1,1,2,1,1,2,1,1,1,1,0,"
19860,19860,17,NM_001252216.2,chr3,+,67991543,68545621,68006626,68544503,5,"67991543,68006623,68417279,68538755,68544485,","67991804,68006744,68417420,68538880,68545621,",0,TAFA1,cmpl,cmpl,"-1,0,1,1,0,"
6533,6533,17,NM_032682.6,chr3,-,70954707,71583978,70959246,71198381,21,"70954707,70965889,70970735,70972554,70976940,70977642,70977827,70987993,71000971,71015548,71041327,71046941,71052536,71053635,71112535,71198201,71299819,71359149,71493425,71581548,71583909,","70959391,70966056,70970805,70972676,70977042,70977722,70978029,70988077,71001059,71015653,71041532,71047095,71052626,71053773,71112637,71198392,71299880,71359244,71493555,71581697,71583978,",0,FOXP1,cmpl,cmpl,"2,0,2,0,0,1,0,0,2,2,1,0,0,0,0,0,-1,-1,-1,-1,-1,"
17320,17320,18,NM_001128929.3,chr3,+,75906674,77649964,75937493,77646055,27,"75906674,75937480,77098013,77477413,77481098,77493243,77522774,77546337,77550817,77557943,77562650,77563166,77564953,77568312,77574498,77577489,77579946,77588750,77595141,77596622,77602209,77607797,77617512,77622226,77634869,77644703,77646053,","75906960,75937602,77098340,77477571,77481219,77493382,77522902,77546462,77550989,77558149,77562732,77563329,77565120,77568434,77574730,77577614,77580118,77588933,77595184,77596750,77602491,77607954,77617773,77622432,77635043,77644904,77649964,",0,ROBO2,cmpl,cmpl,"-1,0,1,1,0,1,2,1,0,1,0,1,2,1,0,1,0,1,1,2,1,1,2,2,1,1,1,"
17319,17319,18,XM_011533977.3,chr3,-,78597238,79767998,78598912,79589911,32,"78597238,78600112,78606732,78614647,78617634,78627320,78631160,78633934,78635772,78639743,78646147,78647628,78651731,78657097,78659685,78661029,78661992,78667882,78668133,78668483,78670095,78685745,78688647,78693347,78714396,78717274,78717762,78746742,78938600,79125455,79589823,79767460,","78598927,78600309,78607041,78614800,78618041,78627569,78631305,78634042,78636108,78639898,78646190,78647655,78651929,78657269,78659807,78661261,78662114,78668049,78668302,78668565,78670301,78685917,78688772,78693356,78714524,78717413,78717883,78746900,78938927,79125539,79589961,79767998,",0,ROBO1,cmpl,cmpl,"0,1,1,1,2,2,1,1,1,2,1,1,1,0,1,0,1,2,1,0,1,0,1,1,2,1,0,1,1,1,0,-1,"
2324,2324,19,NM_001381964.1,chr3,+,84958988,86074429,84959607,86066783,11,"84958988,84959589,85802046,85883290,85886189,85912372,85935766,85961468,85979163,86065604,86066664,","84959492,84959668,85802196,85883443,85886327,85912543,85935857,85961647,85979283,86065730,86074429,",0,CADM2,cmpl,cmpl,"-1,0,1,1,1,1,1,2,1,1,1,"
5626,5626,20,XM_017006214.2,chr3,+,96814593,97761532,96866864,97748701,18,"96814593,96866824,97226263,97243951,97405149,97448124,97448567,97475351,97479293,97483933,97532357,97592611,97610792,97637872,97720260,97735924,97747422,97748586,","96815008,96866889,97226419,97244287,97405274,97448172,97448730,97475460,97479364,97484059,97532543,97592737,97610854,97638082,97720410,97736118,97747572,97761532,",0,EPHA6,cmpl,cmpl,"-1,0,1,1,1,0,0,1,2,1,1,1,1,0,0,0,2,2,"
22471,22471,182,NM_001348802.3,chr3,-,114314499,115147288,114339004,114351858,11,"114314499,114350273,114380216,114389004,114500351,114693527,114801100,114900303,114974365,115144812,115147218,","114339426,114351878,114380404,114389105,114500391,114693575,114801174,114900342,114974416,115144907,115147288,",0,ZBTB20,cmpl,cmpl,"1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,"
11321,11321,22,NM_001318915.2,chr3,-,115802373,116445487,115810316,116445031,9,"115802373,115816613,115834561,115841844,115842457,115852482,116019514,116086323,116444876,","115810414,115816646,115834597,115841993,115842578,115852617,116019640,116086556,116445487,",0,LSAMP,cmpl,cmpl,"1,1,1,2,1,1,1,2,0,"
8998,8998,191,XM_006713813.4,chr3,+,124033368,124726325,124033740,124719470,60,"124033368,124227989,124234828,124264497,124268742,124298790,124325979,124329860,124334264,124347142,124384844,124395134,124398696,124413469,124422811,124430655,124434333,124438887,124441944,124446160,124446762,124455176,124456609,124461889,124462523,124474662,124477244,124482807,124488203,124490693,124491322,124492739,124496310,124562842,124632419,124633848,124637207,124650807,124655600,124657447,124657733,124658430,124659364,124660922,124661850,124666448,124667011,124671659,124674360,124678189,124679457,124693803,124694331,124696133,124697592,124699868,124702037,124712934,124717246,124718924,","124033813,124228064,124234943,124264690,124269255,124298913,124326171,124329992,124334495,124347265,124385036,124395304,124398871,124413665,124422978,124430775,124434525,124439037,124442059,124446276,124446885,124455359,124456728,124461956,124462633,124474732,124477334,124482900,124488315,124490884,124491424,124492882,124496413,124563089,124632703,124633953,124637303,124650938,124655667,124657551,124657803,124658517,124659457,124660973,124661928,124666634,124667183,124671898,124674614,124678313,124679517,124693831,124694503,124696255,124697724,124700033,124702116,124713135,124717385,124726325,",0,KALRN,cmpl,cmpl,"0,1,1,2,0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,1,0,0,0,2,0,2,0,0,0,1,0,0,2,0,1,0,0,0,2,0,2,0,0,0,0,0,0,1,0,2,0,0,1,2,1,1,1,2,2,0,"
3594,3594,25,NM_022131.3,chr3,+,139935184,140577397,139935374,140566253,17,"139935184,140175950,140403628,140404557,140421124,140448518,140459520,140466609,140532323,140546514,140556512,140558639,140562137,140562810,140563079,140563960,140566052,","139935483,140176073,140403824,140404766,140421274,140448704,140459769,140466731,140532486,140546681,140556661,140558857,140562308,140562956,140563203,140564145,140577397,",0,CLSTN2,cmpl,cmpl,"0,1,1,2,1,1,1,1,0,1,0,2,1,1,0,1,0,"
18750,18750,26,NM_173653.4,chr3,-,143265221,143848468,143266701,143848322,16,"143265221,143268874,143363483,143382059,143467036,143493652,143495334,143552361,143574087,143578584,143652254,143693191,143795000,143796825,143832018,143848147,","143266929,143268980,143363563,143382114,143467190,143493764,143495448,143552450,143574193,143578723,143652360,143693307,143795077,143796903,143832221,143848468,",0,SLC9A9,cmpl,cmpl,"0,2,0,2,1,0,0,1,0,2,1,2,0,0,1,0,"
8814,8814,3,NM_001197114.2,chr3,+,159069318,159897359,159069432,159896774,10,"159069318,159245842,159262547,159764442,159866162,159886206,159887707,159888819,159892096,159896722,","159069441,159245907,159262683,159765138,159866281,159886324,159887905,159888943,159892190,159897359,",0,IQCJ-SCHIP1,cmpl,cmpl,"0,0,2,0,0,2,0,0,1,2,"
17814,17814,3,NM_001197108.2,chr3,+,159273243,159897359,159273820,159896774,7,"159273243,159866162,159886206,159887707,159888819,159892096,159896722,","159273883,159866281,159886324,159887905,159888943,159892190,159897359,",0,SCHIP1,cmpl,cmpl,"0,0,2,0,0,1,2,"
11892,11892,234,XM_005247213.4,chr3,-,169083506,169663712,169084908,169663372,17,"169083506,169088999,169089999,169092957,169095075,169100884,169102059,169107925,169112786,169115382,169121055,169122579,169127843,169131428,169143697,169381186,169663335,","169085043,169089183,169090236,169093102,169095245,169100962,169102226,169107952,169112874,169116739,169121212,169122727,169128060,169131531,169143832,169381524,169663712,",0,MECOM,cmpl,cmpl,"0,2,2,1,2,2,0,0,2,1,0,2,1,0,0,1,0,"
13299,13299,29,XM_047447712.1,chr3,+,173395951,174294372,173604598,174281303,6,"173395951,173604278,173807679,174275314,174278860,174280480,","173396227,173605091,173807832,174275500,174279650,174294372,",0,NLGN1,cmpl,cmpl,"-1,0,1,1,1,2,"
12817,12817,29,XM_017006080.3,chr3,+,174440981,175810548,175096797,175803203,15,"174440981,174737640,175096789,175233930,175256410,175324174,175447228,175463400,175466978,175471638,175576040,175627290,175737305,175755219,175803004,","174441032,174737746,175097291,175234204,175256530,175324325,175447372,175463493,175467184,175471758,175576187,175627386,175737399,175755418,175810548,",0,NAALADL2,cmpl,cmpl,"-1,-1,0,2,0,0,1,1,1,0,0,0,0,1,2,"
11178,11178,31,NM_001387672.1,chr3,+,188153020,188890671,188406120,188874479,10,"188153020,188406111,188484591,188524664,188609160,188708266,188760112,188866199,188872642,188874350,","188153363,188406313,188484704,188524787,188609844,188708393,188760282,188866378,188872763,188890671,",0,LPP,cmpl,cmpl,"-1,0,1,0,0,0,1,0,2,0,"
6322,6322,256,NM_004113.6,chr3,-,192139389,192727541,192144008,192727193,6,"192139389,192170457,192335360,192360427,192727180,192727483,","192144127,192170656,192335464,192360538,192727323,192727541,",0,FGF12,cmpl,cmpl,"1,0,1,1,0,-1,"
19052,19052,9,NM_020777.3,chr4,+,7192537,7742827,7192646,7740264,27,"7192537,7396287,7531529,7638327,7654133,7661499,7664352,7667123,7676049,7682742,7689485,7697197,7703279,7704176,7712732,7714239,7715182,7718011,7723696,7725153,7726779,7728349,7729586,7733321,7734271,7737068,7740199,","7193126,7396355,7531629,7638492,7654207,7661564,7664471,7667213,7676229,7682889,7689588,7697274,7703371,7704284,7712853,7714373,7715311,7718183,7723883,7725287,7726903,7728462,7729712,7733421,7734374,7737172,7742827,",0,SORCS2,cmpl,cmpl,"0,0,2,0,0,2,1,0,0,0,0,1,0,2,2,0,2,2,0,1,0,1,0,0,1,2,1,"
9084,9084,11,NM_147182.4,chr4,-,20728605,21948772,20730081,20850644,9,"20728605,20732005,20732680,20734627,20749661,20758820,20850542,21762920,21948570,","20730129,20732068,20732785,20734735,20749732,20758890,20850667,21763032,21948772,",0,KCNIP4,cmpl,cmpl,"0,0,0,0,1,0,0,-1,-1,"
15734,15734,11,NM_001330751.2,chr4,-,23792020,24472905,23795821,24091536,15,"23792020,23801729,23802223,23812746,23813020,23813689,23824279,23824462,23828399,23829462,23831556,23884751,24091467,24258202,24472374,","23795925,23801881,23802345,23812867,23813125,23814605,23824353,23824508,23828604,23829585,23831751,23884931,24091635,24258267,24472905,",0,PPARGC1A,cmpl,cmpl,"1,2,0,2,2,1,2,1,0,0,0,0,0,-1,-1,"
388,388,16,NM_001387542.1,chr4,+,61200325,62078335,61497293,62070908,22,"61200325,61497120,61587226,61676825,61732753,61813808,61892655,61895730,61909559,61912718,61934839,61935922,61946913,61948099,61979679,61983382,61996290,61998173,62031441,62037730,62044452,62070108,","61201765,61497348,61587440,61676935,61733554,61813889,61892958,61895834,61909745,61912757,61935023,61936045,61947122,61948276,61979772,61983603,61996357,61998265,62031610,62037856,62044549,62078335,",0,ADGRL3,cmpl,cmpl,"-1,0,1,2,1,1,1,1,0,0,0,1,1,0,0,0,2,0,2,0,0,1,"
3204,3204,18,XM_047449975.1,chr4,+,80321264,80963750,80321434,80963612,8,"80321272,80335743,80362753,80583092,80608332,80869992,80944809,80963516,","80321463,80335879,80362884,80583183,80608383,80870135,80944939,80963750,",0,CFAP299,cmpl,cmpl,"0,2,0,2,0,0,2,0,"
1049,1049,19,NM_001025616.3,chr4,+,85475149,86002666,85570541,86000722,10,"85475149,85570521,85721884,85923647,85942065,85972035,85974887,85977569,85994582,86000478,","85475559,85570721,85721972,85923770,85942273,85972168,85974961,85977691,85995657,86002666,",0,ARHGAP24,cmpl,cmpl,"-1,0,0,1,1,2,0,2,1,2,"
11673,11673,155,XM_047415964.1,chr4,-,86010404,86594074,86017227,86593945,13,"86010404,86029196,86031367,86064265,86067772,86098523,86101051,86101893,86103185,86107222,86159297,86194335,86593909,","86017370,86029274,86031431,86064390,86067955,86098595,86101217,86102032,86103244,86107352,86159467,86194407,86594074,",0,MAPK10,cmpl,cmpl,"1,1,0,1,1,1,0,2,0,2,0,0,0,"
2782,2782,19,XM_047415679.1,chr4,+,90127393,91605295,90308284,91599057,10,"90127393,90308243,90312862,90400035,90468233,90628024,90723913,90815761,91085949,91598571,","90127831,90309608,90313047,90400129,90468354,90628232,90723991,90815845,91085994,91605295,",0,CCSER1,cmpl,cmpl,"-1,0,1,0,1,2,0,0,0,0,"
7471,7471,20,XM_047450133.1,chr4,+,92303965,93810456,92304656,93806873,16,"92303965,92590130,93084994,93110747,93207403,93216737,93224613,93238370,93395606,93422770,93455661,93490638,93515215,93626268,93769209,93806714,","92304744,92590286,93085279,93110953,93207457,93216911,93224775,93238490,93395708,93422968,93455974,93490777,93515411,93626435,93769450,93810456,",0,GRID2,cmpl,cmpl,"0,1,1,1,0,0,0,0,0,0,0,1,2,0,2,0,"
19589,19589,20,XM_011531886.4,chr4,-,97441248,98143476,97448750,98143150,14,"97441248,97448739,97712698,97840772,97943896,97972279,97981158,97986885,98105952,98109192,98128427,98132444,98134346,98143041,","97441534,97448888,97712814,97840932,97944007,97972440,97981318,97986993,98106064,98109305,98128592,98132603,98134459,98143476,",0,STPG2,cmpl,cmpl,"-1,0,1,0,0,1,0,0,2,0,0,0,1,0,"
742,742,22,NM_001386187.2,chr4,+,112705621,113383736,112706145,113381471,43,"112705621,113174415,113196367,113199010,113232160,113236986,113240484,113242110,113249763,113255734,113258049,113258312,113264896,113274451,113277836,113278459,113282674,113287604,113288387,113292415,113293439,113302766,113311254,113317706,113318516,113330245,113333053,113335845,113336576,113339225,113341687,113343016,113345899,113348275,113350227,113360822,113363337,113365038,113367565,113369513,113373089,113373284,113381456,","112706217,113174517,113196466,113199109,113232259,113237172,113240583,113242209,113249862,113255932,113258148,113258411,113264995,113274649,113277935,113278558,113282872,113287703,113288486,113292514,113293538,113302839,113311399,113317809,113318620,113330470,113333208,113336057,113336781,113339322,113341916,113343142,113346022,113348308,113350249,113360897,113363469,113365182,113367851,113369805,113373173,113373449,113383736,",0,ANK2,cmpl,cmpl,"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,2,2,1,0,1,2,0,0,0,0,1,1,1,1,2,0,0,0,"
8737,8737,3,XM_047416356.1,chr4,-,142023159,142846535,142028781,142431259,27,"142023159,142082030,142086143,142108092,142112541,142122127,142123291,142124587,142145839,142160357,142173631,142193086,142208424,142208895,142237863,142260491,142270662,142305457,142314711,142402937,142405205,142429172,142431168,142462662,142725838,142754013,142846208,","142028914,142082185,142086256,142108190,142112682,142122245,142123415,142124760,142145996,142160561,142173809,142193195,142208529,142209026,142238011,142260564,142270774,142305537,142314762,142403054,142405324,142429217,142431385,142462726,142725901,142754132,142846535,",0,INPP4B,cmpl,cmpl,"2,0,1,2,2,1,0,1,0,0,2,1,1,2,1,0,2,0,0,0,1,1,0,-1,-1,-1,-1,"
11183,11183,3,XM_005263373.4,chr4,-,150264434,151015727,150265721,151014642,58,"150264434,150277852,150282449,150285932,150302624,150310228,150315560,150321190,150325808,150349991,150415437,150435588,150436723,150467672,150471623,150487731,150490917,150588047,150590712,150597082,150599006,150683550,150735257,150761782,150798080,150806270,150808319,150817123,150828179,150831816,150844099,150844657,150848817,150849421,150850723,150851884,150867670,150868181,150870524,150871344,150872662,150893051,150896393,150897738,150900048,150905837,150906296,150908333,150908659,150914194,150915607,150916400,150916616,150921197,150928515,150928833,151014426,151015472,","150265812,150278004,150282646,150286034,150302792,150310384,150315623,150321383,150325898,150350159,150415590,150435708,150436864,150467785,150471739,150487834,150491035,150588184,150590859,150597115,150599131,150683717,150735366,150761847,150798142,150806404,150808398,150817257,150828621,150831976,150844207,150844779,150848998,150849575,150850902,150852943,150867863,150868305,150870606,150871453,150872755,150893149,150896456,150897818,150900217,150905990,150906405,150908467,150908857,150914341,150915727,150916527,150916738,150921293,150928616,150929065,151014861,151015727,",0,LRBA,cmpl,cmpl,"2,0,1,1,1,1,1,0,0,0,0,0,0,1,2,1,0,1,1,1,2,0,2,0,1,2,1,2,1,0,0,1,0,2,0,0,2,1,0,2,2,0,0,1,0,0,2,0,0,0,0,2,0,0,1,0,0,-1,"
6605,6605,28,NM_020116.5,chr4,-,161383896,162164000,161385746,162111396,16,"161383896,161455003,161459211,161481019,161500015,161510397,161538165,161542531,161587454,161656327,161759410,161775877,161920403,162033624,162111270,162163614,","161386449,161455128,161459319,161481169,161500134,161510424,161538300,161542693,161587575,161656494,161759531,161776074,161920652,162033658,162111412,162164000,",0,FSTL5,cmpl,cmpl,"2,0,0,0,1,1,1,1,0,1,0,1,1,0,0,-1,"
11701,11701,28,XM_017008335.2,chr4,-,163524297,164384019,163528747,163988599,8,"163524297,163545595,163585748,163613313,163700812,163988500,164111587,164383186,","163529046,163545743,163585929,163613393,163700863,163988709,164111662,164384019,",0,MARCHF1,cmpl,cmpl,"1,0,2,0,0,0,-1,-1,"
6768,6768,29,NM_001034845.3,chr4,+,171813403,173041559,171814580,173040100,13,"171813403,171814411,172229655,172311613,172348522,172809360,172813539,172882789,172931160,172952036,173009177,173021475,173039932,","171813990,171814718,172229764,172311752,172348689,172809546,172813723,172882907,172931268,172952258,173009294,173021625,173041559,",0,GALNTL6,cmpl,cmpl,"-1,0,0,1,2,1,1,2,0,0,0,0,0,"
20213,20213,30,XM_047415944.1,chr4,+,181447612,182803024,182324020,182800351,30,"181447612,181739486,181867751,182041663,182323945,182600923,182628650,182653770,182673004,182679665,182680247,182680542,182681813,182688165,182714086,182728964,182730199,182730877,182736807,182738400,182743169,182751799,182753449,182754384,182773471,182774917,182789092,182792273,182796636,182799595,","181447772,181739649,181867832,182041743,182324252,182601161,182628889,182653893,182673219,182679876,182680349,182680737,182682014,182688351,182714233,182729181,182730319,182731139,182737075,182738544,182743419,182752032,182753604,182755259,182773647,182775153,182789389,182793885,182796767,182803024,",0,TENM3,cmpl,cmpl,"-1,-1,-1,-1,0,1,2,1,1,0,1,1,1,1,1,1,2,2,0,1,1,2,1,0,2,1,0,0,1,0,"
4205,4205,10,XM_005248251.4,chr5,-,10971835,11904446,10973452,11903853,23,"10971835,10981772,10988110,10992550,11017973,11022768,11082695,11083880,11098574,11110857,11117449,11159575,11199447,11236690,11346371,11364695,11384664,11397030,11411535,11412034,11564943,11732135,11903816,","10973713,10981846,10988242,10992677,11018058,11022979,11082846,11083955,11098748,11111043,11117567,11159759,11199661,11236823,11346627,11364890,11385229,11397203,11411652,11412069,11565056,11732272,11904446,",0,CTNND2,cmpl,cmpl,"0,1,1,0,2,1,0,0,0,0,2,1,0,2,1,1,0,1,1,2,0,1,0,"
2949,2949,11,NM_001349558.2,chr5,-,19471295,20575713,19473225,19838986,16,"19471295,19483300,19502991,19520656,19543868,19571578,19591056,19612433,19721346,19746941,19838758,19981059,19991872,20255443,20338091,20575461,","19473716,19483552,19503109,19520778,19544005,19571832,19591244,19612601,19721466,19747236,19839242,19981178,19992014,20255505,20338239,20575713,",0,CDH18,cmpl,cmpl,"1,1,0,1,2,0,1,1,1,0,0,-1,-1,-1,-1,-1,"
2944,2944,11,XM_047416602.1,chr5,-,21750672,22853344,21751736,22078676,17,"21750672,21755590,21760557,21764977,21783357,21802166,21816944,21842160,21854670,21975090,22078445,22172340,22212497,22405256,22505269,22810616,22853057,","21752236,21755842,21760675,21765099,21783494,21802420,21817132,21842328,21854790,21975385,22078862,22172409,22212643,22405351,22505364,22810709,22853344,",0,CDH12,cmpl,cmpl,"1,1,0,1,2,0,1,1,1,0,0,-1,-1,-1,-1,-1,-1,"
14958,14958,16,XM_024446110.2,chr5,-,58969037,60522128,58974663,60185598,18,"58969037,58975656,58976349,58977190,58988492,58989754,58990803,58991831,58993371,59038858,59180594,59185188,59193499,59215776,59988487,60147747,60185556,60522050,","58975080,58975839,58976472,58977345,58988592,58989919,58990902,58992004,58993465,59038971,59180644,59185262,59193536,59215968,59988717,60147894,60185687,60522128,",0,PDE4D,cmpl,cmpl,"0,0,0,1,0,0,0,1,0,1,2,0,2,2,0,0,0,-1,"
11745,11745,0,NM_001393525.1,chr5,+,66596392,67169593,66596655,67167051,28,"66596392,66759708,66788669,66899950,67054403,67090161,67095596,67100434,67102535,67104365,67110097,67114086,67118681,67121016,67130209,67131812,67133513,67134522,67136562,67142114,67142420,67144668,67145143,67152636,67153457,67160455,67162606,67163146,","66597018,66759862,66788794,66899982,67054492,67090231,67095675,67100592,67102611,67104575,67110199,67114219,67118749,67121102,67130418,67131951,67133646,67134688,67136664,67142237,67142533,67144796,67145379,67152866,67153580,67160592,67162788,67169593,",0,MAST4,cmpl,cmpl,"0,0,1,0,2,1,2,0,2,0,0,0,1,0,2,1,2,0,1,1,1,0,2,1,0,0,2,1,"
390,390,159,XM_017009967.2,chr5,+,90558796,91164437,90558895,91163900,89,"90558796,90614834,90617803,90622596,90625129,90627210,90628561,90629209,90635113,90637724,90642635,90642855,90643802,90644705,90645967,90647497,90651603,90652345,90653208,90657904,90672545,90674053,90675242,90676079,90679548,90681314,90683585,90685779,90689860,90690796,90692604,90693889,90696936,90703664,90704388,90705378,90706230,90708815,90710980,90711183,90712286,90716466,90720047,90720934,90724831,90725085,90725548,90728668,90729641,90745045,90745590,90750550,90753573,90754982,90756453,90756978,90759408,90763304,90774185,90776452,90777904,90778426,90778864,90781429,90783123,90783837,90788070,90789701,90790872,90802738,90805283,90807601,90810232,90815618,90823424,90828943,90840577,90848636,90853283,90854061,90855740,90863756,90965414,90985343,91072446,91102218,91150029,91153220,91163781,","90558917,90615019,90617953,90622701,90625243,90627776,90628832,90629539,90635290,90637948,90642762,90643041,90643983,90644869,90646091,90647764,90651730,90652563,90653952,90658278,90672722,90674234,90675445,90676209,90679629,90681454,90684195,90685995,90690076,90691041,90692786,90694701,90697146,90703795,90704488,90705579,90706394,90708909,90711059,90711322,90712428,90716729,90720223,90721059,90724989,90725232,90725656,90728933,90729764,90745265,90745795,90750697,90753829,90755185,90756630,90757161,90759588,90763469,90774303,90776576,90778043,90778609,90779097,90781578,90783325,90784057,90788310,90789851,90791346,90802882,90805458,90807737,90811338,90815736,90823596,90829186,90840985,90848821,90853533,90854201,90855901,90863857,90965531,90985522,91072604,91102340,91150221,91153398,91164437,",0,ADGRV1,cmpl,cmpl,"0,1,0,0,0,0,2,0,0,0,2,0,0,1,0,1,1,2,1,1,0,0,1,0,1,1,0,1,1,1,0,2,1,1,0,1,1,0,1,2,0,1,0,2,1,0,0,0,1,1,2,0,0,1,0,0,0,0,0,1,2,0,0,2,1,2,0,0,0,0,0,1,2,1,2,0,0,0,2,0,2,1,0,0,2,1,0,0,1,"
11854,11854,163,NM_024717.7,chr5,-,94703689,95285094,94707495,95284575,23,"94703689,94708511,94710817,94714776,94779109,94799012,94868332,94870416,94870871,94871314,94873138,94888878,94894648,94909250,94912805,94917895,94923961,94931952,94940083,94942347,94953218,95017366,95283855,","94707567,94708609,94710927,94714886,94779163,94799132,94868452,94870491,94870973,94871417,94873241,94888972,94894835,94909381,94912976,94917973,94924021,94931991,94940195,94942427,94953361,95017484,95285094,",0,MCTP1,cmpl,cmpl,"0,1,2,0,0,0,0,0,0,2,1,0,2,0,0,0,0,0,2,0,1,0,0,"
2462,2462,20,NM_001423255.1,chr5,+,95961428,96774683,96722677,96771679,31,"95961428,96379565,96675538,96695835,96722638,96727488,96729152,96729611,96730779,96736171,96737848,96740037,96741265,96741493,96742654,96746341,96747344,96748517,96750586,96754059,96754657,96757443,96757582,96762273,96765220,96766052,96767437,96767906,96770530,96771643,96772639,","95961586,96379652,96675601,96695907,96722698,96727530,96729209,96729725,96730860,96736240,96737947,96740118,96741358,96741580,96742756,96746425,96747392,96748613,96750682,96754161,96754741,96757494,96757654,96762372,96765325,96766145,96767482,96767999,96770602,96771702,96774683,",0,CAST,cmpl,cmpl,"-1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,"
6175,6175,21,NM_001163315.3,chr5,-,107859034,108382098,107861719,108381691,9,"107859034,107881036,108020924,108186116,108224120,108348398,108364737,108367830,108380698,","107861860,107881179,108021001,108186247,108224228,108348530,108364995,108367953,108382098,",0,FBXL17,cmpl,cmpl,"0,1,2,0,0,0,0,0,0,"
6604,6604,200,XM_011543283.2,chr5,-,133196454,133842067,133199094,133603983,16,"133196454,133201932,133210190,133217228,133220747,133224189,133225149,133225657,133233416,133249409,133312653,133316458,133400737,133567185,133603857,133841951,","133199797,133202042,133210298,133217378,133220866,133224216,133225284,133225819,133233537,133249576,133312777,133316652,133400986,133567219,133603993,133842067,",0,FSTL4,cmpl,cmpl,"2,0,0,0,1,1,1,1,0,1,0,1,1,0,0,-1,"
19287,19287,25,NM_004598.4,chr5,-,136975297,137499326,136978653,137498558,11,"136975297,136979331,136985139,136988421,136992483,137067714,137112434,137140579,137267009,137498372,137499178,","136978844,136979469,136985202,136988643,136992600,137067829,137112561,137140694,137267055,137498558,137499326,",0,SPOCK1,cmpl,cmpl,"1,1,1,1,1,0,2,1,0,0,-1,"
18143,18143,27,XM_047417519.1,chr5,+,155727831,156767788,156329576,156759390,11,"155727831,155870343,156123855,156329533,156344488,156508600,156589230,156594931,156647463,156757580,156759216,","155728990,155870424,156124019,156329579,156344677,156508702,156589318,156595051,156647536,156757704,156767788,",0,SGCD,cmpl,cmpl,"-1,-1,-1,0,0,0,0,1,1,2,0,"
20212,20212,3,XM_047417419.1,chr5,+,166979028,168264157,167284837,168262810,29,"166979028,167073241,167284763,167375197,167952587,167992943,168047426,168062059,168090573,168098025,168118291,168124849,168126753,168162610,168190336,168195175,168198852,168199863,168203688,168204371,168215039,168216767,168218124,168226087,168227894,168244419,168246756,168260282,168262048,","166979523,167073356,167285063,167375473,167952822,167993182,168047549,168062265,168090769,168098127,168118486,168125050,168126966,168162757,168190547,168195295,168199114,168200131,168203832,168204621,168215272,168216922,168218999,168226263,168228130,168244716,168248371,168260413,168264157,",0,TENM2,cmpl,cmpl,"-1,-1,0,1,1,2,1,1,0,1,1,1,1,1,1,2,2,0,1,1,2,1,0,2,1,0,0,1,0,"
18780,18780,29,NM_001271946.2,chr5,-,168661739,169301139,168666453,169300709,36,"168661739,168669782,168671197,168673176,168683965,168685686,168686978,168692606,168696291,168700581,168707975,168710894,168712282,168722255,168722932,168724415,168748301,168749471,168752954,168753863,168760861,168762538,168772780,168774234,168785906,168789559,168795506,168806445,168817299,168823259,168844583,168883264,169193478,169244704,169251387,169300512,","168666689,168669991,168671483,168673331,168684096,168685927,168687116,168692700,168696431,168700679,168708121,168711058,168712354,168722327,168723004,168724484,168748434,168749635,168753098,168754007,168760936,168762689,168772944,168774378,168785978,168789631,168795578,168806587,168817463,168823331,168844655,168883336,169193550,169244776,169251459,169301139,",0,SLIT3,cmpl,cmpl,"1,2,1,2,0,2,2,1,2,0,1,2,2,2,2,2,1,2,2,2,2,1,2,2,2,2,2,1,2,2,2,2,2,2,2,0,"
7075,7075,9,NM_001500.4,chr6,-,1623805,2245605,1624168,2245422,11,"1623805,1624471,1726415,1742467,1930102,1959866,1960773,2115770,2117468,2124686,2245320,","1624231,1624540,1726512,1742586,1930230,1959971,1960966,2115880,2117556,2124731,2245605,",0,GMDS,cmpl,cmpl,"0,0,2,0,1,1,0,1,0,0,0,"
15141,15141,85,NM_001322308.3,chr6,+,12716766,13287837,12718744,13287078,14,"12716766,12718698,12749643,13053364,13160203,13182518,13205814,13227815,13230036,13272859,13278267,13283421,13286145,13287062,","12716896,12718847,12749790,13053529,13160284,13182686,13206136,13228063,13230193,13272915,13278329,13283562,13286222,13287837,",0,PHACTR1,cmpl,cmpl,"-1,0,1,1,1,1,1,2,1,2,1,0,0,2,"
3004,3004,11,XM_011514718.1,chr6,+,20534456,21232404,20546350,21231039,15,"20534456,20535350,20546345,20548592,20649292,20739518,20758594,20781144,20846074,20955418,21000226,21065047,21198020,21201109,21230847,","20534574,20535394,20546523,20548705,20649377,20739615,20758643,20781265,20846178,20955585,21000372,21065228,21198104,21201274,21232404,",0,CDKAL1,cmpl,cmpl,"-1,-1,0,2,1,2,0,1,2,1,0,2,0,0,0,"
15616,15616,14,NM_001318876.2,chr6,+,43517088,44461400,43517109,44461379,11,"43517088,43517305,43519332,43519705,43520065,43520274,43520624,43520931,43529248,44441889,44461319,","43517178,43517377,43519440,43519838,43520185,43520427,43520774,43521048,43529271,44441913,44461400,",0,POLR1C,cmpl,cmpl,"0,0,0,0,1,1,1,1,1,0,0,"
19680,19680,14,NM_181356.3,chr6,-,44826725,45377934,44829815,45322916,13,"44826725,44932652,44953309,44954494,44961752,45003652,45014800,45020545,45105921,45321795,45322878,45365200,45377767,","44829857,44932763,44953417,44954607,44961828,45003792,45014891,45020632,45106006,45321891,45322967,45365301,45377934,",0,SUPT3H,cmpl,cmpl,"0,0,0,1,0,1,0,0,2,2,0,-1,-1,"
9203,9203,16,NM_001350622.2,chr6,-,61679960,62286225,61680962,62285948,10,"61679960,61697194,61732681,61816954,61894634,61901243,61978065,62047877,62177184,62285857,","61681060,61697253,61732764,61817005,61894833,61901371,61978212,62047994,62177312,62286225,",0,KHDRBS2,cmpl,cmpl,"1,2,0,0,2,0,0,0,1,0,"
5841,5841,16,NM_001292009.2,chr6,-,63719979,65707226,63720595,65495410,44,"63719979,63726518,63741912,63762460,63778005,63788104,63789057,63806189,63864185,63984382,63999074,64066337,64081855,64230591,64306969,64388689,64436173,64439161,64590222,64593116,64617417,64626120,64813377,64821644,64822650,64886696,64902112,64902403,64912483,64945792,64997581,65057613,65295862,65334979,65344037,65353457,65384385,65402477,65405173,65490593,65494662,65495858,65639777,65707134,","63721797,63726680,63741975,63762633,63778180,63788249,63789224,63806372,63864358,63984603,63999183,64066491,64082002,64230824,64307082,64388840,64436265,64439352,64591989,64593309,64617533,64626245,64813577,64821723,64822822,64886842,64902220,64902500,64912743,64945914,64997703,65057727,65296119,65335146,65344177,65353617,65384500,65402605,65405367,65490707,65495607,65495993,65639892,65707226,",0,EYS,cmpl,cmpl,"1,1,1,2,1,0,1,1,2,0,2,1,1,2,0,2,0,1,1,0,1,2,0,2,1,2,2,1,2,0,1,1,2,0,1,0,2,0,1,1,0,-1,-1,-1,"
367,367,17,NM_001704.3,chr6,+,68635281,69389506,68638675,69388891,32,"68635281,68637390,68638660,68930558,68936518,68943829,68956023,68956644,68974762,68975233,68993767,69014037,69018390,69048184,69049270,69062933,69075994,69233289,69235031,69239123,69324871,69327819,69330505,69332922,69338915,69339332,69354232,69355820,69360868,69372405,69382830,69388702,","68636000,68637562,68639432,68930669,68936680,68943994,68956188,68956809,68974864,68975340,68993962,69014106,69018499,69048334,69049346,69063036,69076038,69233416,69235135,69239226,69325022,69327889,69330572,69333008,69339014,69339504,69354328,69355860,69361512,69372441,69382935,69389506,",0,ADGRB3,cmpl,cmpl,"-1,-1,0,1,1,1,1,1,1,1,0,0,0,1,1,2,0,2,0,2,0,1,2,0,2,2,0,0,1,0,0,0,"
9132,9132,142,XM_047419077.1,chr6,+,72622063,73198853,72622189,73195414,12,"72622063,73003907,73041935,73077321,73077761,73111307,73120482,73133420,73169745,73190572,73192564,73194451,","72622587,73003998,73042062,73077497,73077887,73111403,73120577,73133641,73169854,73190704,73192691,73198853,",0,KCNQ5,cmpl,cmpl,"0,2,0,1,0,0,0,2,1,2,2,0,"
7475,7475,21,NM_021956.5,chr6,+,101393707,102070083,101399277,102068511,17,"101393707,101398984,101621948,101626379,101676622,101682552,101686179,101799647,101802330,101818369,101859286,101889639,101924600,101928414,102035340,102055329,102068346,","101393837,101399392,101622116,101626637,101676804,101682606,101686353,101799791,101802438,101818483,101859493,101889863,101924719,101928632,102035566,102055580,102070083,",0,GRIK2,cmpl,cmpl,"-1,0,1,1,1,0,0,0,0,0,0,0,2,1,0,1,0,"
13268,13268,23,XM_017010318.3,chr6,+,123803864,124825640,123804200,124823229,6,"123803864,124283004,124658185,124791338,124818386,124823219,","123804254,124283142,124658386,124791399,124818468,124825640,",0,NKAIN2,cmpl,cmpl,"0,0,0,0,1,2,"
16473,16473,195,NM_001291981.2,chr6,-,127968784,128520599,127970226,128520358,33,"127968784,127973021,127973663,127976656,127976922,127981115,127982830,127983241,127985720,127990768,127991293,127992672,127995248,127995461,127996900,127998719,128001195,128003196,128005083,128009129,128064757,128067518,128078812,128082436,128083714,128089689,128184431,128218921,128240034,128242520,128322038,128397565,128520258,","127970280,127973157,127973827,127976782,127977054,127981289,127982980,127983377,127985875,127990885,127991391,127992709,127995266,127995538,127996988,127998904,128001207,128003232,128005244,128009268,128064794,128067792,128078918,128082638,128083824,128089992,128184725,128219096,128240150,128242602,128322310,128397688,128520599,",0,PTPRK,cmpl,cmpl,"0,2,0,0,0,0,0,2,0,0,1,0,0,1,0,1,1,1,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,"
10051,10051,24,NM_001079823.2,chr6,+,128883137,129516566,128883245,129516347,64,"128883137,129049917,129059783,129098172,129143900,129146958,129148978,129154504,129165575,129177705,129190204,129192679,129250111,129252083,129260710,129267105,129270623,129280060,129287846,129291613,129297684,129300735,129312860,129314654,129315475,129315761,129316037,129320537,129328277,129342342,129349297,129353163,129366218,129369891,129383121,129391490,129393044,129401223,129402323,129403820,129427751,129438645,129440815,129443062,129445666,129452987,129454154,129456334,129460199,129464289,129465144,129473213,129478692,129481262,129486473,129491900,129492314,129502658,129503090,129505199,129507488,129512362,129514372,129516189,","128883357,129050088,129059896,129098415,129144080,129147048,129149096,129154683,129165675,129177866,129190345,129192853,129250213,129252295,129260822,129267219,129270751,129280147,129288058,129291720,129297865,129300872,129313097,129314798,129315655,129315950,129316171,129320655,129328412,129342467,129349384,129353357,129366361,129369990,129383233,129391653,129393255,129401340,129402487,129403959,129427854,129438762,129440998,129443068,129445821,129453131,129454288,129456494,129460324,129464452,129465289,129473352,129478813,129481439,129486622,129492077,129492483,129502771,129503280,129505355,129507642,129512493,129514595,129516566,",0,LAMA2,cmpl,cmpl,"0,1,1,0,0,0,0,1,0,1,0,0,0,0,2,0,0,2,2,1,0,1,0,0,0,0,0,2,0,0,2,2,1,0,0,1,2,0,0,2,0,1,1,1,1,0,0,2,0,2,0,1,2,0,0,2,2,0,2,0,0,1,0,1,"
21962,21962,26,NM_007124.3,chr6,+,144285334,144853034,144291828,144850997,75,"144285334,144291736,144403122,144421877,144423548,144423985,144426286,144428777,144429580,144435934,144437564,144438744,144440351,144444280,144447210,144447601,144448599,144451369,144453781,144458769,144459173,144461196,144462653,144473719,144474603,144479811,144482208,144485384,144487547,144488672,144490070,144490928,144493300,144499256,144510943,144513908,144514649,144516228,144516810,144521979,144523015,144531051,144533084,144537581,144539293,144542794,144548639,144550964,144554687,144557156,144577098,144678405,144700086,144730356,144748245,144751805,144754719,144757928,144771906,144774289,144781921,144789193,144793833,144797823,144803035,144820881,144827347,144827610,144828789,144835779,144836300,144839172,144840739,144846804,144850988,","144285821,144291907,144403184,144421970,144423626,144424078,144426459,144428893,144429741,144436138,144437746,144438895,144440471,144444382,144447318,144447781,144448769,144451493,144453869,144459011,144459354,144461342,144462866,144473833,144474759,144479982,144482388,144485519,144487697,144488834,144490199,144491102,144493456,144499427,144511123,144514037,144514820,144516387,144516948,144522171,144523188,144531202,144533260,144537717,144539443,144542870,144548854,144551082,144554893,144557311,144577288,144678578,144700243,144730486,144748514,144751952,144754798,144757989,144771968,144774364,144782123,144789279,144793991,144797990,144803147,144821018,144827386,144827676,144828855,144835938,144836541,144839284,144840832,144846827,144853034,",0,UTRN,cmpl,cmpl,"-1,0,1,0,0,0,0,2,1,0,0,2,0,0,0,0,0,2,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,2,0,0,1,0,1,0,2,0,2,0,1,0,0,1,2,1,1,2,1,0,2,0,2,2,2,2,2,0,1,1,0,"
16072,16072,28,NM_004562.3,chr6,-,161347416,162727766,161350098,162727668,12,"161347416,161360087,161386793,161548853,161569354,161785771,161973301,162054090,162201130,162262524,162443309,162727661,","161350211,161360205,161386877,161549003,161569416,161785908,161973417,162054174,162201252,162262765,162443473,162727766,",0,PRKN,cmpl,cmpl,"1,0,0,0,1,2,0,0,1,0,1,0,"
14617,14617,228,NM_001080378.2,chr6,+,162727131,163315500,162728235,163314987,6,"162727131,162728159,162814146,163062149,163089258,163314826,","162727279,162728391,162814281,163062321,163089408,163315500,",0,PACRG,cmpl,cmpl,"-1,0,0,0,1,1,"
14946,14946,28,XM_017010194.3,chr6,-,165327288,165988052,165333121,165910865,24,"165327288,165336122,165339277,165343390,165379193,165388297,165392645,165395180,165396316,165413500,165416188,165418634,165428657,165430286,165431421,165432973,165435236,165448927,165450241,165482314,165543439,165711018,165910807,165986107,","165333127,165336215,165339358,165343502,165379366,165388453,165392796,165395264,165396459,165413687,165416281,165418777,165428709,165430345,165431472,165433129,165435377,165448977,165450362,165482343,165543568,165711153,165910932,165988052,",0,PDE10A,cmpl,cmpl,"0,0,0,2,0,0,2,2,0,2,2,0,2,0,0,0,0,1,0,1,1,1,0,-1,"
16474,16474,73,NM_001291981.2,chr6_KI270801v1_alt,-,313982,869933,315424,869692,33,"313982,318219,318861,321854,322120,326313,328028,328439,330918,335966,336491,337870,340446,340659,342098,343917,346393,348394,350281,358462,414091,416852,428146,431770,433048,439023,533765,568255,589368,591854,671372,746899,869592,","315478,318355,319025,321980,322252,326487,328178,328575,331073,336083,336589,337907,340464,340736,342186,344102,346405,348430,350442,358601,414128,417126,428252,431972,433158,439326,534059,568430,589484,591936,671644,747022,869933,",0,PTPRK,cmpl,cmpl,"0,2,0,0,0,0,0,2,0,0,1,0,0,1,0,1,1,1,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,"
17898,17898,9,NM_152744.4,chr7,+,3301251,4269000,3301586,4265384,45,"3301251,3619079,3639003,3641957,3821449,3950922,3951729,3958930,3962656,3967317,3969256,3971465,3974368,3987185,4010965,4012094,4017170,4049347,4051637,4067837,4076997,4079462,4110662,4113288,4114036,4127380,4129907,4132324,4145721,4149261,4158447,4161785,4174221,4175774,4178484,4205878,4208098,4210024,4220108,4221238,4233254,4237646,4241792,4245675,4265123,","3301884,3619239,3639110,3642105,3821583,3951034,3951920,3959014,3962851,3967434,3969424,3971568,3974545,3987322,4011113,4012235,4017352,4049463,4051830,4067936,4077189,4079584,4110772,4113439,4114274,4127496,4130097,4132423,4145916,4149463,4158551,4161856,4174357,4175834,4178586,4205994,4208285,4210162,4220270,4221364,4233419,4237784,4241913,4245805,4269000,",0,SDK1,cmpl,cmpl,"0,1,2,1,2,1,2,1,1,1,1,1,2,2,1,2,2,1,0,1,1,1,0,2,0,1,0,1,1,1,2,1,0,1,1,1,0,1,1,1,1,1,1,2,0,"
4755,4755,10,XM_011515154.3,chr7,-,14145048,14974858,14149130,14841263,26,"14145048,14176838,14178030,14338514,14345300,14478160,14574211,14580861,14583051,14607433,14613339,14621377,14630235,14672928,14682552,14682752,14685244,14694074,14698094,14701680,14718541,14736040,14753927,14757654,14841193,14974695,","14149238,14176899,14178151,14338710,14345391,14478225,14574372,14580951,14583137,14607508,14613413,14621494,14630271,14673027,14682669,14682841,14685362,14694194,14698169,14701730,14718685,14736194,14753948,14757731,14841450,14974858,",0,DGKB,cmpl,cmpl,"0,2,1,0,2,0,1,1,2,2,0,0,0,0,0,1,0,0,0,1,1,0,0,1,0,-1,"
7833,7833,11,NM_001321868.2,chr7,+,18086824,19002416,18162324,18996062,26,"18086824,18162228,18496261,18585280,18590344,18591515,18593907,18634626,18644670,18647784,18648465,18666212,18727579,18749004,18762156,18767105,18793344,18829160,18829460,18835466,18835899,18874477,18935808,18954145,18975805,18996022,","18087213,18162349,18496324,18585522,18590486,18591642,18594029,18634742,18644793,18647998,18648683,18666476,18727757,18749138,18762277,18767155,18793452,18829216,18829548,18835586,18835997,18874596,18935942,18954230,18975953,19002416,",0,HDAC9,cmpl,cmpl,"-1,0,1,1,0,1,2,1,0,0,1,0,0,1,0,1,0,0,2,0,0,2,1,0,1,2,"
3972,3972,12,NM_182899.5,chr7,+,28299320,28825894,28494929,28819279,10,"28299320,28494905,28507615,28570364,28718752,28724221,28804198,28809186,28818070,28819115,","28299441,28494999,28507737,28570537,28718879,28724332,28804522,28809414,28818179,28825894,",0,CREB5,cmpl,cmpl,"-1,0,1,0,2,0,0,0,0,1,"
14951,14951,103,NM_001322059.2,chr7,-,31616776,32428224,31790245,32428131,18,"31783509,31809030,31815923,31823072,31824866,31828291,31837179,31837869,31847967,31850640,31864941,31873291,31877969,31878995,31880746,32169784,32209488,32427821,","31790259,31809108,31816154,31823248,31824987,31828373,31837300,31837971,31848096,31850741,31865082,31873408,31878036,31879178,31880860,32169956,32209539,32428224,",0,PDE1C,cmpl,cmpl,"1,1,1,2,1,0,2,2,2,0,0,0,2,2,2,1,1,0,"
5490,5490,108,XM_011515654.3,chr7,-,36852905,37449326,36855550,37342690,23,"36852905,36861658,36870392,36878009,36887559,36894853,37013298,37096618,37133129,37211385,37213334,37216644,37222614,37224878,37233094,37244355,37259180,37271831,37314849,37315919,37342612,37428790,37448859,","36855751,36861736,36870475,36878117,36887672,36895017,37013435,37096727,37133234,37211517,37213457,37216695,37222693,37225030,37233194,37244391,37259350,37271882,37314922,37315960,37342763,37429756,37449326,",0,ELMO1,cmpl,cmpl,"0,0,1,1,2,0,1,0,0,0,0,0,2,0,2,2,0,0,2,0,0,-1,-1,"
19646,19646,111,XM_047420843.1,chr7,+,40135004,40882597,40135020,40881766,14,"40135004,40180946,40181954,40188494,40189543,40194939,40237634,40274512,40316759,40449286,40459100,40496283,40749433,40881680,","40135120,40180998,40182028,40188580,40189594,40195060,40237726,40274656,40316855,40449358,40459198,40496386,40749497,40882597,",0,SUGCT,cmpl,cmpl,"0,1,2,1,0,0,1,0,0,0,0,2,0,1,"
1486,1486,17,XM_047420162.1,chr7,+,69598474,70793506,69599653,70790996,16,"69598474,69899285,70118131,70134535,70435751,70698568,70762869,70764754,70766113,70771548,70777102,70781614,70784941,70785954,70787208,70789747,","69599962,69899498,70118233,70134571,70435781,70698620,70763341,70765005,70766334,70771644,70777174,70781756,70785019,70786038,70787431,70793506,",0,AUTS2,cmpl,cmpl,"0,0,0,0,0,0,1,2,1,0,0,0,1,1,1,2,"
6756,6756,17,NM_022479.3,chr7,+,71132143,71713599,71132802,71712146,11,"71132143,71335549,71388234,71415888,71420907,71571284,71665410,71669971,71677210,71710760,71712017,","71133040,71335733,71388401,71416063,71421105,71571402,71665596,71670109,71677306,71710928,71713599,",0,GALNT17,cmpl,cmpl,"0,1,2,1,2,2,0,0,0,0,0,"
2354,2354,17,XM_017012677.2,chr7,-,71779490,72504279,71787774,72504113,6,"71779490,71810335,72023656,72106150,72278685,72504111,","71787902,71810492,72023769,72106294,72278810,72504279,",0,CALN1,cmpl,cmpl,"1,0,1,1,2,0,"
11575,11575,18,XM_017012840.3,chr7,-,78017054,79453667,78019314,79453320,25,"78017054,78026067,78065573,78078946,78125693,78127196,78132888,78135020,78160024,78167915,78178010,78185628,78194873,78201161,78255942,78343777,78345443,78345921,78369155,78489760,78501576,78521429,78627119,79007089,79453019,","78019976,78026104,78065662,78079085,78125837,78127416,78133060,78135206,78160273,78168108,78178102,78185670,78195063,78201193,78256581,78343960,78345572,78346043,78369213,78489840,78501787,78521645,78627239,79007206,79453667,",0,MAGI2,cmpl,cmpl,"1,0,1,0,0,2,1,1,1,0,1,1,0,1,1,1,1,2,1,2,1,1,1,1,0,"
17964,17964,153,XM_047419751.1,chr7,-,83955776,84492725,83961370,84194586,21,"83955776,83963204,83977131,83981320,83985435,84001954,84005338,84007352,84011021,84011182,84014208,84046323,84060464,84110469,84129122,84134793,84194474,84295041,84307206,84371823,84492459,","83961826,83963347,83977196,83981478,83985477,84002046,84005558,84007497,84011091,84011297,84014351,84046443,84060558,84110589,84129185,84134951,84194668,84295131,84307292,84371900,84492725,",0,SEMA3A,cmpl,cmpl,"0,1,2,0,0,1,0,2,1,0,1,1,0,0,0,1,0,-1,-1,-1,-1,"
23192,23192,19,NM_181646.5,chr7,+,88759699,89338528,88759976,89337032,4,"88759699,89218154,89327343,89333362,","88760084,89218295,89327474,89338528,",0,ZNF804B,cmpl,cmpl,"0,0,0,2,"
2981,2981,159,NM_001287135.2,chr7,+,90596320,91210590,90596627,91118180,15,"90596320,90604217,90726566,90747680,90790572,90863174,90899290,90917600,90955696,90984147,91045896,91079431,91112541,91118064,91207164,","90596718,90604249,90726812,90747775,90790652,90863269,90899353,90917724,90955817,90984241,91045960,91079480,91112681,91118208,91210590,",0,CDK14,cmpl,cmpl,"0,1,0,0,2,1,0,0,1,2,0,1,2,1,-1,"
10240,10240,21,NM_199000.3,chr7,+,104328602,104908561,104328779,104906215,3,"104328602,104736674,104906186,","104329224,104736911,104908561,",0,LHFPL3,cmpl,cmpl,"0,1,1,"
8697,8697,22,XM_047420927.1,chr7,-,110662643,111562492,110663711,111521447,7,"110662643,110963499,111417258,111487237,111521312,111532517,111561850,","110663721,110963565,111417342,111487341,111521449,111532585,111562492,",0,IMMP2L,cmpl,cmpl,"2,2,2,0,0,-1,-1,"
2329,2329,23,XM_017012796.3,chr7,-,122318410,122886460,122320164,122663539,33,"122318410,122325476,122345573,122360787,122360929,122379367,122386294,122387025,122388582,122393195,122393440,122407539,122414067,122416060,122436359,122438340,122441511,122451373,122471374,122474380,122480851,122490080,122491311,122513248,122554549,122581178,122615180,122621480,122629247,122663236,122736954,122885393,122885998,","122320338,122325581,122345681,122360820,122361013,122379442,122386309,122387173,122388738,122393315,122393582,122407696,122414076,122416164,122436380,122438464,122441575,122451475,122471562,122474517,122480860,122490281,122491420,122513315,122554689,122581290,122615299,122621717,122629328,122663569,122737068,122885445,122886460,",0,CADPS2,cmpl,cmpl,"0,0,0,0,0,0,0,2,2,2,1,0,0,1,1,0,2,2,0,1,1,1,0,2,0,2,0,0,0,0,-1,-1,-1,"
7507,7507,24,NM_001371083.1,chr7,-,126438597,127252941,126439118,127243204,12,"126438597,126446125,126532951,126609361,126769864,126902541,126903971,126904547,127106495,127242694,127248219,127252796,","126439168,126446372,126533887,126609498,126770065,126902679,126904126,126904683,127106712,127243515,127248323,127252941,",0,GRM8,cmpl,cmpl,"1,0,0,1,1,1,2,1,0,0,-1,-1,"
15509,15509,199,XM_047421017.1,chr7,-,132123339,132648688,132130478,132508693,33,"132123339,132133048,132140598,132145118,132146509,132147899,132148542,132159472,132164141,132165133,132168303,132174777,132179686,132180585,132181380,132182096,132185298,132187470,132194061,132198484,132202645,132203322,132210942,132223526,132226160,132227450,132228345,132241065,132298090,132489291,132507505,132565464,132576421,","132130574,132133199,132140811,132145288,132146700,132147999,132148646,132159632,132164288,132165200,132168572,132174920,132179921,132180732,132181620,132182190,132185463,132187607,132194179,132198636,132202836,132203419,132211143,132223641,132226260,132227604,132228469,132241166,132298222,132489474,132508779,132565647,132576470,",0,PLXNA4,cmpl,cmpl,"0,2,2,0,1,0,1,0,0,2,0,1,0,0,0,2,2,0,2,0,1,0,0,2,1,0,2,0,0,0,0,-1,-1,"
5814,5814,200,NM_021807.4,chr7,+,133253077,134065761,133253101,134064528,18,"133253077,133274981,133288921,133305876,133317283,133356329,133374827,133475327,133480049,133630044,133817324,133895598,133917582,133937890,133997491,134004911,134007675,134064290,","133253187,133275171,133289116,133306061,133317390,133356573,133375002,133475473,133480138,133630141,133817544,133895735,133917738,133938069,133997633,134005090,134007835,134065761,",0,EXOC4,cmpl,cmpl,"0,2,0,0,2,1,2,0,2,1,2,0,2,2,1,2,1,2,"
3707,3707,26,NM_014141.6,chr7,+,146116800,148420998,146116876,148415616,24,"146116800,146774270,146839710,147043906,147108146,147120978,147128692,147132244,147300140,147395608,147485934,147562137,147639105,147903564,147977861,148118117,148147490,148172241,148217287,148229645,148267032,148383648,148409390,148415416,","146116973,146774381,146839904,147044054,147108350,147121163,147128836,147132509,147300290,147395780,147486041,147562257,147639306,147903721,147977989,148118288,148147709,148172478,148217524,148229779,148267126,148383888,148409471,148420998,",0,CNTNAP2,cmpl,cmpl,"0,1,1,0,1,1,0,0,1,1,2,1,1,1,2,1,1,1,1,1,0,1,1,1,"
5068,5068,27,NM_001364498.2,chr7,+,153748132,154894285,153748948,154892480,27,"153748132,153748754,154446213,154474938,154540531,154566841,154637820,154669359,154727766,154769416,154772844,154794078,154795844,154801354,154803863,154804916,154806993,154853779,154867994,154872623,154875905,154880887,154885632,154887675,154889271,154889456,154892333,","153748319,153749008,154446328,154475037,154540626,154566916,154637873,154669441,154727887,154769571,154772942,154794202,154795883,154801462,154803955,154804964,154807112,154853827,154868093,154872693,154876100,154880942,154885744,154887734,154889344,154889530,154894285,",0,DPP6,cmpl,cmpl,"-1,0,0,1,1,0,0,2,0,1,0,2,0,0,0,2,2,1,1,1,2,2,0,1,0,1,0,"
16477,16477,27,NM_002847.5,chr7,-,157539055,158587823,157540713,158587669,23,"157539055,157548945,157568901,157571439,157576612,157578020,157595237,157604001,157621361,157656356,157682724,157898672,158081297,158110828,158133676,158136654,158138293,158166930,158192326,158205170,158316818,158489734,158587557,","157540785,157549019,157568966,157571493,157576779,157578140,157595315,157604075,157621509,157656551,157682937,157898737,158081377,158110915,158134059,158136695,158138515,158167291,158192495,158205273,158316932,158489785,158587823,",0,PTPRN2,cmpl,cmpl,"0,1,2,2,0,0,0,1,0,0,0,1,2,2,0,1,1,0,2,1,1,1,0,"
4866,4866,9,NM_001346810.2,chr8,+,737627,1708476,737807,1701406,15,"737627,907911,1258850,1501365,1548625,1565682,1626739,1632826,1668328,1669742,1676532,1678213,1691534,1697146,1701187,","737825,907966,1258883,1501431,1549683,1565894,1626887,1633046,1668678,1669784,1676618,1678629,1691626,1697299,1708476,",0,DLGAP2,cmpl,cmpl,"0,0,1,1,1,0,2,0,1,0,0,2,1,0,0,"
4078,4078,9,NM_033225.6,chr8,-,2935360,4994914,2938584,4994416,70,"2935360,2942471,2949298,2950230,2951113,2954223,2955588,2957695,2961140,2962465,2963221,2965774,2966569,2973116,2974450,2978611,2998010,2999957,3018476,3029318,3052461,3087096,3091515,3096848,3106527,3107717,3108602,3110157,3118398,3142464,3151396,3157896,3162158,3181109,3187868,3188886,3189911,3199713,3201611,3205503,3214496,3219254,3223728,3230039,3284143,3307694,3308311,3343293,3347991,3359151,3367031,3369253,3387493,3396193,3399390,3406026,3407898,3409422,3468711,3493622,3574944,3586135,3616709,3708413,3753929,3997902,4031904,4419952,4637341,4994331,","2938744,2942604,2949386,2950343,2951275,2954268,2955768,2957807,2961214,2962639,2963395,2965954,2966746,2973299,2974624,2978800,2998184,3000131,3018650,3029513,3052647,3087285,3091662,3097037,3106641,3107798,3108748,3110335,3118587,3142674,3151513,3157966,3162277,3181214,3187965,3189011,3190115,3199809,3201725,3205620,3214691,3219442,3223867,3230231,3284346,3307821,3308503,3343450,3348161,3359340,3367247,3369370,3387682,3396381,3399529,3406221,3408225,3409605,3468824,3493726,3575066,3586260,3616797,3708491,3754042,3998110,4032099,4420065,4637558,4994914,",0,CSMD1,cmpl,cmpl,"2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,2,1,1,2,1,0,"
18146,18146,10,NM_139167.4,chr8,-,14084844,15238431,14090442,15237623,8,"14084844,14102375,14108162,14164579,14237591,14324102,14554731,15237584,","14090637,14102499,14108235,14164702,14237679,14324204,14554926,15238431,",0,SGCZ,cmpl,cmpl,"0,2,1,1,0,0,0,0,"
16276,16276,11,NM_001412866.1,chr8,-,18527302,19084805,18535742,19084529,17,"18527302,18556208,18572527,18575127,18600363,18632612,18655641,18735234,18765448,18799294,18801269,18804521,18804703,18867673,18871625,18936033,19084205,","18535958,18556352,18572672,18575285,18600434,18632806,18655685,18735315,18765538,18799353,18801382,18804602,18804898,18868069,18872733,18936142,19084805,",0,PSD3,cmpl,cmpl,"0,0,2,0,1,2,0,0,0,1,2,2,2,2,1,0,0,"
13576,13576,12,NM_001322202.2,chr8,+,31639244,32774046,32754445,32764402,9,"31639244,32595827,32605561,32727948,32754371,32756402,32759305,32760199,32763747,","31639431,32596005,32605683,32728078,32754474,32756529,32759436,32760406,32774046,",0,NRG1,cmpl,cmpl,"-1,-1,-1,-1,0,2,0,2,2,"
21803,21803,13,XM_047421381.1,chr8,+,35235474,35796540,35235784,35790563,15,"35235474,35549291,35568097,35595553,35683546,35686544,35722209,35726151,35731011,35748526,35750581,35759319,35766901,35774298,35790358,","35235887,35549510,35568241,35595657,35683727,35686709,35722356,35726529,35731096,35748695,35750809,35759469,35767066,35774477,35796540,",0,UNC5D,cmpl,cmpl,"0,1,1,1,0,1,1,1,1,2,0,0,0,0,2,"
18992,18992,1,NM_001287813.3,chr8,+,49909795,50796692,50394238,50792829,20,"49909795,49910891,50172560,50394211,50402209,50438542,50449667,50450555,50450687,50502777,50530176,50536677,50553049,50590878,50656908,50658591,50704599,50708885,50752000,50792670,","49909904,49911044,50172635,50394265,50402344,50438599,50449725,50450599,50450729,50502880,50530259,50536808,50553179,50590917,50657025,50658663,50704752,50708978,50752111,50796692,",0,SNTG1,cmpl,cmpl,"-1,-1,-1,0,0,0,0,1,0,0,1,0,2,0,0,0,0,0,0,0,"
3606,3606,131,XM_024447079.2,chr8,+,60964847,61501629,61299827,61499542,9,"60964847,60966169,61131769,61292317,61299676,61376604,61454140,61458306,61499454,","60965361,60966237,61131860,61292454,61300282,61376779,61454251,61458542,61501629,",0,CLVS1,cmpl,cmpl,"-1,-1,-1,-1,0,2,0,0,2,"
13269,13269,16,XM_017013359.2,chr8,+,62248853,62999652,62249073,62999334,6,"62248853,62579538,62589713,62746931,62918452,62999230,","62249127,62579676,62589794,62747129,62918513,62999652,",0,NKAIN3,cmpl,cmpl,"0,0,0,0,0,1,"
16716,16716,153,XM_024447066.2,chr8,+,84182786,84921844,84529321,84920911,8,"84182786,84529298,84774578,84849979,84862295,84873283,84887603,84920893,","84182944,84529577,84774654,84850027,84862453,84873397,84887776,84921844,",0,RALYL,cmpl,cmpl,"-1,0,1,2,2,1,1,0,"
3636,3636,19,XM_017013149.2,chr8,+,86866414,87428652,86866495,87428637,11,"86866438,86887541,86905080,86939595,87205992,87236918,87284677,87286538,87351684,87353635,87428545,","86866583,86887611,86905194,86939754,87206138,87237112,87284815,87286671,87351794,87353786,87428652,",0,CNBD1,cmpl,cmpl,"0,1,2,2,2,1,0,0,1,0,1,"
19557,19557,20,XM_017013756.2,chr8,-,98387878,98942610,98434253,98942470,13,"98429935,98437102,98526741,98547968,98579663,98596031,98706466,98707146,98749275,98767242,98774738,98883646,98942377,","98434318,98437208,98526917,98548161,98579789,98596169,98706634,98707311,98749390,98767371,98774819,98883834,98942610,",0,STK3,cmpl,cmpl,"1,0,1,0,0,0,0,0,2,2,2,0,0,"
22072,22072,20,NM_017890.5,chr8,+,99013273,99877580,99013788,99875666,62,"99013273,99013759,99038422,99096311,99102952,99111097,99115699,99121176,99134631,99135014,99135595,99136664,99142973,99147840,99156548,99170038,99192875,99274197,99275080,99384207,99391556,99431536,99442400,99467413,99481598,99501686,99502835,99507769,99511103,99520898,99556449,99575657,99577489,99641810,99661353,99699524,99717170,99720344,99720862,99766773,99776774,99778681,99784314,99809374,99817539,99818450,99818712,99819411,99819920,99821293,99823831,99832368,99835196,99835538,99848775,99853450,99859303,99861775,99868288,99870784,99871447,99875417,","99013347,99013935,99038566,99096432,99103120,99111279,99115874,99121445,99134727,99135137,99135733,99136752,99143165,99148010,99156743,99170163,99193057,99274332,99275254,99384317,99391704,99431664,99442635,99467634,99481802,99501858,99502950,99507911,99511512,99521010,99556653,99575784,99577633,99642498,99661491,99699932,99717373,99720552,99721047,99766970,99776956,99779031,99784476,99809530,99817803,99818534,99818888,99819582,99820122,99821482,99823978,99832652,99835324,99835738,99848894,99854256,99859480,99861946,99868465,99870887,99871697,99877580,",0,VPS13B,cmpl,cmpl,"-1,0,0,0,1,1,0,1,0,0,0,0,1,1,0,0,2,1,1,1,0,1,0,1,0,0,1,2,0,1,2,2,0,0,1,1,1,0,1,0,2,1,0,0,0,0,0,2,2,0,0,0,2,1,0,2,1,1,1,1,2,0,"
17130,17130,21,NM_001348497.2,chr8,+,103500609,104256094,103500886,104251820,23,"103500609,103697085,103766226,103885297,103910320,103912052,103915494,103916413,103918440,103921671,103931262,103936550,103942772,103961064,103975349,103989304,104014505,104015423,104244915,104248700,104249486,104251023,104251601,","103501062,103697296,103766537,103886223,103910529,103912172,103915594,103916537,103918487,103921784,103931393,103936722,103942926,103961133,103975506,103989421,104014615,104015456,104245057,104248813,104249588,104251163,104256094,",0,RIMS2,cmpl,cmpl,"0,2,0,2,1,0,0,1,2,1,0,2,0,1,1,2,2,1,1,2,1,1,0,"
4080,4080,22,NM_198123.2,chr8,-,112222927,113436939,112224770,113436854,71,"112222927,112228755,112231544,112234364,112237189,112241719,112244393,112247019,112254252,112255253,112263638,112265410,112281173,112287063,112289364,112291509,112292536,112295832,112301792,112304720,112306006,112310977,112313905,112314428,112318836,112319900,112335328,112336651,112337542,112341476,112346096,112351174,112352415,112380351,112383566,112390663,112406523,112408317,112408918,112472590,112492488,112503789,112506690,112517033,112550670,112552593,112556762,112573500,112587065,112636816,112638695,112645108,112650160,112656153,112666276,112682441,112685405,112689867,112800161,112829685,112859144,112921626,112947789,112954683,112975836,113019066,113098755,113173721,113278591,113314570,113436676,","112224930,112228891,112231632,112234477,112237348,112241785,112244573,112247131,112254326,112255427,112263812,112265590,112281350,112287246,112289538,112291695,112292710,112296006,112301966,112304915,112306192,112311166,112314052,112314617,112318950,112319981,112335474,112336829,112337731,112341686,112346213,112351244,112352534,112380456,112383663,112390788,112406727,112408413,112409032,112472707,112492683,112503977,112506829,112517225,112550873,112552720,112556954,112573657,112587235,112637005,112638911,112645225,112650349,112656341,112666415,112682636,112685732,112690050,112800274,112829789,112859266,112921751,112947877,112954761,112976148,113019179,113098963,113173916,113278704,113314793,113436939,",0,CSMD3,cmpl,cmpl,"2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,1,2,1,1,2,1,0,"
21106,21106,206,NM_031466.8,chr8,-,139727724,140458579,139731060,140451373,23,"139727724,139731978,139885878,139910146,139988725,140023936,140221458,140252776,140275657,140283888,140287607,140290992,140300468,140311247,140360049,140370963,140397619,140405576,140426614,140435111,140439051,140450789,140458280,","139731228,139732202,139885969,139910300,139988836,140024079,140221583,140252929,140275821,140284021,140287734,140291078,140300614,140311374,140360193,140371180,140397745,140405698,140426641,140435240,140439197,140451383,140458579,",0,TRAPPC9,cmpl,cmpl,"0,1,0,2,2,0,1,1,2,1,0,1,2,1,1,0,0,1,1,1,2,0,-1,"
7037,7037,9,XM_047422890.1,chr9,-,3824126,4490465,3828271,4348261,12,"3824126,3829309,3856008,3879426,3898690,3932359,3937027,4117767,4125733,4347080,4348231,4489627,","3828408,3829492,3856184,3879595,3898835,3932470,3937189,4118881,4125941,4347183,4348412,4490465,",0,GLIS3,cmpl,cmpl,"1,1,2,1,0,0,0,2,1,0,0,-1,"
16467,16467,1,NM_002839.4,chr9,-,8314245,10613002,8317873,8733843,46,"8314245,8319830,8331581,8338921,8340342,8341089,8341692,8375935,8376606,8389231,8404536,8436591,8449724,8460410,8465465,8470994,8484118,8485226,8485761,8492861,8497241,8499646,8500753,8504260,8507300,8517847,8521276,8523512,8524924,8526626,8527344,8528590,8633316,8636698,8733779,9018696,9183303,9397448,9574731,9734532,9766809,9938506,10033717,10340962,10612397,10612687,","8317942,8319966,8331736,8339047,8340469,8341268,8341978,8376090,8376726,8389407,8404660,8436689,8449837,8460571,8465675,8471085,8484378,8485324,8486349,8492979,8497268,8499840,8501059,8504405,8507434,8518429,8521546,8523524,8525035,8526644,8527353,8528779,8633458,8636844,8733946,9018735,9183363,9397482,9574781,9734571,9766851,9938610,10033790,10341017,10612505,10613002,",0,PTPRD,cmpl,cmpl,"0,2,0,0,2,0,2,0,0,1,0,1,2,0,0,2,0,1,1,0,0,1,1,0,1,1,1,1,1,1,1,1,0,1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,"
326,326,11,XM_017015312.3,chr9,+,17906632,18910950,17906826,18908548,29,"17906632,18163861,18504828,18533246,18574029,18622242,18635942,18639253,18657638,18661934,18680311,18681811,18684715,18706746,18721535,18753297,18770601,18775742,18776780,18795396,18817108,18826283,18829842,18887830,18889567,18892388,18905781,18906691,18908441,","17906922,18163981,18504956,18533292,18574266,18622369,18636017,18639411,18657750,18662073,18680516,18681959,18684800,18707048,18721665,18753508,18770781,18775896,18777906,18795524,18817237,18826463,18829977,18888043,18889748,18892596,18905891,18906912,18910950,",0,ADAMTSL1,cmpl,cmpl,"0,0,0,2,0,0,1,1,0,1,2,0,1,2,1,2,0,0,1,2,1,1,1,1,1,2,0,2,1,"
18445,18445,11,XM_017014592.2,chr9,-,19507454,20307892,19516152,19786866,15,"19507454,19520893,19528048,19550136,19573350,19576923,19597228,19619583,19622260,19785936,19849648,19891130,20004249,20301225,20307652,","19516402,19521060,19528138,19550268,19573469,19577022,19597279,19619692,19622299,19787019,19849787,19891228,20004387,20301364,20307892,",0,SLC24A2,cmpl,cmpl,"2,0,0,0,1,1,1,0,0,0,-1,-1,-1,-1,-1,"
10335,10335,12,XM_047422812.1,chr9,-,27937616,29213601,27948850,27950671,8,"27937616,28295207,28372835,28475939,28670199,28913791,28947817,29212921,","27950706,28295366,28372868,28476025,28670280,28913874,28947914,29213601,",0,LINGO2,cmpl,cmpl,"0,-1,-1,-1,-1,-1,-1,-1,"
21314,21314,17,NM_001366142.2,chr9,-,70529059,71446971,70535428,71446835,27,"70529059,70537121,70549541,70552843,70553159,70591030,70598418,70603341,70610608,70615907,70618866,70620075,70621243,70625190,70625481,70635210,70639059,70640559,70681505,70761600,70784104,70827846,70843002,70846377,70862907,70864431,71446652,","70535451,70537405,70549674,70553043,70553310,70591205,70598670,70603470,70610749,70616075,70619095,70620365,70621273,70625331,70625517,70635261,70639194,70640660,70681578,70761724,70784279,70828018,70843127,70846591,70863112,70864511,71446971,",0,TRPM3,cmpl,cmpl,"1,2,1,2,1,0,0,0,0,0,2,0,0,0,0,0,0,1,0,2,1,0,1,0,2,0,0,"
14665,14665,22,XM_047423419.1,chr9,+,109640786,110172512,109780488,110168421,8,"109780197,109867490,109880550,109923734,109925060,110015953,110136126,110168398,","109780533,109867571,109880681,109923849,109925082,110016039,110138539,110172512,",0,PALM2AKAP2,cmpl,cmpl,"0,0,0,2,0,1,0,1,"
1289,1289,184,NM_001365068.1,chr9,-,116423111,117415057,116425850,117414938,23,"116423111,116440608,116442452,116487358,116618323,116620309,116651527,116725770,116728991,116733398,116805631,116820616,116863582,116975207,116976113,116976700,117008091,117039818,117096043,117141325,117214357,117291325,117414496,","116426088,116440792,116442553,116487500,116618472,116620443,116651793,116725950,116729096,116733523,116805820,116820783,116863733,116975345,116976188,116976785,117008259,117039965,117096151,117141478,117214742,117291513,117415057,",0,ASTN2,cmpl,cmpl,"2,1,2,1,2,0,1,1,1,2,2,0,2,2,2,1,1,1,1,1,0,1,0,"
4709,4709,23,NM_001352964.2,chr9,-,123379657,123930126,123381431,123929905,24,"123379657,123383654,123387729,123403401,123411775,123440359,123450692,123452275,123454738,123457347,123457792,123557569,123583168,123609435,123630375,123652012,123667025,123671290,123676719,123757702,123769513,123792586,123878950,123929888,","123382625,123383913,123387858,123403490,123411829,123440491,123450749,123452347,123454779,123457435,123457897,123557695,123583270,123609481,123630476,123652123,123667079,123671371,123676789,123757822,123769563,123792630,123879021,123930126,",0,DENND1A,cmpl,cmpl,"0,2,2,0,0,0,0,0,1,0,0,0,0,2,0,0,0,0,2,2,0,1,2,0,"
1070,1070,10,NM_013427.3,chrX,-,11137543,11665920,11138862,11664828,13,"11137543,11142232,11143979,11156528,11169504,11178099,11179301,11182062,11186235,11188727,11196924,11254547,11664240,","11139530,11142313,11144248,11156626,11169684,11178248,11179452,11182118,11186431,11188984,11196996,11254707,11665920,",0,ARHGAP6,cmpl,cmpl,"1,1,2,0,0,1,0,1,0,1,1,0,0,"
6580,6580,10,NM_001368395.3,chrX,+,11822438,12724523,11865188,12721858,19,"11822438,11865085,11877894,12498679,12609720,12614778,12674862,12683482,12686096,12690194,12694334,12701873,12704358,12706825,12707468,12710398,12716068,12717500,12720533,","11822715,11865216,11878018,12498796,12609881,12614881,12674908,12683587,12686204,12690326,12694454,12702010,12704485,12706915,12707651,12710537,12717133,12718790,12724523,",0,FRMPD4,cmpl,cmpl,"-1,0,1,2,2,1,2,0,0,0,0,0,2,0,0,0,1,1,1,"
8637,8637,12,NM_014271.4,chrX,+,28587445,29956718,28789343,29955820,11,"28587445,28789319,29282937,29396257,29399154,29668429,29917463,29919948,29941650,29954521,29955101,","28588047,28789425,29283217,29396444,29399308,29668504,29917596,29920094,29941794,29954692,29956718,",0,IL1RAPL1,cmpl,cmpl,"-1,0,1,2,0,1,1,2,1,1,1,"
4894,4894,12,NM_000109.4,chrX,-,31119221,33339388,31121918,33339265,79,"31119221,31126641,31134101,31146290,31147274,31169442,31172347,31173538,31177931,31178668,31180369,31182737,31203960,31206581,31209497,31223046,31260954,31323597,31348555,31444480,31478105,31478982,31496787,31507280,31627672,31657989,31679374,31729630,31773959,31819974,31836717,31875187,31929595,31932079,31968338,32216915,32287528,32310081,32342099,32343133,32345942,32348405,32362787,32364581,32365019,32380509,32386309,32389500,32390070,32411751,32438240,32441179,32448455,32454661,32463438,32464585,32468497,32472163,32484918,32491276,32501754,32518007,32545158,32565701,32573529,32573744,32595756,32614302,32644131,32644963,32697869,32699111,32809492,32816467,32823294,32844782,32849727,33020138,33339258,","31121930,31126673,31134194,31146414,31147518,31169601,31172413,31173604,31177970,31178805,31180481,31182904,31204118,31206667,31209699,31223121,31261016,31323658,31348634,31444627,31478374,31479103,31496944,31507453,31627862,31658144,31679586,31729748,31774192,31820083,31836819,31875373,31929745,31932227,31968514,32217063,32287701,32310276,32342282,32343286,32346080,32348528,32362958,32364710,32365199,32380680,32386465,32389674,32390181,32411913,32438390,32441314,32448638,32454832,32463594,32464699,32468710,32472309,32485099,32491518,32501842,32518131,32545334,32565881,32573637,32573846,32595876,32614453,32644313,32645152,32697998,32699293,32809611,32816640,32823387,32844860,32849820,33020200,33339388,",0,DMD,cmpl,cmpl,"0,1,1,0,2,2,2,2,2,0,2,0,1,2,1,1,2,1,0,0,1,0,2,0,2,0,1,0,1,0,0,0,0,2,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,2,0,0,0,0,0,2,0,0,0,1,2,0,0,0,0,1,0,"
4421,4421,155,XM_017029255.2,chrX,+,86148450,86832602,86148620,86832155,11,"86148450,86514278,86651035,86695020,86714547,86739746,86812855,86813129,86814687,86816033,86832105,","86149108,86514391,86651167,86695179,86714720,86739882,86813004,86813277,86814834,86816099,86832602,",0,DACH2,cmpl,cmpl,"0,2,1,1,1,0,1,0,1,1,1,"
14785,14785,2,XM_011530914.3,chrX,+,91779374,92623230,91835504,92618940,8,"91779374,91835460,91876780,92201374,92263113,92387734,92468298,92618263,","91779684,91836044,91879273,92201455,92263143,92387933,92468322,92623230,",0,PCDH11X,cmpl,cmpl,"-1,0,0,0,0,0,1,1,"
4821,4821,20,NM_006729.5,chrX,+,96684841,97604997,96685058,97599317,27,"96684841,96735757,96738585,96758153,96881578,96912327,96912482,96916437,96918508,96930732,96937232,96939265,96942017,96945526,96948934,96957827,96965092,97072940,97075166,97099693,97114725,97141664,97247714,97348115,97383908,97429649,97599252,","96685190,96735790,96738762,96758258,96881718,96912402,96912552,96916574,96918617,96930843,96937351,96939382,96942136,96945591,96949039,96958148,96965207,97073042,97075261,97099795,97114965,97141794,97247839,97348280,97384044,97429745,97604997,",0,DIAPH2,cmpl,cmpl,"0,0,0,0,0,2,2,0,2,0,0,2,2,1,0,0,0,1,1,0,0,0,1,0,0,1,1,"
8638,8638,21,NM_017416.2,chrX,+,104566198,105767829,104658913,105767661,11,"104566198,104658894,105195474,105233817,105267387,105484312,105717366,105740545,105748959,105755176,105766963,","104567051,104658995,105195748,105234004,105267541,105484387,105717496,105740691,105749103,105755347,105767829,",0,IL1RAPL2,cmpl,cmpl,"-1,0,1,2,0,1,1,2,1,1,1,"
20211,20211,23,XM_017029213.3,chrX,-,124375902,125204312,124380535,124963753,35,"124375902,124382669,124383633,124385676,124392051,124405030,124406316,124420310,124422271,124453336,124470724,124481731,124487208,124497015,124503559,124520516,124523363,124529863,124546873,124561670,124563748,124565374,124641790,124645142,124646708,124651913,124653583,124671682,124705012,124736956,124894295,124895980,124963536,125185642,125203799,","124381294,124382812,124384854,124386064,124392348,124405266,124406489,124420821,124422638,124453491,124470823,124481964,124487229,124497265,124503703,124520784,124523625,124529983,124547090,124561817,124563772,124565560,124641991,124645337,124646810,124652124,124653783,124671835,124705251,124737197,124894352,124896241,124963817,125185709,125204312,",0,TENM1,cmpl,cmpl,"0,1,1,0,0,1,2,1,0,1,1,2,2,1,1,0,2,2,1,1,1,1,1,1,1,0,1,1,2,1,1,1,0,-1,-1,"
6323,6323,205,NM_001139501.2,chrX,-,138614726,139205023,138632849,138857641,8,"138614726,138635456,138702983,138708817,138857511,138990507,139204058,139204920,","138632986,138635655,138703087,138708928,138857679,138990617,139204271,139205023,",0,FGF13,cmpl,cmpl,"1,0,1,1,0,-1,-1,-1,"
14786,14786,9,XM_017030080.2,chrY,+,5000295,5742228,5032696,5737942,10,"5000295,5030898,5031214,5031905,5032669,5056888,5098214,5501056,5581774,5737271,","5000605,5031067,5031346,5032011,5032728,5057459,5100707,5501255,5581798,5742228,",0,PCDH11Y,cmpl,cmpl,"-1,-1,-1,-1,0,2,0,0,1,1,"
1 Unnamed: 0 bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
2 2378 2378 9 XM_047416024.1 chr1 + 6785453 7769706 6785550 7766522 20 6785453,6825091,7091303,7249490,7640399,7661725,7663352,7670910,7677598,7732447,7736343,7736930,7737254,7738297,7744834,7745844,7747709,7751198,7752458,7766458, 6785575,6825210,7091371,7249626,7640553,7661866,7665199,7671037,7677733,7732599,7736540,7737009,7737570,7738482,7745022,7746091,7747781,7751392,7752533,7769706, 0 CAMTA1 cmpl cmpl 0,1,0,2,0,1,1,0,1,1,0,2,0,1,0,2,0,0,2,2,
3 9028 9028 10 XM_005245795.6 chr1 + 13892823 15118043 13893635 15114635 17 13892823,14180434,14598982,14960683,15034748,15043988,15056090,15060171,15063571,15065629,15094179,15094814,15101542,15103358,15104022,15112426,15114470, 13893756,14180592,14599223,14960875,15034885,15044159,15056280,15060302,15063622,15065753,15094385,15094933,15101774,15103460,15104189,15112541,15118043, 0 KAZN cmpl cmpl 0,1,0,1,1,0,0,1,0,0,1,0,2,0,0,2,0,
4 4079 4079 1 NM_052896.5 chr1 - 33513997 34165842 33519517 34165813 70 33513997,33519464,33519811,33521462,33523306,33524881,33527195,33533049,33533795,33537021,33537435,33540524,33541129,33542719,33546036,33550176,33567592,33569373,33571531,33572505,33577295,33580752,33583641,33586503,33587087,33600864,33602368,33605281,33605862,33611040,33614503,33616905,33617498,33622166,33623369,33624518,33625050,33626485,33633421,33635213,33636359,33646647,33652322,33657945,33662889,33692929,33698752,33700516,33709088,33714586,33716285,33724196,33724515,33725348,33726546,33739139,33743279,33772568,33788599,33792422,33810742,33819712,33820468,33825696,33846883,33918093,33935759,34032593,34088976,34165746, 33516570,33519677,33519950,33521550,33523419,33525043,33527258,33533229,33533907,33537095,33537609,33540698,33541309,33542896,33546219,33550350,33567766,33569547,33571726,33572691,33577484,33580899,33583830,33586617,33587168,33601010,33602546,33605470,33605988,33611250,33614620,33616975,33617617,33622271,33623466,33624643,33625254,33626581,33633535,33635330,33636554,33646835,33652461,33658137,33663092,33693056,33698944,33700673,33709258,33714775,33716501,33724313,33724704,33725536,33726685,33739334,33743606,33772751,33788712,33792526,33810864,33819837,33820556,33825774,33846996,33918301,33935954,34032706,34089193,34165842, 0 CSMD2 cmpl cmpl -1,2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,2,1,1,2,1,0,
5 469 469 14 XM_017002595.3 chr1 - 48522510 50023954 48522580 50023796 13 48522510,48539641,48587003,48590832,48634492,48653336,48663151,48867190,49045583,49245769,49697312,49851395,50023762, 48522692,48539738,48587166,48590985,48634604,48653451,48663241,48867230,49045800,49245864,49697437,49851518,50023954, 0 AGBL4 cmpl cmpl 2,1,0,0,2,1,1,0,2,0,1,1,0,
6 5886 5886 121 XM_047442743.1 chr1 - 50437027 50960267 50441439 50788105 20 50437027,50475463,50490587,50491720,50535368,50539591,50567076,50582617,50583651,50584684,50596120,50655441,50705785,50738862,50744683,50787999,50801630,50857928,50959014,50959766, 50441523,50475679,50490665,50491801,50535457,50539728,50567231,50582699,50583715,50584811,50596216,50655528,50705891,50738954,50744775,50788205,50801677,50857997,50959111,50960267, 0 FAF1 cmpl cmpl 0,0,0,0,1,2,0,2,1,0,0,0,2,0,1,0,-1,-1,-1,-1,
7 4417 4417 15 NM_001379461.1 chr1 - 56994777 58546726 57010694 57291030 21 56994777,57010679,57011144,57014882,57023530,57025980,57062889,57069359,57071022,57071521,57072282,57136542,57145289,57290963,57649591,57883998,58150510,58343351,58506059,58527260,58546702, 56998128,57010790,57011272,57015431,57023639,57026043,57062943,57069425,57071061,57071641,57072414,57136641,57145429,57291166,57649665,57884162,58150588,58343403,58506209,58527335,58546726, 0 DAB1 cmpl cmpl -1,0,1,1,0,0,0,0,0,0,0,0,1,0,-1,-1,-1,-1,-1,-1,-1,
8 14956 14956 16 NM_001297440.2 chr1 + 65792509 66374579 65913351 66372678 16 65792509,65913244,66247459,66257646,66257792,66266037,66332507,66355526,66361614,66363167,66363406,66365666,66367695,66367942,66368786,66372312, 65792630,65913356,66247654,66257683,66257863,66266087,66332620,66355620,66361793,66363266,66363571,66365766,66367850,66368065,66368969,66374574, 0 PDE4B cmpl cmpl -1,0,2,2,0,2,1,0,1,0,0,0,1,0,0,0,
9 11282 11282 139 NM_001366838.3 chr1 + 69567921 70144364 69568639 70121887 26 69567921,69678380,69760190,69792042,69825747,69834779,69838226,69931506,69980378,69986241,69994560,70011796,70012973,70016464,70018718,70021004,70023125,70028170,70036120,70036443,70038112,70053025,70076076,70089726,70107751,70121779, 69568641,69678478,69760393,69792160,69825826,69834869,69838283,69931570,69980453,69986386,69994633,70011926,70013089,70016534,70018818,70021129,70023374,70028371,70036232,70036624,70039793,70053145,70076298,70089819,70107826,70144364, 0 LRRC7 cmpl cmpl 0,2,1,0,1,2,2,2,0,0,1,2,0,2,0,1,0,0,0,1,2,0,0,0,0,0,
10 13105 13105 141 NM_173808.3 chr1 - 71395942 72282539 71407445 72282494 7 71395942,71592816,71611025,71698007,71776171,71935078,72282318, 71407570,71592968,71611146,71698139,71776297,71935311,72282539, 0 NEGR1 cmpl cmpl 1,2,1,1,1,2,0,
11 19473 19473 18 NM_001349109.3 chr1 + 76074745 76637339 76074866 76634191 4 76074745,76313804,76412007,76634127, 76074884,76313999,76412417,76637339, 0 ST6GALNAC3 cmpl cmpl 0,0,0,2,
12 387 387 18 NM_001393349.1 chr1 + 81306131 81993932 81836984 81991145 26 81306131,81445020,81580875,81761810,81836884,81907016,81936727,81942033,81942968,81950188,81951017,81951956,81952986,81955876,81966057,81966403,81968025,81969177,81970313,81971851,81979868,81981807,81984582,81985258,81986900,81990390, 81306509,81445089,81580980,81761852,81837057,81907230,81936837,81942045,81943769,81950482,81951121,81952142,81953025,81956060,81966183,81966609,81968199,81969387,81970534,81971918,81979960,81981976,81984711,81985355,81987029,81993932, 0 ADGRL2 cmpl cmpl -1,-1,-1,-1,0,1,2,1,1,1,1,0,0,0,1,1,0,0,0,2,0,2,0,0,1,1,
13 5084 5084 20 XM_005270562.3 chr1 - 97077742 97921059 97078975 97920922 22 97077742,97082329,97098488,97193068,97234851,97305258,97306176,97373560,97382392,97450058,97549559,97573759,97593217,97595058,97679094,97691716,97699350,97721509,97740391,97828113,97883263,97920883, 97079146,97082470,97098632,97193248,97234994,97305378,97306297,97373644,97382461,97450223,97549744,97573970,97593387,97595166,97679182,97691798,97699547,97721671,97740479,97828196,97883374,97921059, 0 DPYD cmpl cmpl 0,0,0,0,1,1,0,0,0,0,1,0,1,1,0,2,0,0,2,0,0,0,
14 5008 5008 29 XM_017000984.2 chr1 + 171841497 172418466 171841656 172418317 20 171841497,171921747,171987655,171988944,172032401,172033104,172038318,172042008,172044384,172048611,172068818,172081831,172092823,172131174,172253572,172308727,172379017,172387132,172388572,172418280, 171841817,171921821,171987805,171989148,172032500,172033265,172038461,172042144,172044452,172048750,172068905,172081902,172092875,172131288,172253682,172308839,172379182,172387359,172388809,172418466, 0 DNM3 cmpl cmpl 0,2,1,1,1,1,0,2,0,2,0,0,2,0,0,2,0,0,2,2,
15 16657 16657 239 XM_047436039.1 chr1 + 174159519 174995308 174219157 174990001 25 174159519,174219124,174220971,174231144,174241482,174250474,174252479,174272413,174275832,174278612,174304985,174370978,174393994,174637374,174683521,174699524,174702112,174752312,174811831,174957456,174969276,174976077,174978806,174982833,174989848, 174159657,174219184,174221164,174231355,174241657,174250632,174252590,174272480,174275935,174278779,174305127,174371072,174394145,174637488,174683596,174699650,174702256,174752354,174811960,174957549,174969387,174976182,174978890,174982905,174995308, 0 RABGAP1L cmpl cmpl -1,0,0,1,2,0,2,2,0,1,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0,
16 21862 21862 34 NM_206933.4 chr1 - 215622890 216423448 215625780 216422336 72 215622890,215628813,215634458,215639154,215640557,215647521,215648527,215650591,215670971,215674099,215680148,215728029,215741374,215743176,215758594,215759659,215766680,215779842,215782041,215782737,215786669,215790058,215798906,215813735,215816996,215837990,215844293,215845823,215867006,215877757,215878763,215888425,215900074,215900754,215934615,215965316,215970624,215993019,215998886,216000402,216046430,216048533,216070100,216072888,216073096,216078088,216083455,216084697,216086718,216089012,216097082,216175251,216190222,216196552,216198314,216199626,216207272,216217386,216231952,216246584,216250902,216289279,216292174,216321882,216323473,216324167,216325304,216327590,216364952,216418513,216421851,216423213, 215625870,215629035,215634703,215639238,215640734,215647730,215648766,215650801,215671293,215675616,215680376,215728384,215741537,215743335,215758752,215759843,215766788,215780041,215782196,215782935,215786874,215790282,215799125,215813904,215817195,215838103,215844496,215846033,215867170,215877880,215879098,215889054,215900217,215900905,215934795,215965479,215970776,215993167,215999058,216000562,216046592,216048647,216070292,216072969,216073300,216078362,216083586,216084877,216086820,216089139,216097213,216175482,216190367,216196722,216198584,216200121,216207431,216217550,216232136,216247226,216251098,216289410,216292370,216321976,216323695,216324352,216325599,216327654,216365085,216418679,216422540,216423448, 0 USH2A cmpl cmpl 0,0,1,1,1,2,0,0,2,0,0,2,1,1,2,1,1,0,1,1,0,1,1,0,2,0,1,1,2,2,0,1,2,1,1,0,1,0,2,1,1,1,1,1,1,0,1,1,1,0,1,1,0,1,1,1,1,2,1,1,0,1,0,2,2,0,2,1,0,2,0,-1,
17 5754 5754 34 XM_017000625.2 chr1 - 216503245 217137702 216506938 216905339 9 216503245,216519151,216564218,216567987,216650972,216677075,216905247,216939581,217137666, 216507183,216519421,216564401,216568098,216651089,216677491,216905683,216939673,217137702, 0 ESRRG cmpl cmpl 1,1,1,1,1,2,0,-1,-1,
18 17643 17643 299 XM_017002028.2 chr1 + 237042183 237833988 237042521 237832647 106 237042183,237270496,237330877,237364357,237369533,237374716,237377322,237387280,237388086,237417048,237423091,237441318,237445400,237454390,237456599,237469091,237491805,237492953,237496510,237500710,237503288,237506709,237511687,237530426,237548430,237550543,237566566,237569144,237589792,237590639,237591738,237593475,237594099,237595497,237602024,237610761,237614038,237617285,237623764,237625660,237627806,237631426,237633577,237634888,237638356,237639014,237640896,237643326,237648443,237649876,237651410,237654273,237655820,237657943,237659984,237660809,237666511,237667882,237674095,237674730,237678047,237680455,237687454,237698964,237700228,237701977,237705212,237706948,237708857,237709479,237711744,237717197,237718461,237723127,237726272,237727086,237730259,237732045,237733704,237742295,237743599,237756287,237757696,237759775,237760954,237770806,237772011,237773519,237778665,237781564,237783674,237785968,237787987,237791428,237792104,237793866,237795288,237798036,237801855,237806136,237808900,237819035,237828380,237830529,237831513,237832551, 237042569,237270616,237330982,237364372,237369608,237374795,237377435,237387380,237388183,237417123,237423248,237441483,237445522,237454574,237456735,237469187,237491924,237493087,237496752,237500903,237503505,237506814,237511791,237530510,237548590,237550691,237566775,237569319,237590001,237590992,237591853,237593636,237594129,237595657,237602111,237610988,237614843,237617486,237623870,237625804,237628080,237631541,237633710,237634992,237638492,237639201,237641002,237643447,237648613,237650097,237651501,237654414,237655984,237658022,237660074,237660947,237666589,237667958,237674219,237674846,237678112,237680577,237687504,237699025,237700467,237702059,237705343,237707269,237709098,237709567,237711837,237717368,237718521,237723262,237726308,237727199,237730356,237732149,237733756,237742349,237743623,237756387,237757776,237759852,237761028,237770887,237772100,237773648,237778770,237781646,237784972,237786036,237788135,237791515,237792323,237793997,237795331,237798170,237801916,237806283,237809035,237819192,237828445,237830630,237831565,237833988, 0 RYR2 cmpl cmpl 0,0,0,0,0,0,1,0,1,2,2,0,0,2,0,1,1,0,2,1,2,0,0,2,2,0,1,0,1,0,2,0,2,2,0,0,2,0,0,1,1,2,0,1,0,1,2,0,1,0,2,0,0,2,0,0,0,0,1,2,1,0,2,1,2,1,2,1,1,2,0,0,0,0,0,0,2,0,2,0,0,0,1,0,2,1,1,0,0,0,1,0,2,0,0,0,2,0,2,0,0,0,1,0,2,0,
19 3358 3358 301 XM_047443244.1 chr1 + 239386567 239915450 239907451 239909224 4 239386567,239545640,239678185,239907432, 239387227,239545749,239678288,239915450, 0 CHRM3 cmpl cmpl -1,-1,-1,0,
20 17061 17061 37 NM_001374808.1 chr1 - 240774741 241357230 240800646 241098762 19 240774741,240800640,240802903,240806139,240811917,240813617,240814715,240816316,240827097,240868586,240868775,240870054,240930716,240936599,240983078,241098665,241101832,241355698,241356898, 240776213,240800721,240802993,240806326,240812043,240813728,240814777,240816415,240827172,240868668,240868852,240870119,240930768,240936706,240983129,241098762,241101978,241355826,241357205, 0 RGS7 cmpl cmpl -1,0,0,2,2,2,0,0,0,2,0,1,0,1,1,0,-1,-1,-1,
21 9259 9259 38 NM_018012.4 chr1 + 245154984 245709432 245155424 245702606 15 245154984,245156281,245366833,245419578,245540766,245602576,245607650,245609265,245611792,245646120,245684232,245685404,245698105,245698886,245702457, 245155487,245156683,245367367,245419745,245540950,245602783,245607744,245609528,245611976,245646280,245684395,245688807,245698308,245699037,245709432, 0 KIF26B cmpl cmpl 0,0,0,0,2,0,0,1,0,1,2,0,1,0,1,
22 18940 18940 38 NM_001167740.2 chr1 - 245749346 246507279 245749562 246507217 12 245749346,245764040,245858495,245863798,245915529,245927930,245929869,246327200,246330479,246335366,246355030,246507053, 245749664,245764149,245858670,245863886,245915640,245928033,245929937,246327337,246330537,246335474,246355094,246507279, 0 SMYD3 cmpl cmpl 0,2,1,0,0,2,0,1,0,0,2,0,
23 337 337 74 NM_018702.4 chr10 - 1177312 1737525 1183192 1737150 10 1177312,1184860,1199965,1216950,1233693,1242130,1270954,1363027,1379073,1737050, 1183369,1185039,1200147,1217119,1233845,1242299,1271069,1363917,1379160,1737525, 0 ADARB2 cmpl cmpl 0,1,2,1,2,1,0,1,1,0,
24 3080 3080 10 NM_001326317.2 chr10 + 10462549 11336675 11165504 11329053 15 10462549,10682455,10919963,11165485,11217424,11249152,11257737,11266597,11270665,11275056,11288417,11314138,11321206,11325835,11328925, 10462586,10682494,10919999,11165682,11217507,11249201,11257872,11266677,11270824,11275120,11288552,11314258,11321386,11325979,11336675, 0 CELF2 cmpl cmpl -1,-1,-1,0,1,0,1,1,0,0,1,1,1,1,1,
25 6571 6571 86 NM_018027.5 chr10 - 13643705 14330924 13651904 14330102 25 13643705,13651902,13654415,13656635,13659322,13660315,13663452,13666096,13670405,13674910,13693897,13701339,13707036,13737843,13740193,13740511,13747735,13761646,13762623,13782921,13796495,13810813,13858846,14330057,14330596, 13647035,13651974,13654512,13657522,13659490,13660553,13663509,13666325,13670528,13675044,13694039,13701478,13707113,13737930,13740251,13740577,13747819,13761669,13762680,13783006,13796588,13810908,13858912,14330183,14330924, 0 FRMD4A cmpl cmpl -1,2,1,2,2,1,1,0,0,1,0,2,0,0,2,2,2,0,0,2,2,0,0,0,-1,
26 11589 11589 91 XM_011519454.2 chr10 + 19046926 19734478 19048959 19734237 41 19046926,19048958,19066718,19087839,19088023,19103978,19123491,19124523,19128220,19133855,19136573,19146197,19155074,19165636,19175207,19203727,19204307,19204897,19209267,19257683,19280046,19283018,19323948,19327562,19331368,19347770,19352005,19387527,19389451,19450306,19491516,19498484,19531193,19567501,19595193,19607776,19615856,19692281,19692457,19730705,19734156, 19046982,19049137,19066859,19087934,19088185,19104075,19123593,19124670,19128387,19133948,19136781,19146344,19155172,19165810,19175328,19203880,19204413,19205265,19209680,19257771,19280223,19283181,19324105,19327673,19331582,19348018,19352297,19387773,19389609,19450490,19491645,19498646,19531351,19567703,19595457,19607902,19615923,19692361,19692554,19730781,19734478, 0 MALRD1 cmpl cmpl -1,0,1,1,0,0,1,1,1,0,0,1,1,0,0,1,1,2,1,0,1,1,2,0,0,1,0,1,1,0,1,1,1,0,1,1,1,2,1,2,0,
27 9222 9222 11 NM_001098500.3 chr10 + 23694726 24547843 24219795 24546324 19 23694726,24007224,24219625,24380868,24432994,24438385,24473227,24494499,24495146,24501378,24513258,24520122,24521781,24524322,24527935,24531829,24533069,24544980,24545826, 23695234,24007374,24219909,24381067,24433193,24438479,24474060,24494604,24495196,24501545,24513434,24520253,24521929,24524764,24528119,24531993,24533237,24545103,24547843, 0 KIAA1217 cmpl cmpl -1,-1,0,0,1,2,0,2,2,1,0,2,1,2,0,1,0,0,0,
28 14702 14702 13 NM_019619.4 chr10 - 34109560 34815296 34111168 34814995 25 34109560,34119612,34131462,34269656,34284134,34317106,34331116,34336198,34337274,34341626,34347955,34359146,34360070,34372497,34374873,34377966,34382539,34384128,34399329,34401825,34450316,34470084,34516978,34696317,34814875, 34111562,34119740,34131583,34269899,34284245,34317338,34331344,34336243,34337426,34341816,34348115,34359317,34360259,34372536,34375002,34378106,34382922,34384254,34399413,34401917,34450448,34470263,34517159,34696419,34815296, 0 PARD3 cmpl cmpl 2,0,2,2,2,1,1,1,2,1,0,0,0,0,0,1,2,2,2,0,0,1,0,0,0,
29 860 860 118 XM_006717951.4 chr10 - 47467992 47991796 47468846 47991772 12 47467992,47471261,47472132,47473969,47474304,47474944,47475492,47476231,47477080,47478532,47479797,47991679, 47468906,47471384,47472191,47474065,47474398,47475004,47475572,47476322,47477194,47478627,47479888,47991796, 0 ANXA8 cmpl cmpl 0,0,1,1,0,0,1,0,0,1,0,0,
30 16070 16070 15 NM_001098512.3 chr10 + 50990887 52298350 50991378 52293900 18 50990887,51153163,51467722,51804584,51907506,52054483,52062536,52133839,52161888,52251569,52271349,52272391,52280788,52282152,52288725,52288930,52290223,52293801, 50991644,51153330,51467836,51804690,51907570,52054561,52062631,52133905,52161963,52251666,52271489,52272481,52280930,52282316,52288848,52288993,52290290,52298350, 0 PRKG1 cmpl cmpl 0,2,1,1,2,0,0,2,2,2,0,2,2,0,2,2,2,0,
31 14788 14788 15 NM_001354404.2 chr10 - 53802770 55627942 53821857 54664262 35 53821098,53827392,53828564,53831314,53840319,53857174,53866641,53903242,53938814,53940865,53959731,53961751,53995648,54020191,54022891,54066756,54079330,54089983,54132874,54153099,54183443,54185133,54195682,54213935,54236822,54317270,54329595,54346364,54369119,54378781,54664171,54897449,55166575,55627624,55627864, 53823358,53827548,53828573,53831533,53840496,53857263,53866857,53903370,53938955,53940975,53959844,53961892,53995765,54020416,54023197,54066885,54079424,54090063,54133007,54153293,54183593,54185268,54195889,54214048,54236931,54317441,54329706,54346484,54369275,54378942,54664290,54897500,55166651,55627753,55627942, 0 PCDH15 cmpl cmpl 2,2,2,2,2,0,0,1,1,2,0,0,0,0,0,0,2,0,2,0,0,0,0,1,0,0,0,0,0,1,0,-1,-1,-1,-1,
32 743 743 130 NM_001204403.2 chr10 - 60026297 60733528 60042690 60733319 44 60026297,60042671,60055657,60059339,60059697,60063110,60064156,60067934,60080536,60082614,60083491,60084601,60085156,60086676,60088146,60105904,60108829,60114224,60134270,60138963,60166590,60166823,60172307,60172899,60173087,60181328,60186714,60196144,60196526,60198339,60200128,60203001,60205791,60208035,60213411,60234687,60261858,60263834,60270130,60278773,60279049,60279537,60615185,60733262, 60029826,60042759,60056036,60059430,60060006,60063254,60064288,60068009,60080618,60082737,60083617,60084830,60085253,60086884,60088358,60106059,60109054,60114331,60134373,60139087,60166653,60166896,60172403,60172998,60173186,60181427,60186912,60196243,60196625,60198537,60200227,60203100,60205890,60208233,60213510,60234786,60261957,60264020,60270229,60278872,60279148,60279639,60615224,60733528, 0 ANK3 cmpl cmpl -1,0,2,1,1,1,1,1,0,0,0,2,1,0,1,2,2,0,2,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
33 4199 4199 0 XM_047425124.1 chr10 - 65912522 67763594 65920329 67648770 19 65912522,65966611,65988691,66069307,66103156,66280469,66379151,66520616,66621691,66766263,66775443,67180316,67219606,67521841,67539502,67606856,67647414,67648739,67763433, 65920617,65966746,65988797,66069489,66103249,66280621,66379352,66520773,66621784,66766416,66775524,67180520,67219870,67521961,67539669,67607049,67647518,67648816,67763594, 0 CTNNA3 cmpl cmpl 0,0,2,0,0,1,1,0,0,0,0,0,0,0,1,0,1,0,-1,
34 408 408 17 XM_017015705.2 chr10 + 74151220 74709290 74151278 74708356 9 74151220,74200763,74224537,74314666,74394140,74398470,74589281,74670182,74708320, 74151343,74200838,74224591,74314745,74394313,74398579,74589317,74670269,74709290, 0 ADK cmpl cmpl 0,2,2,2,0,2,0,0,0,
35 11205 11205 2 NM_001305581.2 chr10 + 75431623 76560168 75431724 76557288 7 75431623,75438393,76036007,76047163,76058665,76324400,76557208, 75431754,75438494,76036134,76047303,76058783,76324485,76560168, 0 LRMDA cmpl cmpl 0,0,2,0,2,0,1,
36 9117 9117 18 XM_017016207.3 chr10 - 76869601 77637808 76877868 77637642 32 76869601,76887290,76889450,76891524,76909965,76914056,76914935,76944772,76949141,76953800,76969973,77001406,77011966,77019012,77025445,77027822,77039527,77073096,77079480,77084636,77086487,77090399,77108480,77110172,77112366,77120972,77183420,77184822,77251194,77403861,77493797,77637264, 76877893,76887515,76889569,76891719,76910096,76914137,76915049,76944965,76949366,76953924,76970067,77001580,77012043,77019099,77025457,77027891,77039637,77073252,77079550,77084719,77086593,77090510,77108572,77110343,77112442,77121048,77183532,77184916,77251256,77404023,77493929,77637808, 0 KCNMA1 cmpl cmpl 2,2,0,0,1,1,1,0,0,2,1,1,2,2,2,2,0,0,2,0,2,2,0,0,2,1,0,2,0,0,0,0,
37 13578 13578 18 XM_047424512.1 chr10 + 81875193 82987179 81875340 82985605 9 81875193,82358738,82738576,82951468,82958948,82973787,82978949,82984782,82985097, 81876163,82358868,82738650,82951571,82959075,82973915,82979120,82984854,82987179, 0 NRG3 cmpl cmpl 0,1,2,1,2,0,2,2,2,
38 7470 7470 19 NM_017551.3 chr10 - 85599551 86366795 85602272 86366392 16 85599551,85613406,85619866,85647201,85723002,85724351,85727854,85729512,85854495,85856028,85869009,85916185,86138818,86206363,86363940,86366313, 85602701,85613647,85620033,85647397,85723141,85724676,85728052,85729614,85854615,85856190,85869180,85916239,86139024,86206648,86364096,86366795, 0 GRID1 cmpl cmpl 0,2,0,2,1,0,0,0,0,0,0,0,1,1,1,0,
39 8254 8254 20 XM_047425614.1 chr10 - 98457076 99315951 98459573 99144331 12 98457076,98482635,98490050,98614903,98620601,98641846,98693899,98721656,98743882,99144237,99232347,99315928, 98459739,98482782,98490196,98615018,98620708,98641940,98693947,98721828,98744056,99144399,99232505,99315951, 0 HPSE2 cmpl cmpl 2,2,0,2,0,2,2,1,1,0,-1,-1,
40 19053 19053 21 NM_014978.3 chr10 + 104641289 105265242 104641327 105263374 27 104641289,104842791,104915832,104977334,105043054,105089774,105105396,105139396,105147616,105157137,105158891,105164302,105167257,105178065,105199998,105201119,105211136,105214441,105216935,105223115,105245541,105247218,105252774,105255701,105256818,105262330,105263309, 104641954,104842859,104915932,104977493,105043128,105089839,105105515,105139486,105147796,105157284,105158994,105164379,105167349,105178173,105200116,105201253,105211250,105214613,105217122,105223249,105245665,105247331,105252906,105255801,105256924,105262491,105265242, 0 SORCS3 cmpl cmpl 0,0,2,0,0,2,1,0,0,0,0,1,0,2,2,0,2,2,0,1,0,1,0,0,1,2,1,
41 19051 19051 21 XM_017015617.1 chr10 - 106573662 107181138 106574101 107181066 27 106573662,106579090,106579368,106597350,106607165,106611910,106618148,106620427,106629201,106652381,106667688,106671236,106672867,106675048,106677312,106679255,106679631,106688191,106699213,106706544,106709222,106730049,106761587,106776533,106829573,106956512,107181063, 106574181,106579251,106579474,106597450,106607297,106612023,106618272,106620561,106629388,106652553,106667802,106671367,106672985,106675156,106677404,106679332,106679734,106688338,106699393,106706634,106709341,106730114,106761661,106776692,106829673,106956580,107181138, 0 SORCS1 cmpl cmpl 1,2,1,0,0,1,0,1,0,2,2,0,2,2,0,1,0,0,0,0,1,2,0,0,2,0,0,
42 1465 1465 22 XM_011539588.3 chr10 + 115093364 115948999 115093544 115944779 29 115093364,115120184,115121698,115127592,115129326,115160039,115165557,115171036,115215696,115241570,115265192,115266796,115268325,115281354,115286215,115300033,115301854,115315517,115334281,115394658,115426249,115461940,115467173,115469171,115519262,115549457,115727247,115847876,115944657, 115093636,115120268,115121812,115127721,115129535,115160214,115165645,115171292,115215880,115241725,115265277,115267005,115268444,115281487,115286397,115300247,115302043,115315736,115334419,115394752,115426302,115462035,115467252,115469329,115519324,115549536,115727355,115847991,115948999, 0 ATRNL1 cmpl cmpl 0,2,2,2,2,1,2,0,1,2,1,2,1,0,1,0,1,1,1,1,2,1,0,1,0,2,0,0,1,
43 5022 5022 194 NM_001377548.1 chr10 + 126905427 127452516 126905517 127451427 51 126905427,126977947,126981917,126987520,126990454,126996747,126998091,126999353,127000171,127008731,127012294,127018709,127023199,127024684,127026351,127031649,127032136,127037718,127042624,127043063,127052680,127061667,127106230,127110247,127125473,127127668,127248007,127257334,127339005,127343645,127354668,127362063,127373780,127374057,127380081,127381277,127384789,127403054,127404324,127409036,127409312,127410839,127415151,127418364,127419665,127425873,127433282,127439026,127444125,127447393,127451331, 126905563,126977988,126981973,126987617,126990603,126996883,126998249,126999435,127000307,127008804,127012374,127018835,127023324,127024783,127026424,127031753,127032320,127037816,127042714,127043164,127052815,127061776,127106301,127110354,127125601,127127764,127248109,127257429,127339084,127343746,127354727,127362212,127373866,127374214,127380122,127381368,127384909,127403144,127404429,127409178,127409391,127410924,127415238,127418541,127419749,127426011,127433428,127439225,127444279,127447545,127452516, 0 DOCK1 cmpl cmpl 0,1,0,2,0,2,0,2,0,1,2,1,1,0,0,1,0,1,0,0,2,2,0,2,1,0,0,0,2,0,2,1,0,2,0,2,0,0,0,0,1,2,0,0,0,0,0,2,0,1,0,
44 17755 17755 82 NM_001424318.1 chr11 - 9778667 10303837 9780417 10300496 41 9778667,9781506,9784350,9785124,9787633,9789108,9790555,9795830,9807999,9808900,9812531,9816839,9829355,9832223,9839497,9842624,9845564,9846955,9850022,9852675,9853539,9856457,9858225,9895942,9961956,9963772,9968340,9989496,9992414,9992989,9993920,9998265,10000913,10002556,10028451,10029764,10031047,10042843,10193901,10300405,10303295, 9780516,9781638,9784438,9785318,9787738,9789342,9790683,9795957,9808185,9809002,9812708,9817024,9829496,9832420,9839696,9842770,9845740,9847083,9850218,9852749,9853712,9856720,9858396,9896011,9962106,9963882,9968545,9989595,9992543,9993103,9993998,9998379,10001022,10002689,10028557,10029875,10031170,10042981,10193987,10300498,10303837, 0 SBF2 cmpl cmpl 0,0,2,0,0,0,1,0,0,0,0,1,1,2,1,2,0,1,0,1,2,0,0,0,0,1,0,0,0,0,0,0,2,1,0,0,0,0,1,0,-1,
45 19080 19080 88 NM_001367872.1 chr11 - 15966448 16738477 15972808 16341248 17 15966448,15986203,15988996,16014941,16046513,16049754,16055751,16097608,16111802,16183885,16186782,16234581,16318445,16341011,16612080,16714829,16738424, 15973112,15986420,15989230,16015050,16046701,16049938,16055901,16097688,16111923,16183954,16186955,16234671,16318653,16341252,16612260,16714905,16738477, 0 SOX6 cmpl cmpl 2,1,1,0,1,0,0,1,0,0,1,1,0,0,-1,-1,-1,
46 12885 12885 11 XM_047427831.1 chr11 + 19345235 20121601 19350952 20118258 37 19345235,19350372,19832483,19842870,19868924,19879868,19892433,19933175,19939660,19946400,19948690,19984124,20035958,20043980,20044967,20048727,20054079,20055768,20062306,20068185,20068323,20077551,20077992,20080063,20083006,20090864,20092205,20093098,20095671,20097576,20100936,20103254,20103652,20105530,20107663,20114591,20118132, 19345311,19351027,19832601,19842923,19868997,19880127,19892594,19934277,19939773,19946509,19949080,19984247,20036097,20044272,20045670,20049195,20054240,20055957,20062359,20068209,20068398,20077635,20078104,20080209,20083179,20091018,20092368,20093199,20095767,20097745,20101172,20103409,20103724,20105727,20107782,20114795,20121601, 0 NAV2 cmpl cmpl -1,0,0,1,0,1,2,1,2,1,2,2,2,0,1,2,2,1,1,0,0,0,0,1,0,2,0,1,0,0,1,0,2,2,1,0,0,
47 13130 13130 11 NM_001288714.1 chr11 + 20669550 21575686 20669723 21575022 19 20669550,20677931,20783679,20885443,20918181,20919251,20927307,20928376,20937785,20947335,20960431,21113588,21229331,21370852,21534373,21560188,21570763,21573184,21574971, 20669778,20678060,20783830,20885540,20918254,20919334,20927442,20928479,20937859,20947435,20960560,21113714,21229454,21370948,21534514,21560382,21570940,21573409,21575686, 0 NELL1 cmpl cmpl 0,1,1,2,0,1,0,0,1,0,1,1,1,1,1,1,0,0,0,
48 11397 11397 96 NM_001252008.2 chr11 + 24497052 25082638 24738227 25078658 12 24497052,24729172,24732117,24738220,24763245,24905990,24914475,24976590,24983125,25050037,25077328,25078553, 24497305,24729286,24732188,24738302,24763308,24906053,24914538,24976665,24983293,25050130,25077406,25082638, 0 LUZP2 cmpl cmpl -1,-1,-1,0,0,0,0,0,0,0,0,0,
49 11268 11268 13 XM_047427350.1 chr11 - 40114198 41459652 40114369 40116292 10 40114198,40140800,40241518,40319627,40648141,40933634,41222796,41330938,41346263,41459430, 40116334,40140853,40241598,40319721,40648278,40933723,41223008,41345575,41346346,41459652, 0 LRRC4C cmpl cmpl 0,-1,-1,-1,-1,-1,-1,-1,-1,-1,
50 18207 18207 140 XM_047426616.1 chr11 - 70467853 71253228 70472868 71147326 23 70467853,70485313,70490275,70492334,70502205,70502795,70659827,70661595,70698687,70798442,70807001,70820363,70896500,71056480,71075158,71092421,71094536,71109940,71113292,71118828,71147119,71224696,71253034, 70473439,70487720,70490387,70492465,70502286,70502931,70659952,70661678,70698763,70798556,70807171,70820682,70896567,71056558,71075275,71092589,71094688,71110049,71113364,71119032,71147338,71224796,71253228, 0 SHANK2 cmpl cmpl 2,1,0,1,1,0,1,2,1,1,2,1,0,0,0,0,1,0,0,0,0,-1,-1,
51 20214 20214 148 NM_001098816.3 chr11 - 78652828 79441030 78658057 79069944 34 78652828,78661448,78668936,78672032,78676151,78688053,78701525,78708360,78712481,78720369,78722667,78726078,78729375,78732315,78738450,78756804,78770991,78778601,78786897,78805291,78812121,78814293,78854103,78855963,78862961,78889784,78891237,78903267,79064737,79069721,79148709,79215807,79297487,79440508, 78658816,78661591,78670551,78672329,78676387,78688226,78702403,78708515,78712714,78720390,78722917,78726222,78729643,78732577,78738570,78757021,78771138,78778628,78787083,78805492,78812316,78814395,78854314,78856178,78863132,78890020,78891336,78903523,79065007,79070009,79148806,79215909,79297543,79441030, 0 TENM4 cmpl cmpl 0,1,0,0,1,2,0,1,2,2,1,1,0,2,2,1,1,1,1,1,1,1,0,1,1,2,2,1,1,0,-1,-1,-1,-1,
52 4861 4861 2 XM_047426495.1 chr11 - 83455011 85628373 83459817 85626617 28 83455011,83462001,83466707,83469200,83471625,83472726,83484128,83532707,83541681,83633210,83786689,83833613,83874419,83930327,83962884,83965323,83980505,84059314,84098922,84163460,84251237,84534569,85111660,85154555,85285219,85308984,85598656,85626598, 83459924,83462093,83466817,83469373,83471727,83472777,83484228,83532783,83541858,83633325,83786792,83833770,83874488,83930483,83963023,83965468,83980642,84059484,84099047,84163511,84251291,84534731,85111735,85154651,85285365,85309023,85598788,85628373, 0 DLG2 cmpl cmpl 1,2,0,1,1,1,0,2,2,1,0,2,2,2,1,0,1,2,0,0,0,0,0,0,1,1,1,0,
53 7504 7504 157 NM_001143831.3 chr11 - 88504641 89065982 88508591 89047872 10 88504641,88525308,88567052,88590600,88597183,88604717,88653167,88849905,89047211,89065775, 88509504,88525404,88567992,88590727,88597352,88604964,88653403,88850155,89048072,89065982, 0 GRM5 cmpl cmpl 2,2,1,0,2,1,2,1,0,-1,
54 6146 6146 2 XM_017017186.2 chr11 + 92224817 92896473 92524671 92891113 28 92224817,92524633,92697383,92761855,92764878,92765506,92774040,92789942,92792766,92797835,92805152,92806361,92809842,92831621,92834869,92836565,92837662,92840561,92843933,92857213,92859164,92866740,92880730,92882737,92886999,92889188,92889855,92890490, 92225174,92524948,92697445,92762170,92765089,92765575,92774180,92790218,92792977,92801909,92805349,92806515,92810076,92832011,92835084,92836703,92837806,92840759,92844732,92857348,92859322,92867209,92880884,92883393,92887113,92889248,92889891,92896473, 0 FAT3 cmpl cmpl -1,0,1,0,0,1,1,0,0,1,1,0,1,1,1,0,0,0,0,1,1,0,1,2,1,1,1,1,
55 3704 3704 20 XM_047427130.1 chr11 + 99020948 100358885 99556214 100356220 23 99020948,99556144,99844851,99845086,99916053,99956805,100002033,100061211,100070423,100071704,100074143,100191125,100193487,100224691,100255759,100271091,100297624,100299161,100308358,100340462,100341092,100350701,100356116, 99021270,99556269,99844975,99845262,99916149,99957009,100002136,100061393,100070560,100071834,100074294,100191253,100193663,100224812,100255918,100271241,100297695,100299396,100308468,100340649,100341205,100350870,100358885, 0 CNTN5 cmpl cmpl -1,0,1,2,1,1,1,2,1,0,1,2,1,0,1,1,1,0,1,0,1,0,1,
56 9625 9625 24 XM_011543027.3 chr11 - 126423357 127000870 126424579 127000509 17 126423357,126425637,126429178,126431343,126435267,126436810,126440448,126444978,126446758,126449008,126456348,126463156,126473308,126521314,126526537,126562834,127000454, 126425023,126425724,126429288,126431526,126435303,126437009,126440549,126445105,126446886,126449157,126456454,126463307,126473466,126521464,126526687,126562912,127000870, 0 KIRREL3 cmpl cmpl 0,0,1,1,1,0,1,0,1,2,1,0,1,1,1,1,0,
57 13653 13653 24 NM_001048209.2 chr11 + 131370614 132336822 131370806 132335146 8 131370614,131911563,132146281,132212021,132307688,132310111,132314551,132335045, 131370888,131911648,132146514,132212147,132307823,132310232,132314703,132336822, 0 NTM cmpl cmpl 0,1,2,1,1,1,2,1,
58 13870 13870 24 NM_001012393.5 chr11 - 132414980 133532501 132420192 133532324 8 132414980,132436085,132436658,132437221,132529060,132657086,132942925,133532263, 132420293,132436237,132436779,132437359,132529186,132657319,132943010,133532501, 0 OPCML cmpl cmpl 1,2,1,1,1,2,1,0,
59 2293 2293 9 XM_017019953.2 chr12 + 1970779 2697950 1971062 2691199 47 1970779,2115223,2120324,2448975,2457566,2486103,2493189,2504435,2512811,2549942,2556950,2566421,2567568,2581589,2582821,2584502,2585375,2585834,2593212,2595873,2597436,2601853,2605080,2605678,2606610,2606983,2608510,2610540,2611902,2633628,2648474,2651639,2653834,2655146,2664824,2665580,2666685,2668932,2674540,2677093,2677732,2679443,2682549,2685735,2686165,2688446,2690899, 1971201,2115545,2120430,2449115,2457706,2486262,2493386,2504539,2512984,2550033,2556977,2566582,2567794,2581797,2582942,2584617,2585496,2585904,2593345,2596003,2597496,2601960,2605168,2605786,2606663,2607130,2608712,2610699,2612013,2633712,2648507,2651768,2653900,2655238,2664990,2665708,2666782,2669035,2674642,2677221,2677867,2679796,2682678,2685842,2686269,2688779,2697950, 0 CACNA1C cmpl cmpl 0,1,2,0,2,1,1,0,2,1,2,2,1,2,0,1,2,0,1,2,0,0,2,0,0,2,2,0,0,0,0,0,0,0,2,0,2,0,1,1,0,0,2,2,1,0,0,
60 19079 19079 11 XM_047429457.1 chr12 - 23529503 24562650 23534218 23896023 21 23529503,23536452,23543210,23546315,23563257,23575660,23604386,23640811,23665443,23734683,23740866,23755637,23845982,23895792,24213342,24277215,24331276,24368562,24407484,24460595,24562337, 23534522,23536669,23543384,23546424,23563403,23575838,23604533,23640897,23665567,23734752,23741039,23755724,23846193,23896024,24213417,24277312,24331396,24368639,24407566,24460776,24562650, 0 SOX5 cmpl cmpl 2,1,1,0,1,0,0,1,0,0,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,
61 20573 20573 14 XM_047429662.1 chr12 + 43795801 44399108 43844651 44388672 9 43795801,43795974,43844623,43944209,44143524,44211289,44299579,44376594,44388025, 43795820,43796150,43844928,43944342,44143624,44211387,44299739,44376724,44389758, 0 TMEM117 cmpl cmpl -1,-1,0,1,2,0,2,0,1,
62 19861 19861 16 XM_024448962.2 chr12 - 61708272 62260034 61710405 62259544 6 61708272,61753621,61754871,61867319,62258762,62259478, 61710417,61753746,61755024,61867426,62258842,62260034, 0 TAFA2 cmpl cmpl 0,1,1,2,0,0,
63 7487 7487 136 XM_005268754.5 chr12 - 66347430 67069338 66349018 67069107 25 66347430,66353416,66371693,66377016,66377173,66379279,66392307,66392676,66394207,66406282,66420719,66432547,66444583,66445321,66455408,66456186,66462923,66465274,66515618,66517900,66529830,66539077,66541814,66596846,67069049, 66349246,66353563,66371927,66377061,66377285,66379436,66392502,66392816,66394352,66406428,66420789,66432628,66444729,66445508,66455564,66456342,66463093,66465422,66515764,66517976,66529914,66539223,66541950,66596927,67069338, 0 GRIP1 cmpl cmpl 0,0,0,0,2,1,1,2,1,2,1,1,2,1,1,1,2,1,2,1,1,2,1,1,0,
64 21121 21121 17 XM_017019244.2 chr12 + 72087265 72670758 72286810 72663195 20 72087265,72105647,72286680,72377994,72469757,72473066,72499497,72542290,72562164,72562852,72568567,72575254,72575486,72618890,72621107,72621643,72652321,72653015,72656926,72663051, 72087439,72105752,72286954,72378121,72469912,72473180,72499635,72542356,72562230,72563040,72568656,72575388,72575542,72619038,72621205,72621751,72652489,72653156,72657008,72670758, 0 TRHDE cmpl cmpl -1,-1,0,0,1,0,0,0,0,0,2,1,0,2,0,2,2,2,2,0,
65 12886 12886 18 XM_047429826.1 chr12 + 77571861 78213010 77572194 78210517 35 77571861,77940318,77941080,77966228,77968518,77998336,78006418,78021746,78049992,78050763,78058995,78116771,78118026,78119236,78128705,78137176,78140281,78146368,78148841,78159202,78168754,78175305,78177140,78179528,78180870,78185600,78188247,78188608,78189983,78197246,78198604,78199334,78200472,78204934,78210397, 77572266,77940436,77941133,77966301,77968702,77998476,78007445,78021862,78050101,78051147,78059115,78116904,78118297,78119945,78128866,78137365,78140334,78146392,78148919,78159286,78168866,78175427,78177313,78179682,78181045,78185698,78188343,78188777,78190219,78197401,78198676,78199531,78200591,78205138,78213010, 0 NAV3 cmpl cmpl 0,0,1,0,1,2,1,2,1,2,2,2,0,1,2,1,1,0,0,0,0,1,0,2,0,1,0,0,1,0,2,2,1,0,0,
66 19765 19765 148 NM_001135805.2 chr12 + 78863981 79452008 79217519 79449124 12 78863981,78864997,78977798,79047296,79217502,79285786,79292007,79296068,79299383,79353501,79444072,79448917, 78864335,78865109,78977931,79047362,79217685,79285971,79292130,79296236,79299551,79353619,79444206,79452008, 0 SYT1 cmpl cmpl -1,-1,-1,-1,0,1,0,0,0,0,1,0,
67 12048 12048 19 NM_001351285.2 chr12 - 85955666 86839000 85979288 85989546 9 85955666,85983522,85989399,86049673,86334064,86435156,86495250,86727208,86838665, 85980430,85983670,85989552,86049723,86334127,86435265,86495315,86727241,86839000, 0 MGAT4C cmpl cmpl 1,0,0,-1,-1,-1,-1,-1,-1,
68 820 820 20 XM_006719507.5 chr12 - 98734785 99984936 98735559 99984237 27 98734785,98751354,98773041,98781116,98782125,98798933,98800996,98807843,98829173,98832028,99053156,99084924,99154288,99244341,99246274,99399630,99443672,99504475,99655066,99772921,99775547,99779870,99782021,99806403,99812154,99825308,99984103, 98735634,98751522,98773179,98781203,98782137,98799005,98801125,98807918,98829353,98832136,99053309,99085023,99154395,99244414,99246864,99399811,99443809,99504641,99655210,99773088,99775661,99779972,99782097,99806700,99812311,99825389,99984936, 0 ANKS1B cmpl cmpl 0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,1,1,1,0,0,2,2,0,
69 20593 20593 196 NM_133448.3 chr12 - 129071725 129904025 129073874 129903339 9 129071725,129078533,129081758,129084496,129209519,129337633,129531058,129699809,129903260, 129075059,129078725,129082032,129084702,129209663,129337817,129531205,129700698,129904025, 0 TMEM132D cmpl cmpl 0,0,2,0,0,2,2,1,0,
70 2294 2294 73 XM_054332314.1 chr12_KZ208916v1_fix + 311695 1046066 313206 1039315 47 311695,457367,462468,797091,805682,834219,841305,852551,860927,898058,905066,914537,915684,929705,930937,932618,933491,933950,941328,943989,945552,949969,953196,953794,954726,955099,956626,958656,960018,981744,996590,999755,1001950,1003262,1012940,1013696,1014801,1017048,1022656,1025209,1025848,1027559,1030665,1033851,1034281,1036562,1039015, 313345,457689,462574,797231,805822,834378,841502,852655,861100,898149,905093,914698,915910,929913,931058,932733,933612,934020,941461,944119,945612,950076,953284,953902,954779,955246,956828,958815,960129,981828,996623,999884,1002016,1003354,1013106,1013824,1014898,1017151,1022758,1025337,1025983,1027912,1030794,1033958,1034385,1036895,1046066, 0 CACNA1C cmpl cmpl 0,1,2,0,2,1,1,0,2,1,2,2,1,2,0,1,2,0,1,2,0,0,2,0,0,2,2,0,0,0,0,0,0,0,2,0,2,0,1,1,0,0,2,2,1,0,0,
71 1450 1450 97 NM_001411005.1 chr13 + 25371973 26025851 25372212 26019985 36 25371973,25468976,25529998,25530561,25532271,25533272,25537987,25540318,25541918,25543290,25551337,25553792,25554990,25558972,25559720,25563955,25570766,25571609,25574807,25577068,25578814,25579807,25581818,25589634,25699172,25769045,25774848,25837162,25839545,25860194,25860803,25862300,25961574,25968574,26012530,26019887, 25372288,25469121,25530098,25530660,25532317,25533313,25538061,25540388,25542046,25543402,25551503,25553920,25555068,25559061,25559765,25564031,25570872,25571692,25574857,25577138,25578899,25579947,25581957,25589699,25699345,25769229,25774959,25837285,25839624,25860256,25860860,25862408,25961663,25968679,26012622,26025851, 0 ATP8A2 cmpl cmpl 0,1,2,0,0,1,0,2,0,2,0,1,0,0,2,2,0,1,0,2,0,1,0,1,0,2,0,0,0,1,0,0,0,2,2,1,
72 12591 12591 12 NM_001384605.1 chr13 + 28819962 29505947 29024698 29503206 16 28819962,28839777,29024456,29033884,29100772,29281703,29324612,29359261,29439982,29480149,29487899,29492645,29497237,29498417,29501096,29502992, 28820285,28839850,29026903,29034125,29100970,29281865,29324711,29359473,29440049,29480364,29488005,29492719,29497336,29498537,29501194,29505947, 0 MTUS2 cmpl cmpl -1,-1,0,0,1,1,1,1,0,1,0,1,0,0,0,2,
73 19501 19501 1 NM_001243476.3 chr13 - 33103136 33676794 33105592 33524267 18 33103136,33106757,33109872,33110685,33111777,33112720,33118064,33126080,33127372,33128928,33142309,33165336,33167550,33439690,33524237,33661276,33663889,33676677, 33105710,33106934,33110090,33110907,33111892,33112931,33118263,33126240,33127546,33130289,33142373,33165418,33167622,33439724,33524372,33661343,33664137,33676794, 0 STARD13 cmpl cmpl 2,2,0,0,2,1,0,2,2,0,2,1,1,0,0,-1,-1,-1,
74 12892 12892 13 XM_047430269.1 chr13 + 34942269 35672736 34942820 35670991 58 34942269,35040932,35044946,35045305,35048562,35050268,35056009,35058716,35069907,35070718,35098296,35109289,35110809,35117413,35118227,35118376,35123481,35142268,35155773,35156082,35157077,35159015,35161749,35164355,35171271,35173463,35176995,35182359,35183975,35195863,35208699,35211052,35232491,35290388,35309527,35349107,35352156,35432268,35452091,35472399,35550476,35550929,35554986,35566904,35583897,35593327,35606425,35628080,35645868,35646258,35649654,35651804,35654854,35655578,35665084,35667373,35668367,35670900, 34943114,35041164,35045047,35045401,35048684,35050395,35056129,35058863,35070105,35070852,35098405,35109442,35110978,35117493,35118290,35118474,35123574,35142377,35155855,35156206,35157270,35160032,35161967,35164509,35171452,35173594,35177103,35182528,35184071,35196302,35208836,35211179,35232619,35290450,35309592,35349216,35352323,35432393,35452235,35472536,35550594,35551032,35555102,35567017,35584038,35593447,35606578,35628248,35645931,35646348,35649847,35651876,35655010,35655749,35665186,35667570,35668519,35672736, 0 NBEA cmpl cmpl 0,0,1,0,0,2,0,0,0,0,2,0,0,1,0,0,2,2,0,1,2,0,0,2,0,1,0,0,1,1,2,1,2,1,0,2,0,2,1,1,0,1,2,1,0,0,0,0,0,0,0,1,1,1,1,1,0,2,
75 5570 5570 114 NM_001347966.2 chr13 - 43213129 43786972 43213989 43412914 18 43213129,43224052,43236635,43265397,43269469,43298345,43322383,43326418,43344537,43355918,43359850,43361278,43411915,43412844,43484008,43667478,43761728,43786651, 43214121,43224138,43236738,43265454,43269577,43298530,43322501,43326525,43344750,43356152,43360057,43361452,43412053,43412988,43484152,43667544,43761837,43786972, 0 ENOX1 cmpl cmpl 0,1,0,0,0,1,0,1,1,1,1,1,1,0,-1,-1,-1,-1,
76 14795 14795 0 NM_203487.3 chr13 - 66302833 67230336 66304654 67228440 5 66302833,66631209,66903503,67225404,67229779, 66305028,66631411,66903605,67228575,67230336, 0 PCDH9 cmpl cmpl 1,0,0,0,-1,
77 9640 9640 143 NM_001400139.1 chr13 - 73686088 74306045 73695489 73995022 8 73686088,73715367,73764937,73813151,73845826,73943980,73994989,74305995, 73695671,73715525,73765000,73813287,73846373,73944070,73995053,74306045, 0 KLF12 cmpl cmpl 1,2,2,1,0,0,0,-1,
78 7298 7298 2 NM_004466.6 chr13 + 91398620 92867237 91399046 92866439 8 91398620,91448760,91693186,91728531,91756294,91907936,92144829,92866281, 91399209,91448922,91693881,91728665,91756420,91908057,92144989,92867237, 0 GPC5 cmpl cmpl 0,1,1,0,2,2,0,1,
79 7299 7299 20 XM_047429990.1 chr13 + 93216528 94408020 93545312 94403217 9 93216528,93545262,93830153,94027728,94286348,94305979,94382413,94398465,94403014, 93226682,93545421,93830545,94027894,94286479,94306123,94382550,94398641,94408020, 0 GPC6 cmpl cmpl -1,0,1,0,1,0,0,2,1,
80 8282 8282 20 NM_153456.4 chr13 + 96090106 96839562 96090862 96833198 2 96090106,96832489, 96091569,96839562, 0 HS6ST3 cmpl cmpl 0,2,
81 6324 6324 21 NM_001321938.2 chr13 - 101710803 102402443 101722830 102220709 7 101710803,101726611,101868724,101875185,102220696,102401470,102401953, 101722967,101726810,101868828,101875296,102220933,102401598,102402443, 0 FGF14 cmpl cmpl 1,0,1,1,0,-1,-1,
82 12844 12844 175 NM_001080396.3 chr13 - 107163509 107867496 107170496 107866596 3 107163509,107210583,107865681, 107170786,107210755,107867496, 0 NALF1 cmpl cmpl 1,0,0,
83 12739 12739 2 XM_047430183.1 chr13 + 108495715 109208005 108665923 109206836 35 108495715,108665885,108712660,108727439,108785634,108793515,108806678,108820336,108823124,108844345,108855442,108866176,108883058,108888371,108898015,108910002,108957687,108961538,108962423,108964760,108992375,109008896,109019710,109046915,109052299,109055045,109055389,109100784,109120369,109125111,109127281,109140263,109164900,109179541,109206608, 108495924,108666149,108712731,108727583,108785743,108793640,108806804,108820412,108823278,108844493,108855553,108866242,108883186,108888477,108898133,108910150,108957799,108961656,108962495,108964902,108992448,109009049,109019911,109046991,109052475,109055126,109055595,109100887,109120466,109125358,109127550,109141376,109165059,109179633,109208005, 0 MYO16 cmpl cmpl -1,0,1,0,0,1,0,0,1,2,0,0,0,2,0,1,2,0,1,1,2,0,0,0,1,0,0,2,0,1,2,1,1,1,0,
84 13458 13458 1 XM_017021585.2 chr14 + 32934784 33804173 32934845 33801109 11 32934784,33215181,33367185,33560120,33676210,33735213,33774336,33778465,33793896,33797456,33799733, 32935003,33215426,33367268,33560210,33676385,33735332,33774530,33778572,33794044,33797581,33804173, 0 NPAS3 cmpl cmpl 0,2,1,0,0,1,0,2,1,2,1,
85 11874 11874 14 NM_001113498.3 chr14 - 46839622 47675605 46841930 47674796 17 46840091,46845765,46855023,46873432,46874044,46877488,46882043,46920011,46957373,47035010,47061248,47096853,47131713,47144077,47218020,47301410,47674516, 46842019,46845871,46855154,46873591,46874200,46877509,46882221,46920160,46957643,47035304,47061578,47097123,47131846,47144274,47218195,47301550,47675605, 0 MDGA2 cmpl cmpl 1,0,1,1,1,1,0,1,1,1,1,1,0,1,0,1,0,
86 7307 7307 0 XM_047430879.1 chr14 + 66508146 67735355 66508527 67735340 15 66508146,66681106,66776463,66824473,66842677,66879938,66916002,66922665,66924193,66965190,66985681,66987935,67023632,67058648,67735194, 66508591,66681185,66776521,66824566,66842716,66880033,66916069,66922938,66924292,66965325,66985738,66988007,67023675,67058786,67735355, 0 GPHN cmpl cmpl 0,1,2,0,0,0,2,0,0,0,0,0,0,1,1,
87 16685 16685 17 NM_001321818.2 chr14 + 67819778 68683096 67823543 68682944 11 67819778,67823541,67825463,67835079,67865002,67885868,67887020,68291883,68411423,68468171,68682936, 67819853,67823627,67825577,67835196,67865139,67885988,67887204,68291980,68411527,68468250,68683096, 0 RAD51B cmpl cmpl -1,0,0,0,0,2,2,0,1,0,1,
88 17060 17060 17 XM_024449761.2 chr14 + 71867334 72630029 71964791 72563027 22 71867334,71869925,71908164,71964771,72352094,72454527,72458270,72459631,72465757,72470006,72472871,72474624,72476741,72478267,72495151,72510153,72518350,72536185,72540040,72541469,72562416,72562714, 71867623,71869984,71908434,71964875,72352194,72454578,72458377,72459683,72465822,72470083,72472953,72474699,72476840,72478329,72495262,72510279,72518537,72536275,72540094,72541620,72562585,72566530, 0 RGS6 cmpl cmpl -1,-1,-1,0,0,1,1,0,1,0,2,0,0,0,2,2,2,0,0,0,1,2,
89 13605 13605 18 XM_024449753.2 chr14 + 78170372 79868291 78243093 79861964 19 78170372,78242390,78278644,78297830,78645119,78651164,78709216,78714755,78803619,78957241,78966024,78967207,78968172,78988021,79467220,79663777,79697629,79805111,79861662, 78170674,78243802,78278662,78297860,78645421,78651326,78709655,78715139,78803823,78957361,78966406,78967398,78968346,78988141,79467402,79663949,79697937,79805190,79868291, 0 NRXN3 cmpl cmpl -1,0,1,1,1,0,0,1,1,1,1,2,1,1,1,0,1,0,1,
90 6709 6709 12 NM_033223.5 chr15 + 26971180 27541984 26971535 27532881 10 26971180,26977001,27026753,27326808,27328805,27480649,27519971,27527432,27527932,27532599, 26971588,26977150,27026821,27327029,27328888,27480787,27520124,27527629,27527992,27541984, 0 GABRG3 cmpl cmpl 0,2,1,0,2,1,1,1,0,0,
91 5592 5592 12 NM_001387215.1 chr15 - 29117711 29675409 29118994 29252466 12 29117711,29123344,29124686,29126266,29128788,29136365,29137033,29151733,29196429,29252367,29381774,29675098, 29119018,29123655,29124761,29126491,29128864,29136501,29137194,29151841,29196564,29252478,29381831,29675409, 0 ENTREP2 cmpl cmpl 0,1,1,1,0,2,0,0,0,0,-1,-1,
92 17644 17644 1 XM_017022476.2 chr15 + 33310966 33866102 33311045 33865226 102 33310966,33473418,33530591,33533310,33539349,33540790,33543621,33548129,33550159,33562836,33566677,33579975,33581507,33584394,33585997,33601418,33603122,33613182,33623806,33628470,33629939,33631209,33632948,33634585,33635613,33636375,33644310,33646350,33647423,33649071,33652717,33659719,33660196,33662152,33663536,33669353,33670418,33696217,33697881,33699703,33700976,33706918,33722714,33724064,33726385,33728856,33731473,33736234,33738449,33739831,33742365,33746067,33748113,33748467,33749978,33750162,33755064,33756305,33757474,33768657,33769111,33771919,33773533,33780210,33785661,33788217,33800769,33801868,33810478,33810977,33812862,33813466,33815833,33818577,33819755,33820755,33821269,33821522,33822995,33825602,33826251,33826671,33827198,33830962,33834967,33836905,33837630,33840824,33841863,33843487,33844861,33848290,33853044,33853554,33854388,33854765,33857779,33859574,33860594,33861077,33864137,33865130, 33311096,33473538,33530666,33533389,33539462,33540890,33543715,33548204,33550316,33563010,33566799,33580144,33581643,33584490,33586116,33601552,33603364,33613375,33624023,33628575,33630043,33631293,33633108,33634733,33635819,33636550,33644519,33646526,33647460,33649235,33652883,33659806,33660423,33662948,33663737,33669456,33670556,33696491,33697996,33699833,33701080,33707054,33722895,33724176,33726506,33729026,33731694,33736325,33738590,33739995,33742444,33746157,33748260,33748530,33750054,33750286,33755180,33756373,33757596,33768707,33769172,33772158,33773615,33780341,33785982,33788458,33800857,33801961,33810649,33811037,33812994,33813579,33815933,33818684,33819807,33820812,33821369,33821602,33823072,33825676,33826269,33826752,33827287,33831091,33835072,33836987,33838958,33840883,33842035,33843574,33845062,33848421,33853087,33853682,33854449,33854912,33857914,33859731,33860659,33861178,33864189,33866102, 0 RYR3 cmpl cmpl 0,0,0,0,1,0,1,2,2,0,0,2,0,1,1,0,2,1,2,0,0,2,2,0,1,0,1,0,2,0,2,0,0,2,0,0,1,1,2,0,1,0,1,2,0,1,0,2,0,0,2,0,0,0,0,1,2,1,0,2,1,2,1,2,1,1,2,0,0,0,0,0,2,0,2,0,0,1,0,2,1,1,1,0,0,0,1,0,2,0,0,0,2,0,2,0,0,0,1,0,2,0,
93 17982 17982 14 NM_001198999.2 chr15 + 47184088 47774228 47759798 47771785 20 47184088,47412392,47470473,47600864,47759744,47760303,47760977,47761157,47761329,47761660,47762199,47763015,47763849,47764173,47764637,47764882,47765868,47766104,47766576,47770496, 47184418,47412472,47470545,47600896,47759907,47760415,47761038,47761220,47761431,47761751,47762319,47763104,47764067,47764305,47764793,47765056,47766009,47766182,47766677,47774221, 0 SEMA6D cmpl cmpl -1,-1,-1,-1,0,1,2,0,0,0,1,1,0,2,2,2,2,2,2,1,
94 21794 21794 15 XM_017022222.2 chr15 + 53837601 54633440 54012903 54627113 35 53837601,53876877,53878173,54012647,54143017,54143619,54235029,54236429,54237618,54250224,54264167,54265354,54293894,54297810,54300209,54321938,54332042,54333766,54338360,54393047,54414981,54494607,54500078,54500834,54507116,54511752,54525548,54532916,54546721,54549634,54555431,54567799,54622326,54623794,54626827, 53837659,53877058,53878298,54015886,54143040,54143684,54235108,54236435,54237690,54250444,54264395,54265496,54294064,54297926,54300373,54322095,54332111,54333856,54338489,54393181,54415067,54494734,54500175,54500978,54507194,54511830,54525637,54533066,54546845,54549691,54555512,54567947,54622419,54623954,54633440, 0 UNC13C cmpl cmpl -1,-1,-1,0,1,0,2,0,0,0,1,1,2,1,0,2,0,0,0,0,2,1,2,0,0,0,0,2,2,0,0,0,1,1,2,
95 17333 17333 16 XM_047432928.1 chr15 - 60488283 61229302 60497454 60514628 11 60488283,60499891,60500958,60502759,60503534,60505507,60511225,60514615,60531765,60677150,61229052, 60497619,60500004,60501069,60502867,60503667,60505629,60511621,60514757,60531851,60678686,61229302, 0 RORA cmpl cmpl 0,1,1,1,0,1,1,0,-1,-1,-1,
96 20382 20382 17 NM_001394532.1 chr15 + 71096893 71783383 71141527 71777374 18 71096893,71141448,71154862,71215034,71242648,71256612,71411686,71660529,71728548,71731120,71737731,71745105,71746837,71748420,71757901,71765019,71771063,71777231, 71097006,71141556,71154932,71215399,71243096,71256715,71411823,71660734,71728724,71731217,71738007,71745235,71747042,71748594,71758075,71765199,71771208,71783383, 0 THSD4 cmpl cmpl -1,0,2,0,2,0,1,0,1,0,1,1,2,0,0,0,0,1,
97 17780 17780 18 NM_001353010.2 chr15 - 76347903 76905340 76348632 76804624 33 76347903,76351236,76353948,76376161,76381377,76404523,76434077,76471211,76504858,76574157,76621763,76665652,76701757,76702849,76705902,76728594,76733228,76753807,76764960,76765336,76765562,76766917,76771741,76774854,76795279,76800247,76804532,76841733,76851167,76857808,76862415,76883811,76905192, 76348736,76351288,76354140,76376311,76381615,76404679,76434310,76471335,76504974,76574284,76621829,76665789,76701865,76703002,76705984,76728737,76733384,76753948,76765072,76765454,76765638,76767088,76771954,76775117,76795440,76800364,76804633,76841931,76851222,76857879,76862533,76883876,76905340, 0 SCAPER cmpl cmpl 1,0,0,0,2,2,0,2,0,2,2,0,0,0,2,0,0,0,2,1,0,0,0,1,2,2,0,-1,-1,-1,-1,-1,-1,
98 465 465 155 XM_011521227.4 chr15 + 86079619 87031476 86079972 87028840 23 86079619,86142003,86143698,86154429,86158932,86224913,86247670,86256852,86257963,86262777,86264257,86266373,86266989,86269918,86271618,86279638,86295254,86397365,86522809,86546001,86554360,86674272,87028824, 86080023,86142067,86143845,86154561,86159026,86224951,86247879,86257018,86258031,86262894,86264838,86266457,86267076,86270067,86271706,86279783,86295408,86397546,86522939,86546133,86554537,86674436,87031476, 0 AGBL1 cmpl cmpl 0,0,1,1,1,2,1,0,1,0,0,2,2,2,1,2,0,1,2,0,0,0,2,
99 5593 5593 74 NM_001387215.1 chr15_KI270905v1_alt - 1392758 1959533 1394045 1528000 12 1392758,1397973,1399315,1400895,1403417,1411936,1412604,1427301,1471992,1527901,1657276,1959222, 1394069,1398284,1399390,1401120,1403493,1412072,1412765,1427409,1472127,1528012,1657333,1959533, 0 ENTREP2 cmpl cmpl 0,1,1,1,0,2,0,0,0,0,-1,-1,
100 5594 5594 74 NM_001387215.1 chr15_KN538374v1_fix - 1280274 1847049 1281561 1415516 12 1280274,1285489,1286831,1288411,1290933,1299452,1300120,1314817,1359508,1415417,1544792,1846738, 1281585,1285800,1286906,1288636,1291009,1299588,1300281,1314925,1359643,1415528,1544849,1847049, 0 ENTREP2 cmpl cmpl 0,1,1,1,0,2,0,0,0,0,-1,-1,
101 16812 16812 9 NM_001415888.1 chr16 + 5239720 7713340 5239766 7710745 18 5239720,5467215,5598901,5867302,6316994,6654602,7052056,7518146,7579776,7587246,7595548,7597370,7607284,7653814,7664928,7676773,7709055,7710622, 5240105,5467254,5598961,5867335,6317057,6654650,7052098,7518389,7579920,7587300,7595641,7597431,7607338,7653947,7664968,7676838,7709131,7713340, 0 RBFOX1 cmpl cmpl 0,0,0,0,0,0,0,0,0,0,0,0,1,1,2,0,2,0,
102 19019 19019 84 NM_032167.5 chr16 + 11976733 12574287 11976806 12568629 21 11976733,11999296,12002990,12027319,12042896,12046383,12048371,12051846,12061527,12069056,12078832,12126632,12129629,12199600,12277932,12356162,12398445,12403447,12477718,12524701,12568505, 11976813,11999358,12003043,12027444,12043077,12046454,12048620,12052222,12061646,12069132,12078915,12126696,12129758,12199683,12278036,12356279,12398501,12403529,12477859,12524841,12574287, 0 SNX29 cmpl cmpl 0,1,0,2,1,2,1,1,2,1,2,1,2,2,1,0,0,2,0,0,2,
103 18231 18231 85 XM_011522642.3 chr16 + 12901597 13474651 12901941 13474248 5 12901597,12916687,13203393,13350179,13474209, 12902627,12916815,13203549,13350421,13474651, 0 SHISA9 cmpl cmpl 0,2,1,1,0,
104 22592 22592 17 NM_001386735.1 chr16 - 72782884 73891930 72787163 72960145 17 72782884,72793254,72800026,72811576,72811904,72829778,72889730,72950468,72957426,73093234,73130967,73143751,73257046,73318239,73456002,73680179,73891650, 72788848,72798714,72800129,72811777,72812038,72829859,72889962,72950965,72960194,73093598,73131094,73143831,73257136,73318336,73456258,73680240,73891930, 0 ZFHX3 cmpl cmpl 1,1,0,0,1,1,0,1,0,-1,-1,-1,-1,-1,-1,-1,-1,
105 22333 22333 18 NM_001291997.2 chr16 + 78099653 79212667 78115084 79211796 8 78099653,78109777,78114975,78164182,78386859,78424869,78432487,79211607, 78099885,78109835,78115154,78164289,78386948,78425055,78432752,79212667, 0 WWOX cmpl cmpl -1,-1,0,1,0,2,2,0,
106 2945 2945 18 NM_001220490.2 chr16 + 82626968 83800640 83344987 83795030 13 82626968,82858361,83125384,83217344,83344861,83486476,83602453,83670789,83678207,83748107,83779967,83783253,83795022, 82627137,82858473,83125501,83217497,83345006,83486655,83602594,83670972,83678461,83748250,83780201,83783472,83800640, 0 CDH13 cmpl cmpl -1,-1,-1,-1,0,1,0,0,0,2,1,1,1,
107 1260 1260 1 NM_001094.5 chr17 - 33013086 34156768 33013964 34156532 10 33013086,33015970,33017604,33021218,33023860,33025925,33028241,33088862,33111916,34155977, 33014066,33016039,33017684,33021310,33024014,33025982,33028392,33088990,33112067,34156768, 0 ASIC2 cmpl cmpl 0,0,1,2,1,1,0,1,0,0,
108 11247 11247 117 XM_024450773.2 chr17 + 46372791 47049128 46512712 47049061 11 46512467,46517361,46520211,46523083,46523803,46540175,46540806,46546254,46548311,46550414,47049055, 46515321,46517433,46520283,46523155,46523884,46540247,46540881,46546373,46549843,46550519,47049128, 0 LRRC37A2 cmpl cmpl 0,2,2,2,2,2,2,2,1,0,0,
109 2260 2260 122 NM_001082534.2 chr17 - 51630312 52160023 51631583 52157786 10 51630319,51633475,51635854,51649181,51653640,51747632,51930989,52072318,52157725,52159923, 51631606,51633650,51636009,51649254,51653736,51747818,51931132,52072393,52158369,52160023, 0 CA10 cmpl cmpl 1,0,1,0,0,0,1,1,0,-1,
110 1627 1627 16 NM_017679.5 chr17 + 60677850 61392831 60679457 61392125 24 60677850,60679452,60683981,60689685,60709218,60747197,60808003,60868575,60874661,60889694,60902619,60910531,60924406,60947218,60989970,61015750,61034665,61037888,61040791,61074919,61078332,61084466,61368326,61391976, 60677914,60679540,60684036,60689761,60709325,60747279,60808076,60868683,60874738,60889771,60902703,60910702,60924500,60947352,60990235,61015901,61034790,61038054,61040892,61075020,61078529,61084564,61368494,61392831, 0 BCAS3 cmpl cmpl -1,0,2,0,1,0,1,2,2,1,0,0,0,1,0,1,2,1,2,1,0,2,1,1,
111 3122 3122 16 NM_001353129.2 chr17 - 65635536 66192133 65635970 66183299 27 65635536,65637123,65640963,65689128,65743067,65750661,65851803,65902151,65927581,65961462,66005689,66027500,66028312,66029122,66029868,66053735,66062962,66066777,66069914,66096250,66096584,66129745,66132669,66175043,66176829,66183193,66191996, 65635974,65637188,65641065,65689218,65743217,65750724,65852034,65902334,65927689,65961598,66005769,66027560,66028405,66029252,66030023,66053879,66063081,66066877,66070001,66096331,66096632,66129823,66132763,66175216,66177020,66183307,66192133, 0 CEP112 cmpl cmpl 2,0,0,0,0,0,0,0,0,2,0,0,0,2,0,0,1,0,0,0,0,0,2,0,1,0,-1,
112 16815 16815 148 XM_024450593.2 chr17 - 79089344 79665571 79092596 79115715 17 79091946,79094450,79095512,79096652,79097291,79097691,79101583,79103161,79104072,79106650,79115493,79235765,79307723,79482453,79644136,79646195,79665370, 79092641,79094529,79095574,79096833,79097424,79097745,79101644,79103254,79104126,79106788,79115748,79235805,79307824,79482598,79644242,79646334,79665571, 0 RBFOX3 cmpl cmpl 0,2,0,2,1,1,0,0,0,0,0,-1,-1,-1,-1,-1,-1,
113 4865 4865 9 XM_024451288.2 chr18 - 3496031 4455307 3499184 3880068 15 3496031,3502492,3508569,3534193,3567489,3581874,3656083,3729134,3742334,3814058,3879111,4005115,4106580,4151179,4455005, 3499394,3502645,3508661,3534615,3567581,3582248,3656113,3729375,3742512,3814273,3880140,4005201,4107046,4151287,4455307, 0 DLGAP1 cmpl cmpl 0,0,1,2,0,1,1,0,2,0,0,-1,-1,-1,-1,
114 16475 16475 1 NM_002845.4 chr18 + 7567315 8406856 7567818 8406162 31 7567315,7774148,7888105,7906504,7926567,7949180,7955120,8069685,8076454,8085670,8088748,8113485,8114790,8143646,8244057,8247844,8253226,8296367,8314780,8319177,8343422,8370889,8376045,8376461,8378264,8379166,8380295,8384560,8387071,8394475,8406108, 7567891,7774271,7888377,7906583,7926683,7949355,7955414,8069994,8076564,8085872,8088851,8113759,8114827,8143779,8244209,8247919,8253414,8296455,8314857,8319214,8343520,8371006,8376200,8376597,8378414,8379340,8380427,8384686,8387235,8394611,8406856, 0 PTPRM cmpl cmpl 0,1,1,0,1,0,1,1,1,0,1,2,0,1,2,1,1,0,1,0,1,0,0,2,0,0,0,0,0,2,0,
115 4493 4493 15 XM_047437311.1 chr18 + 52340196 53535899 52340787 53530653 29 52340196,52752053,52906043,52923706,52925233,53063304,53066045,53157355,53178961,53205215,53207678,53215547,53305577,53322046,53339712,53386042,53391714,53397307,53402785,53410451,53416123,53435143,53450499,53459231,53467893,53486796,53499297,53526616,53530563, 52340878,52752374,52906328,52923857,52925370,53063459,53066166,53157512,53179116,53205364,53207817,53215597,53305719,53322157,53339907,53386138,53391887,53397446,53402893,53410646,53416156,53435209,53450662,53459458,53468010,53486952,53499510,53526759,53535899, 0 DCC cmpl cmpl 0,1,1,1,2,1,0,1,2,1,0,1,0,1,1,1,1,0,1,1,1,1,1,2,1,1,1,1,0,
116 12786 12786 9 XM_017003604.2 chr2 - 1789112 2331275 1791866 1979777 27 1789112,1792320,1801689,1809075,1839148,1840759,1851640,1886538,1887058,1887487,1889240,1892036,1903079,1910239,1912019,1917204,1922285,1942981,1979164,1979520,1979722,1997190,2053977,2172871,2284403,2326035,2330966, 1792007,1792464,1801799,1809167,1839370,1840843,1851703,1886607,1887121,1887609,1889477,1892287,1903294,1910347,1912110,1917339,1923263,1943334,1979227,1979554,1979777,1997347,2054123,2172988,2284503,2326111,2331275, 0 MYT1L cmpl cmpl 0,0,1,2,2,2,2,2,2,0,0,1,2,2,1,1,1,2,2,1,0,-1,-1,-1,-1,-1,-1,
117 12890 12890 87 XM_017004317.2 chr2 - 14998066 15561334 15137403 15561304 53 14998066,15137355,15178987,15186741,15190263,15218772,15232421,15234544,15238467,15275483,15276850,15287072,15292536,15308215,15309170,15327749,15328198,15330597,15351991,15353552,15356302,15366579,15374607,15379601,15383214,15394226,15396412,15402167,15415545,15417526,15424314,15427710,15461200,15461686,15467328,15467663,15468381,15473221,15474066,15475686,15478225,15488893,15504144,15511211,15534542,15536417,15539222,15551492,15553425,15554060,15556782,15558579,15561187, 14998224,15137445,15179116,15186880,15190403,15218968,15232511,15234747,15238686,15275818,15277101,15287183,15292766,15308353,15309247,15327870,15328312,15330765,15352081,15353710,15356416,15366693,15374720,15379831,15383317,15394349,15396475,15402301,15415719,15417712,15424468,15427794,15461337,15461791,15467407,15467804,15468533,15473347,15474324,15475880,15478289,15489022,15504213,15511350,15534641,15536551,15539356,15551536,15553473,15554138,15556819,15558634,15561334, 0 NBAS cmpl cmpl -1,0,0,2,0,2,2,0,0,1,2,2,0,0,1,0,0,0,0,1,1,1,2,0,2,2,2,0,0,0,2,2,0,0,2,2,0,0,0,1,0,0,0,2,2,0,1,2,2,2,1,0,0,
118 643 643 12 NM_004304.5 chr2 - 29192773 29921586 29193223 29920659 29 29192773,29196769,29197541,29207170,29209785,29213983,29220705,29222343,29222516,29223341,29225460,29226921,29227573,29228883,29232303,29233564,29239679,29251104,29275098,29275401,29296887,29318303,29320750,29328349,29383731,29531914,29694849,29717577,29919992, 29193922,29196860,29197676,29207272,29209878,29214081,29220835,29222408,29222607,29223528,29225565,29227074,29227672,29229066,29232448,29233696,29239830,29251267,29275227,29275496,29297057,29318404,29320882,29328481,29383859,29532116,29695014,29717697,29921586, 0 ALK cmpl cmpl 0,2,2,2,2,0,2,0,2,1,1,1,1,1,0,0,2,1,1,2,0,1,1,1,2,1,1,1,0,
119 16059 16059 14 XM_005264428.2 chr2 + 45651278 46187990 45652100 46184881 16 45651278,45651903,45842999,45976428,45978975,45980295,45984550,46001403,46004541,46007461,46010343,46086207,46145092,46151040,46159605,46184734, 45651703,45652448,45843063,45976588,45979010,45980381,45984680,46001546,46004638,46007661,46010517,46086362,46145231,46151229,46159752,46187990, 0 PRKCE cmpl cmpl -1,0,0,1,2,1,0,1,0,1,0,0,2,0,0,0,
120 13603 13603 1 NM_001135659.3 chr2 - 49918502 51032132 49921943 51028273 24 49918502,49943703,50053270,50054954,50091322,50236788,50465441,50472297,50495904,50497332,50506494,50528624,50531226,50538252,50552586,50620021,50621204,50623313,50921868,50922657,50925937,51026370,51027501,51031980, 49922251,49943791,50053590,50055044,50091494,50236970,50465561,50472471,50496095,50497714,50506617,50528651,50531430,50538636,50553025,50620183,50621249,50623615,50921880,50922687,50925955,51026469,51029194,51032132, 0 NRXN1 cmpl cmpl 1,0,1,1,0,1,1,1,2,1,1,1,1,1,0,0,0,1,1,1,1,1,0,-1,
121 22196 22196 133 XM_047444626.1 chr2 - 63119558 63840826 63121820 63571377 21 63119558,63152913,63174669,63259306,63313247,63378385,63381905,63404047,63433744,63437420,63439756,63484603,63484916,63486541,63487446,63492855,63571374,63650658,63673866,63813621,63840042, 63122056,63152945,63174832,63259409,63313311,63378509,63382094,63404657,63433936,63437554,63439871,63484663,63484987,63486586,63487494,63492940,63571626,63650838,63678253,63813707,63840826, 0 WDPCP cmpl cmpl 1,2,1,0,2,1,1,0,0,1,0,0,1,1,1,0,0,-1,-1,-1,-1,
122 5817 5817 17 NM_001321731.2 chr2 - 72175983 72826033 72182889 72825910 23 72175983,72182852,72184074,72334946,72379728,72465159,72480615,72492317,72495429,72496453,72498453,72499900,72513131,72514633,72515042,72559452,72575491,72718102,72731006,72731154,72733070,72741303,72825797, 72179461,72182905,72184187,72335020,72379870,72465339,72480750,72492429,72495539,72496559,72498551,72499972,72513252,72514680,72515126,72559521,72575668,72718307,72731052,72731245,72733118,72741469,72826033, 0 EXOC6B cmpl cmpl -1,2,0,1,0,0,0,2,0,2,0,0,2,0,0,0,0,2,1,0,0,2,0,
123 11314 11314 146 NM_001134745.3 chr2 - 76747684 77522376 76748694 77521671 4 76747684,77518317,77521667,77522108, 76748916,77519864,77521818,77522376, 0 LRRTM4 cmpl cmpl 0,1,0,-1,
124 4198 4198 18 NM_001399737.1 chr2 + 79185376 80648780 79651556 80647872 22 79185376,79197958,79312708,79373830,79505053,79651551,79744386,79858012,79869815,79874075,79909593,80393210,80419448,80544981,80545906,80555692,80574162,80581705,80589303,80604073,80608183,80647584, 79185431,79198076,79312796,79374013,79505182,79651658,79744582,79858179,79869935,79874342,79909797,80393291,80419601,80545074,80546063,80555893,80574314,80581819,80589485,80604179,80608318,80648780, 0 CTNNA2 cmpl cmpl -1,-1,-1,-1,-1,0,0,1,0,0,0,0,0,0,0,1,1,0,0,2,0,0,
125 447 447 20 XM_047444279.1 chr2 - 99545418 100142590 99551473 100110104 28 99545418,99554310,99554682,99558874,99560364,99565486,99568851,99578326,99582797,99587153,99593194,99601434,99649625,99672537,99727076,99744103,99752220,99837476,100006631,100007147,100008811,100011496,100104401,100105503,100110053,100112385,100129223,100142483, 99551595,99554534,99554732,99558968,99560436,99565623,99568915,99578451,99582999,99587278,99594289,99601621,99649666,99672589,99727128,99744140,99752301,99837524,100007017,100007460,100008932,100011571,100104518,100105583,100110333,100112524,100129306,100142590, 0 AFF3 cmpl cmpl 1,2,0,2,2,0,2,0,2,0,0,2,0,2,1,0,0,0,1,0,2,2,2,0,0,-1,-1,-1,
126 16726 16726 2 XM_047445367.1 chr2 + 108719481 109842301 108719606 109841457 25 108719481,108729131,108730773,108731321,108735531,108736103,108740488,108746710,108748919,108751263,108751527,108751870,108752997,108753425,108753824,108754904,108755175,108758412,108762100,108763236,108769259,108771700,108772488,108772867,109841403, 108719678,108729199,108730885,108731474,108735762,108736249,108740681,108746798,108749129,108751445,108751703,108751994,108753159,108753563,108753971,108755084,108755259,108758548,108762195,108768388,108769337,108771871,108772581,108773046,109842301, 0 RANBP2 cmpl cmpl 0,0,2,0,0,0,2,0,1,1,0,2,0,0,0,0,0,0,1,0,1,1,1,1,0,
127 5065 5065 22 NM_001321913.3 chr2 + 114442640 115845780 115739803 115842345 25 114442640,115343816,115499509,115525897,115689686,115689839,115727815,115739738,115746085,115753173,115762571,115768296,115777207,115777786,115780873,115782351,115791080,115791286,115814792,115815674,115836156,115836506,115836673,115840749,115842210, 114442838,115343912,115499604,115525972,115689739,115689921,115727936,115739893,115746183,115753297,115762610,115768404,115777299,115777834,115780995,115782399,115791179,115791356,115814987,115815729,115836256,115836565,115836746,115840823,115845780, 0 DPP10 cmpl cmpl -1,-1,-1,-1,-1,-1,-1,0,0,2,0,0,0,2,2,1,1,1,2,2,0,1,0,1,0,
128 3714 3714 23 NM_130773.4 chr2 + 124025286 124921219 124025650 124914288 24 124025286,124221704,124242199,124417442,124434483,124446752,124474738,124504291,124524302,124527284,124563216,124609800,124647757,124747228,124763671,124763976,124772798,124789901,124798095,124865305,124869674,124902881,124911466,124914091, 124025732,124221809,124242393,124417590,124434687,124446937,124474879,124504556,124524452,124527456,124563323,124609920,124647958,124747385,124763799,124764147,124773017,124790141,124798320,124865436,124869762,124903100,124911538,124921219, 0 CNTNAP5 cmpl cmpl 0,1,1,0,1,1,0,0,1,1,2,1,1,1,2,1,1,1,1,1,0,1,1,1,
129 12943 12943 24 XM_011511100.4 chr2 - 132671787 133674836 132673023 133517526 19 132671787,132728815,132731736,132773815,132781051,132781939,132790022,132796627,132860491,132868935,132878847,132963719,132994151,133129977,133213715,133303036,133517457,133559049,133674673, 132673305,132728952,132732051,132773894,132781229,132785718,132790205,132796729,132860611,132868974,132878916,132963869,132994239,133130111,133213779,133303110,133517587,133559117,133674836, 0 NCKAP5 cmpl cmpl 0,1,1,0,2,0,0,0,0,0,0,0,2,0,2,0,0,-1,-1,
130 20384 20384 25 NM_001316349.2 chr2 + 136765544 137677718 136882178 137676605 28 136765544,136882143,137056419,137094872,137115123,137160212,137170740,137231043,137232898,137242456,137272532,137275922,137405612,137411608,137450844,137563220,137572405,137616174,137618391,137620608,137642487,137655500,137656795,137657064,137659663,137663382,137667773,137676523, 136765687,136882317,137057230,137095121,137115293,137160368,137170938,137231235,137233133,137242572,137272662,137276026,137405807,137411872,137451023,137563354,137572556,137616316,137618507,137620726,137642633,137655660,137656969,137657160,137659746,137663575,137667861,137677718, 0 THSD7B cmpl cmpl -1,0,1,2,2,1,1,1,1,2,1,2,1,1,1,0,2,0,1,0,1,0,1,1,1,0,1,2,
131 11210 11210 25 NM_018557.3 chr2 - 140231422 142131016 140233185 142130729 91 140231422,140234785,140238151,140239441,140247085,140270241,140274423,140297807,140314934,140321962,140323892,140325761,140334452,140335614,140350796,140352952,140356341,140357978,140358820,140364660,140370709,140371178,140373007,140378179,140385892,140442503,140444329,140444562,140450567,140456454,140457462,140475137,140485342,140487616,140492607,140495564,140501686,140502962,140506795,140509927,140514652,140516888,140525843,140526236,140534020,140536580,140540972,140541778,140598630,140601449,140700249,140701720,140702140,140702426,140715972,140716681,140769212,140770880,140776097,140813656,140839990,140840917,140850101,140851651,140867589,140868098,140883816,140886137,140902919,140907876,140922964,140950234,140951859,140982159,140989531,140993994,141005334,141013555,141015695,141019921,141048985,141055115,141058882,141062050,141188420,141229182,141247225,141254521,141480395,141810278,142130647, 140233326,140234884,140238296,140239532,140247162,140270346,140274598,140297969,140315099,140322088,140324066,140325878,140334559,140335838,140351038,140353072,140356476,140358116,140358946,140364783,140370842,140371285,140373137,140378286,140386009,140442623,140444449,140444679,140450661,140456603,140457651,140475337,140485524,140487739,140492693,140495748,140501874,140503103,140506918,140510056,140514772,140517011,140525993,140526350,140534140,140536709,140541098,140541971,140598835,140601639,140700621,140701845,140702292,140702553,140716102,140716816,140769344,140771006,140776238,140813806,140840085,140841092,140850329,140851783,140867834,140868263,140884021,140886335,140903165,140908077,140923147,140950402,140951940,140982276,140989657,140994135,141005457,141013745,141015915,141020102,141049222,141055259,141059054,141062273,141188583,141229440,141247354,141254641,141480533,141810401,142131016, 0 LRP1B cmpl cmpl 0,0,2,1,2,2,1,1,1,1,1,1,2,0,1,1,1,1,1,1,0,1,0,1,1,1,1,1,0,1,1,2,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,0,2,1,1,2,0,2,1,1,1,1,1,1,2,1,1,1,2,2,1,1,1,1,1,1,1,1,1,1,1,0,2,1,1,1,0,2,1,1,1,1,1,1,0,
132 1039 1039 26 XM_017004500.3 chr2 + 143129418 143768352 143129430 143768172 13 143129418,143202133,143216383,143228580,143250510,143435600,143436912,143487372,143519265,143556407,143624132,143703418,143767988, 143129466,143202202,143216445,143228668,143250600,143435699,143437042,143487495,143519364,143556485,143624267,143703524,143768352, 0 ARHGAP15 cmpl cmpl 0,0,0,2,0,0,0,1,1,1,1,1,2,
133 6752 6752 27 NM_001422883.1 chr2 + 153068292 154456574 154242762 154450551 17 153068292,153078339,153311474,153332573,153333236,153732768,153900935,153944393,154242029,154242697,154245811,154259020,154301408,154395990,154408983,154438591,154450410, 153068361,153078454,153311933,153332640,153333327,153732830,153901007,153944639,154242196,154242905,154245982,154259138,154301589,154396130,154409082,154438726,154456574, 0 GALNT13 cmpl cmpl -1,-1,-1,-1,-1,-1,-1,-1,-1,0,2,2,0,1,0,0,0,
134 1512 1512 3 NM_020981.4 chr2 + 167293000 167874045 167869039 167870020 5 167293000,167490176,167646908,167818671,167868810, 167293334,167490277,167646966,167818793,167874045, 0 B3GALT1 cmpl cmpl -1,-1,-1,-1,0,
135 14949 14949 30 XM_047444688.1 chr2 - 182140040 182716797 182147078 182716764 16 182140040,182147035,182185891,182186467,182188978,182201438,182201687,182205939,182223863,182230005,182231014,182234431,182240109,182264300,182522275,182716690, 182143038,182147152,182186079,182186588,182189060,182201559,182201789,182206065,182223964,182230146,182231131,182234498,182240292,182264414,182522386,182716797, 0 PDE1A cmpl cmpl -1,1,2,1,0,2,2,2,0,0,0,2,2,2,2,0,
136 14703 14703 33 NM_152526.6 chr2 + 204545474 205620162 204545999 205615813 22 204545474,204686180,204965151,205047580,205104425,205113490,205118920,205121590,205124326,205125608,205172210,205176444,205185763,205193204,205245777,205300529,205301463,205401012,205440369,205499895,205553323,205615455, 204546119,204686282,204965323,205047690,205104514,205113577,205119046,205121949,205124466,205125737,205172381,205176577,205185863,205193320,205245822,205300736,205301701,205401123,205440672,205500031,205553403,205620162, 0 PARD3B cmpl cmpl 0,0,0,1,0,2,2,2,1,0,0,0,1,2,1,1,1,2,2,2,0,2,
137 5677 5677 34 XM_017003577.3 chr2 - 211375716 212538802 211383614 212538530 30 211375716,211386852,211387944,211420440,211422006,211424154,211428407,211430944,211561902,211619176,211623921,211630461,211657753,211657949,211665322,211673163,211679051,211701966,211704103,211705317,211712049,211713534,211722392,211725075,211750638,211781457,211788024,211947429,212124751,212538448, 211384060,211387150,211387992,211420611,211422104,211424301,211428483,211431100,211562088,211619275,211624044,211630594,211657828,211657994,211665477,211673257,211679184,211702166,211704194,211705391,211712176,211713648,211722534,211725194,211750704,211781535,211788159,211947616,212124903,212538802, 0 ERBB4 cmpl cmpl 1,0,0,0,1,1,0,0,0,0,0,2,2,2,0,2,1,2,1,2,1,1,0,1,1,1,1,0,1,0,
138 19118 19118 34 XM_011511820.3 chr2 + 213284463 214410501 213284483 214410315 15 213284463,213296063,213297261,213310058,213317218,213340162,213350527,213364075,213375009,213489962,213862484,214013950,214108195,214149139,214410139, 213284619,213296110,213297357,213310177,213317356,213340270,213350645,213364145,213375119,213490090,213862628,214014077,214108261,214149266,214410501, 0 SPAG16 cmpl cmpl 0,1,0,0,2,2,2,0,1,0,2,2,0,0,1,
139 458 458 37 NM_014914.5 chr2 + 235494042 236131793 235494686 236124122 17 235494042,235709178,235717556,235740962,235744697,235750353,235797758,235799366,235807238,235883344,235908737,235968461,236036560,236040750,236049058,236120191,236123918, 235494849,235709237,235717644,235741048,235744839,235750488,235797886,235799522,235807331,235883449,235908906,235968623,236036715,236040841,236049281,236120447,236131793, 0 AGAP1 cmpl cmpl 0,1,0,1,0,1,1,0,0,0,0,1,1,0,1,2,0,
140 15393 15393 1 NM_015192.4 chr20 + 8132265 8884900 8132651 8881849 32 8132265,8150293,8371381,8628293,8646101,8647899,8649373,8657183,8658537,8684931,8697625,8708669,8716263,8717670,8722353,8724655,8727308,8729049,8733237,8737027,8739260,8740343,8741463,8757045,8760406,8765138,8774538,8788448,8788632,8789517,8790174,8881621, 8132750,8150371,8371450,8628431,8646181,8647953,8649449,8657284,8658704,8685078,8697783,8708752,8716348,8717848,8722421,8724752,8727393,8729174,8733392,8737192,8739360,8740448,8741573,8757178,8760460,8765358,8774719,8788525,8788722,8789575,8790261,8884900, 0 PLCB1 cmpl cmpl 0,0,0,0,0,2,2,0,2,1,1,0,2,0,1,0,1,2,1,0,0,1,1,0,1,1,2,0,2,2,0,0,
141 11512 11512 10 NM_080676.6 chr20 + 13995515 16053197 13995763 16049876 17 13995515,14002287,14085620,14493478,14684842,15229939,15431404,15499773,15862744,15885763,15933275,15937475,15967552,15986726,15987065,16041200,16049829, 13995809,14002404,14085728,14493508,14684959,15230061,15431435,15499847,15862826,15885811,15933338,15937544,15967630,15986801,15987158,16041278,16053197, 0 MACROD2 cmpl cmpl 0,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,
142 16482 16482 14 XM_047439848.1 chr20 - 42031889 43189906 42043543 43189733 32 42031889,42043521,42081881,42084681,42085727,42098420,42102123,42104568,42106785,42110332,42115198,42118402,42119934,42128753,42141914,42161351,42199239,42236228,42248686,42282488,42315722,42350627,42352083,42448219,42472265,42677865,42756461,42771434,42780217,42791194,42885806,43189645, 42032336,42043639,42082017,42084845,42085853,42098552,42102297,42104718,42106921,42110487,42115315,42118500,42119971,42128830,42142002,42161539,42199388,42236258,42248822,42282525,42315996,42350730,42352285,42448329,42472562,42678159,42756636,42771550,42780299,42791466,42885932,43189906, 0 PTPRT cmpl cmpl -1,0,2,0,0,0,0,0,2,0,0,1,0,1,0,1,2,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,
143 21370 21370 15 XM_047439879.1 chr20 + 52972357 53495330 52973293 53487145 5 52972357,53253498,53487143,53490865,53494873, 52973333,53256444,53487332,53490947,53495330, 0 TSHZ2 cmpl cmpl 0,1,1,-1,-1,
144 2958 2958 16 NM_001794.5 chr20 + 61252260 61940617 61252513 61936943 16 61252260,61254825,61743562,61773002,61844667,61852753,61873727,61894909,61910421,61923450,61924333,61928189,61929608,61932984,61934055,61936736, 61252570,61254937,61743789,61773182,61844823,61852898,61873900,61895047,61910607,61923704,61924476,61928423,61929842,61933124,61934220,61940617, 0 CDH4 cmpl cmpl 0,0,1,0,0,0,1,0,0,0,2,1,1,1,0,0,
145 12919 12919 93 NM_001352595.2 chr21 + 20998408 21543329 20998563 21537957 15 20998408,21292103,21324382,21335504,21338388,21373862,21410273,21418472,21432107,21466605,21468661,21477290,21508850,21534536,21537845, 20998618,21292241,21324500,21335665,21338534,21374013,21410461,21418569,21432281,21466725,21468783,21477471,21509055,21534656,21543329, 0 NCAM2 cmpl cmpl 0,1,1,2,1,0,1,0,1,1,1,0,1,2,2,
146 5114 5114 111 NM_001389.5 chr21 - 40010998 40847158 40013033 40846661 33 40010998,40042370,40044077,40051957,40055724,40062868,40075036,40078686,40080151,40083907,40085601,40087169,40093720,40124194,40133853,40142557,40144490,40167217,40178926,40187130,40187890,40189041,40276096,40296054,40312080,40338100,40339118,40347669,40353464,40369098,40692809,40708453,40846618, 40013386,40042673,40044275,40052107,40055840,40062899,40075213,40078977,40080340,40084006,40085765,40087287,40093874,40124328,40134009,40142704,40144731,40167288,40179094,40187259,40187987,40189238,40276270,40296174,40312359,40338376,40339415,40347945,40353743,40369245,40692956,40708771,40847158, 0 DSCAM cmpl cmpl 1,1,1,1,2,1,1,1,1,1,2,1,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,
147 5115 5115 73 NM_001389.5 chr21_MU273391v1_fix - 150306 986812 152341 986315 33 150306,181704,183411,191296,195063,202213,214361,218011,219810,223565,225261,226829,233380,263864,273523,282211,284144,306871,318580,326784,327544,328695,415750,435708,451734,477754,478772,487323,493118,508752,832463,848107,986272, 152694,182007,183609,191446,195179,202244,214538,218302,219999,223664,225425,226947,233534,263998,273679,282358,284385,306942,318748,326913,327641,328892,415924,435828,452013,478030,479069,487599,493397,508899,832610,848425,986812, 0 DSCAM cmpl cmpl 1,1,1,1,2,1,1,1,1,1,2,1,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,
148 21455 21455 12 NM_001145418.2 chr22 - 27978013 28679840 27982220 28679723 23 27978013,27985248,27989877,27990788,27992586,27993286,27996134,27998539,28001373,28014247,28030225,28094079,28096189,28098914,28101170,28105278,28107061,28163091,28296197,28297579,28306495,28629551,28679621, 27983851,27985356,27990007,27990812,27992663,27993518,27996259,27999260,28001553,28014392,28030366,28094245,28096408,28099044,28101280,28105802,28108403,28163599,28296328,28297852,28306643,28629830,28679840, 0 TTC28 cmpl cmpl 1,1,0,0,1,0,1,0,0,2,2,1,1,0,1,2,1,0,1,1,0,0,0,
149 19734 19734 104 XM_017028962.3 chr22 - 32507819 33058381 32513691 33006662 14 32507819,32518042,32527917,32528873,32533792,32538035,32541570,32596673,32864914,32868965,32931389,32980644,33006351,33057160, 32513824,32518334,32528005,32529008,32533895,32538110,32541713,32596736,32865004,32869125,32931481,32980702,33006824,33058381, 0 SYN3 cmpl cmpl 2,1,0,0,2,2,0,0,0,2,0,2,0,-1,
150 10078 10078 1 XM_024452302.2 chr22 - 33162227 33922824 33166762 33761476 15 33162227,33283201,33304228,33316084,33337645,33381918,33384191,33432160,33564847,33604434,33626243,33650366,33761370,33856739,33919994, 33166832,33283348,33304507,33316248,33337801,33382044,33384304,33432265,33565019,33604558,33626326,33650668,33761558,33856802,33920476, 0 LARGE1 cmpl cmpl 2,2,2,0,0,0,1,1,0,2,0,1,0,-1,-1,
151 3703 3703 75 XM_006713004.5 chr3 + 2098865 3057959 2571503 3056220 24 2098865,2339177,2571415,2736214,2745521,2819485,2866751,2883144,2887039,2900684,2902875,2925628,2988344,3026101,3030857,3034631,3037178,3038932,3040036,3042309,3042976,3043591,3053806,3056119, 2098978,2339233,2571558,2736341,2745697,2819581,2866949,2883247,2887224,2900821,2903005,2925779,2988472,3026277,3030975,3034790,3037328,3039003,3040271,3042422,3043163,3043704,3053975,3057959, 0 CNTN4 cmpl cmpl -1,-1,0,1,2,1,1,1,2,1,0,1,2,1,0,1,1,1,0,1,0,1,0,1,
152 7506 7506 9 NM_000844.4 chr3 + 6861114 7741533 6861388 7740406 10 6861114,7146451,7298683,7306497,7415022,7452606,7461582,7578421,7680048,7740356, 6861907,7146668,7298825,7306652,7415163,7452807,7461722,7579357,7680295,7741533, 0 GRM7 cmpl cmpl 0,0,1,2,1,1,1,0,0,1,
153 20041 20041 89 XM_047449300.1 chr3 - 17157161 17742631 17160962 17508570 26 17157161,17166766,17167748,17185108,17214206,17238162,17258505,17291894,17307991,17372074,17374470,17374628,17376524,17383912,17403180,17404693,17404871,17406417,17428449,17508473,17562018,17586352,17622647,17623848,17672544,17742480, 17161256,17166928,17167828,17185208,17214370,17238419,17258591,17292001,17308134,17372247,17374540,17374679,17376613,17384015,17403248,17404768,17404961,17406526,17428519,17508605,17562142,17586557,17622765,17623913,17672705,17742631, 0 TBC1D5 cmpl cmpl 0,0,1,0,1,2,0,1,2,0,2,2,0,2,0,0,0,2,1,0,-1,-1,-1,-1,-1,-1,
154 22860 22860 11 XM_017007191.2 chr3 - 21412217 22372763 21421213 22372555 10 21416334,21423962,21425491,21436969,21441685,21510860,21564573,21664885,22168816,22372449, 21421447,21424064,21425670,21437203,21441742,21511023,21564684,21665028,22169035,22372763, 0 ZNF385D cmpl cmpl 0,0,1,1,1,0,0,1,1,0,
155 16751 16751 1 NM_001290216.3 chr3 + 24829320 25597932 25174397 25596616 11 24829320,24858673,25060124,25174118,25461192,25501181,25569757,25580545,25593502,25594519,25596419, 24829403,24858752,25060176,25174575,25461341,25501323,25569918,25580722,25593707,25594678,25597932, 0 RARB cmpl cmpl -1,-1,-1,0,1,0,1,0,0,1,1,
156 16860 16860 12 XM_017006181.2 chr3 + 29281070 30010395 29281681 30003862 13 29281070,29434745,29488440,29587113,29739719,29762909,29868857,29884161,29897378,29936085,29988142,29991081,30003855, 29281756,29434915,29488499,29587205,29739877,29762989,29868964,29884208,29897475,29936196,29988223,29991209,30010395, 0 RBMS3 cmpl cmpl 0,0,2,1,0,2,1,0,2,0,0,0,2,
157 21785 21785 1 NM_017886.4 chr3 - 41246598 41962103 41246928 41954759 37 41246598,41249488,41398078,41455496,41463086,41566024,41615668,41663606,41681507,41681752,41705056,41705253,41715236,41715446,41717727,41754360,41789660,41800131,41819422,41835863,41883873,41895517,41896821,41898431,41900724,41907844,41911316,41911540,41912806,41915976,41918456,41919716,41931843,41935800,41938097,41954621,41962015, 41246992,41249574,41398264,41455595,41463253,41566130,41615717,41663699,41681652,41681804,41705151,41705305,41715293,41715568,41717861,41754488,41789843,41800293,41819506,41835971,41883952,41895564,41897003,41898492,41900829,41907941,41911386,41911659,41912899,41916052,41918540,41919818,41932006,41935940,41938197,41954807,41962103, 0 ULK4 cmpl cmpl 2,0,0,0,1,0,2,2,1,0,1,0,0,1,2,0,0,0,0,0,2,0,1,0,0,2,1,2,2,1,1,1,0,1,0,0,-1,
158 5026 5026 15 XM_047447599.1 chr3 + 50674926 51384198 50675263 51381559 52 50674926,50778674,50841674,50890025,50933980,51064447,51075355,51089242,51090229,51146548,51159243,51160554,51208773,51214121,51225648,51227282,51227981,51228660,51229511,51236344,51237489,51246725,51260155,51270814,51275078,51280105,51310231,51312003,51312475,51312843,51314979,51330137,51333157,51338358,51338934,51341236,51348851,51350287,51354881,51356088,51356406,51356961,51357757,51357960,51360510,51361858,51362526,51374468,51375747,51379448,51380124,51381049, 50675300,50778758,50841715,50890081,50934077,51064596,51075440,51089284,51090384,51146630,51159304,51160702,51208862,51214247,51225773,51227445,51228088,51228832,51229609,51236428,51237590,51246807,51260326,51271007,51275206,51280204,51310326,51312079,51312576,51312902,51315128,51330223,51333253,51338419,51339028,51341385,51348938,51350392,51355023,51356255,51356493,51357141,51357841,51358077,51360632,51361997,51362674,51374587,51375835,51379571,51380207,51384198, 0 DOCK3 cmpl cmpl 0,1,1,0,2,0,2,0,0,2,0,1,2,1,1,0,1,0,1,0,0,2,0,0,1,0,0,2,0,2,1,0,2,2,0,1,0,0,0,1,0,0,0,0,0,2,0,1,0,1,1,0,
159 2304 2304 15 NM_018398.3 chr3 + 54122551 55074557 54122713 55074206 38 54122551,54123512,54320441,54386714,54503491,54562799,54569794,54569953,54581802,54627786,54642127,54752598,54764217,54816852,54837158,54838567,54846392,54871538,54879017,54879349,54880795,54885280,54885488,54887958,54891354,54896748,54899787,54968449,54969799,54984607,54987682,55004762,55007789,55009387,55018205,55073444,55073776,55074113, 54122835,54123594,54320558,54386774,54503654,54562931,54569855,54570104,54581877,54627876,54642241,54752677,54764351,54816870,54837230,54838648,54846467,54871622,54879089,54879411,54880863,54885326,54885586,54888052,54891450,54896870,54899868,54968511,54969844,54984670,54987753,55004838,55007842,55009443,55018317,55073557,55073859,55074557, 0 CACNA2D3 cmpl cmpl 0,2,0,0,0,1,1,2,0,0,0,0,1,0,0,0,0,0,0,0,2,1,2,1,2,2,1,1,0,0,0,2,0,2,1,2,1,0,
160 5681 5681 15 XM_047447942.1 chr3 - 55508310 56468467 55606909 56435007 18 55508310,55606779,55699377,55734749,55888388,55950424,55992056,56007180,56010448,56018893,56080816,56139508,56148976,56170128,56173445,56296018,56434350,56468247, 55511276,55606966,55699512,55734918,55888549,55950560,55992250,56007321,56010589,56019031,56080984,56139676,56149132,56170170,56173520,56296435,56435147,56468467, 0 ERC2 cmpl cmpl -1,0,0,2,0,2,0,0,0,0,0,0,0,0,0,0,0,-1,
161 6362 6362 16 NM_001320900.2 chr3 - 59747276 61251452 59752225 60536962 10 59747276,59922345,60011370,60014006,60536859,60821918,61042046,61196749,61200616,61251300, 59752321,59922414,60011400,60014152,60536979,60822011,61042099,61196843,61200665,61251452, 0 FHIT cmpl cmpl 0,0,0,1,0,-1,-1,-1,-1,-1,
162 16470 16470 16 NM_001375471.1 chr3 + 61561570 62297609 61562287 62293307 29 61561570,61748877,61989624,62003348,62078162,62132601,62157066,62167970,62191468,62195061,62201504,62203172,62218850,62243806,62255123,62262797,62267409,62267684,62269034,62271382,62272945,62273697,62275872,62276971,62277550,62281562,62282726,62292420,62293160, 61562372,61748982,61989804,62003497,62078258,62132668,62157224,62168163,62191653,62195170,62201554,62203950,62218983,62243898,62255215,62262894,62267492,62267819,62269169,62271555,62273081,62273844,62275966,62277048,62277679,62281709,62282869,62292556,62297609, 0 PTPRG cmpl cmpl 0,1,1,1,0,0,1,0,1,0,1,0,1,2,1,0,1,0,0,0,2,0,0,1,0,0,0,2,0,
163 11573 11573 135 NM_001365903.2 chr3 - 65353525 66038918 65357075 66038308 25 65353525,65359063,65361198,65363464,65364664,65364852,65375744,65379260,65381876,65383531,65387142,65391141,65401438,65429519,65430698,65437154,65439878,65442791,65448021,65453257,65470282,65478591,65493511,65621971,66037995, 65357132,65359152,65361337,65363608,65364725,65364946,65375948,65379554,65382069,65383623,65387226,65391358,65401470,65430140,65430881,65437247,65440012,65442849,65448057,65453340,65470487,65478798,65493631,65622088,66038918, 0 MAGI1 cmpl cmpl 0,1,0,0,2,1,1,1,0,1,1,0,1,1,1,1,2,1,1,2,1,1,1,1,0,
164 19860 19860 17 NM_001252216.2 chr3 + 67991543 68545621 68006626 68544503 5 67991543,68006623,68417279,68538755,68544485, 67991804,68006744,68417420,68538880,68545621, 0 TAFA1 cmpl cmpl -1,0,1,1,0,
165 6533 6533 17 NM_032682.6 chr3 - 70954707 71583978 70959246 71198381 21 70954707,70965889,70970735,70972554,70976940,70977642,70977827,70987993,71000971,71015548,71041327,71046941,71052536,71053635,71112535,71198201,71299819,71359149,71493425,71581548,71583909, 70959391,70966056,70970805,70972676,70977042,70977722,70978029,70988077,71001059,71015653,71041532,71047095,71052626,71053773,71112637,71198392,71299880,71359244,71493555,71581697,71583978, 0 FOXP1 cmpl cmpl 2,0,2,0,0,1,0,0,2,2,1,0,0,0,0,0,-1,-1,-1,-1,-1,
166 17320 17320 18 NM_001128929.3 chr3 + 75906674 77649964 75937493 77646055 27 75906674,75937480,77098013,77477413,77481098,77493243,77522774,77546337,77550817,77557943,77562650,77563166,77564953,77568312,77574498,77577489,77579946,77588750,77595141,77596622,77602209,77607797,77617512,77622226,77634869,77644703,77646053, 75906960,75937602,77098340,77477571,77481219,77493382,77522902,77546462,77550989,77558149,77562732,77563329,77565120,77568434,77574730,77577614,77580118,77588933,77595184,77596750,77602491,77607954,77617773,77622432,77635043,77644904,77649964, 0 ROBO2 cmpl cmpl -1,0,1,1,0,1,2,1,0,1,0,1,2,1,0,1,0,1,1,2,1,1,2,2,1,1,1,
167 17319 17319 18 XM_011533977.3 chr3 - 78597238 79767998 78598912 79589911 32 78597238,78600112,78606732,78614647,78617634,78627320,78631160,78633934,78635772,78639743,78646147,78647628,78651731,78657097,78659685,78661029,78661992,78667882,78668133,78668483,78670095,78685745,78688647,78693347,78714396,78717274,78717762,78746742,78938600,79125455,79589823,79767460, 78598927,78600309,78607041,78614800,78618041,78627569,78631305,78634042,78636108,78639898,78646190,78647655,78651929,78657269,78659807,78661261,78662114,78668049,78668302,78668565,78670301,78685917,78688772,78693356,78714524,78717413,78717883,78746900,78938927,79125539,79589961,79767998, 0 ROBO1 cmpl cmpl 0,1,1,1,2,2,1,1,1,2,1,1,1,0,1,0,1,2,1,0,1,0,1,1,2,1,0,1,1,1,0,-1,
168 2324 2324 19 NM_001381964.1 chr3 + 84958988 86074429 84959607 86066783 11 84958988,84959589,85802046,85883290,85886189,85912372,85935766,85961468,85979163,86065604,86066664, 84959492,84959668,85802196,85883443,85886327,85912543,85935857,85961647,85979283,86065730,86074429, 0 CADM2 cmpl cmpl -1,0,1,1,1,1,1,2,1,1,1,
169 5626 5626 20 XM_017006214.2 chr3 + 96814593 97761532 96866864 97748701 18 96814593,96866824,97226263,97243951,97405149,97448124,97448567,97475351,97479293,97483933,97532357,97592611,97610792,97637872,97720260,97735924,97747422,97748586, 96815008,96866889,97226419,97244287,97405274,97448172,97448730,97475460,97479364,97484059,97532543,97592737,97610854,97638082,97720410,97736118,97747572,97761532, 0 EPHA6 cmpl cmpl -1,0,1,1,1,0,0,1,2,1,1,1,1,0,0,0,2,2,
170 22471 22471 182 NM_001348802.3 chr3 - 114314499 115147288 114339004 114351858 11 114314499,114350273,114380216,114389004,114500351,114693527,114801100,114900303,114974365,115144812,115147218, 114339426,114351878,114380404,114389105,114500391,114693575,114801174,114900342,114974416,115144907,115147288, 0 ZBTB20 cmpl cmpl 1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,
171 11321 11321 22 NM_001318915.2 chr3 - 115802373 116445487 115810316 116445031 9 115802373,115816613,115834561,115841844,115842457,115852482,116019514,116086323,116444876, 115810414,115816646,115834597,115841993,115842578,115852617,116019640,116086556,116445487, 0 LSAMP cmpl cmpl 1,1,1,2,1,1,1,2,0,
172 8998 8998 191 XM_006713813.4 chr3 + 124033368 124726325 124033740 124719470 60 124033368,124227989,124234828,124264497,124268742,124298790,124325979,124329860,124334264,124347142,124384844,124395134,124398696,124413469,124422811,124430655,124434333,124438887,124441944,124446160,124446762,124455176,124456609,124461889,124462523,124474662,124477244,124482807,124488203,124490693,124491322,124492739,124496310,124562842,124632419,124633848,124637207,124650807,124655600,124657447,124657733,124658430,124659364,124660922,124661850,124666448,124667011,124671659,124674360,124678189,124679457,124693803,124694331,124696133,124697592,124699868,124702037,124712934,124717246,124718924, 124033813,124228064,124234943,124264690,124269255,124298913,124326171,124329992,124334495,124347265,124385036,124395304,124398871,124413665,124422978,124430775,124434525,124439037,124442059,124446276,124446885,124455359,124456728,124461956,124462633,124474732,124477334,124482900,124488315,124490884,124491424,124492882,124496413,124563089,124632703,124633953,124637303,124650938,124655667,124657551,124657803,124658517,124659457,124660973,124661928,124666634,124667183,124671898,124674614,124678313,124679517,124693831,124694503,124696255,124697724,124700033,124702116,124713135,124717385,124726325, 0 KALRN cmpl cmpl 0,1,1,2,0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,1,0,0,0,2,0,2,0,0,0,1,0,0,2,0,1,0,0,0,2,0,2,0,0,0,0,0,0,1,0,2,0,0,1,2,1,1,1,2,2,0,
173 3594 3594 25 NM_022131.3 chr3 + 139935184 140577397 139935374 140566253 17 139935184,140175950,140403628,140404557,140421124,140448518,140459520,140466609,140532323,140546514,140556512,140558639,140562137,140562810,140563079,140563960,140566052, 139935483,140176073,140403824,140404766,140421274,140448704,140459769,140466731,140532486,140546681,140556661,140558857,140562308,140562956,140563203,140564145,140577397, 0 CLSTN2 cmpl cmpl 0,1,1,2,1,1,1,1,0,1,0,2,1,1,0,1,0,
174 18750 18750 26 NM_173653.4 chr3 - 143265221 143848468 143266701 143848322 16 143265221,143268874,143363483,143382059,143467036,143493652,143495334,143552361,143574087,143578584,143652254,143693191,143795000,143796825,143832018,143848147, 143266929,143268980,143363563,143382114,143467190,143493764,143495448,143552450,143574193,143578723,143652360,143693307,143795077,143796903,143832221,143848468, 0 SLC9A9 cmpl cmpl 0,2,0,2,1,0,0,1,0,2,1,2,0,0,1,0,
175 8814 8814 3 NM_001197114.2 chr3 + 159069318 159897359 159069432 159896774 10 159069318,159245842,159262547,159764442,159866162,159886206,159887707,159888819,159892096,159896722, 159069441,159245907,159262683,159765138,159866281,159886324,159887905,159888943,159892190,159897359, 0 IQCJ-SCHIP1 cmpl cmpl 0,0,2,0,0,2,0,0,1,2,
176 17814 17814 3 NM_001197108.2 chr3 + 159273243 159897359 159273820 159896774 7 159273243,159866162,159886206,159887707,159888819,159892096,159896722, 159273883,159866281,159886324,159887905,159888943,159892190,159897359, 0 SCHIP1 cmpl cmpl 0,0,2,0,0,1,2,
177 11892 11892 234 XM_005247213.4 chr3 - 169083506 169663712 169084908 169663372 17 169083506,169088999,169089999,169092957,169095075,169100884,169102059,169107925,169112786,169115382,169121055,169122579,169127843,169131428,169143697,169381186,169663335, 169085043,169089183,169090236,169093102,169095245,169100962,169102226,169107952,169112874,169116739,169121212,169122727,169128060,169131531,169143832,169381524,169663712, 0 MECOM cmpl cmpl 0,2,2,1,2,2,0,0,2,1,0,2,1,0,0,1,0,
178 13299 13299 29 XM_047447712.1 chr3 + 173395951 174294372 173604598 174281303 6 173395951,173604278,173807679,174275314,174278860,174280480, 173396227,173605091,173807832,174275500,174279650,174294372, 0 NLGN1 cmpl cmpl -1,0,1,1,1,2,
179 12817 12817 29 XM_017006080.3 chr3 + 174440981 175810548 175096797 175803203 15 174440981,174737640,175096789,175233930,175256410,175324174,175447228,175463400,175466978,175471638,175576040,175627290,175737305,175755219,175803004, 174441032,174737746,175097291,175234204,175256530,175324325,175447372,175463493,175467184,175471758,175576187,175627386,175737399,175755418,175810548, 0 NAALADL2 cmpl cmpl -1,-1,0,2,0,0,1,1,1,0,0,0,0,1,2,
180 11178 11178 31 NM_001387672.1 chr3 + 188153020 188890671 188406120 188874479 10 188153020,188406111,188484591,188524664,188609160,188708266,188760112,188866199,188872642,188874350, 188153363,188406313,188484704,188524787,188609844,188708393,188760282,188866378,188872763,188890671, 0 LPP cmpl cmpl -1,0,1,0,0,0,1,0,2,0,
181 6322 6322 256 NM_004113.6 chr3 - 192139389 192727541 192144008 192727193 6 192139389,192170457,192335360,192360427,192727180,192727483, 192144127,192170656,192335464,192360538,192727323,192727541, 0 FGF12 cmpl cmpl 1,0,1,1,0,-1,
182 19052 19052 9 NM_020777.3 chr4 + 7192537 7742827 7192646 7740264 27 7192537,7396287,7531529,7638327,7654133,7661499,7664352,7667123,7676049,7682742,7689485,7697197,7703279,7704176,7712732,7714239,7715182,7718011,7723696,7725153,7726779,7728349,7729586,7733321,7734271,7737068,7740199, 7193126,7396355,7531629,7638492,7654207,7661564,7664471,7667213,7676229,7682889,7689588,7697274,7703371,7704284,7712853,7714373,7715311,7718183,7723883,7725287,7726903,7728462,7729712,7733421,7734374,7737172,7742827, 0 SORCS2 cmpl cmpl 0,0,2,0,0,2,1,0,0,0,0,1,0,2,2,0,2,2,0,1,0,1,0,0,1,2,1,
183 9084 9084 11 NM_147182.4 chr4 - 20728605 21948772 20730081 20850644 9 20728605,20732005,20732680,20734627,20749661,20758820,20850542,21762920,21948570, 20730129,20732068,20732785,20734735,20749732,20758890,20850667,21763032,21948772, 0 KCNIP4 cmpl cmpl 0,0,0,0,1,0,0,-1,-1,
184 15734 15734 11 NM_001330751.2 chr4 - 23792020 24472905 23795821 24091536 15 23792020,23801729,23802223,23812746,23813020,23813689,23824279,23824462,23828399,23829462,23831556,23884751,24091467,24258202,24472374, 23795925,23801881,23802345,23812867,23813125,23814605,23824353,23824508,23828604,23829585,23831751,23884931,24091635,24258267,24472905, 0 PPARGC1A cmpl cmpl 1,2,0,2,2,1,2,1,0,0,0,0,0,-1,-1,
185 388 388 16 NM_001387542.1 chr4 + 61200325 62078335 61497293 62070908 22 61200325,61497120,61587226,61676825,61732753,61813808,61892655,61895730,61909559,61912718,61934839,61935922,61946913,61948099,61979679,61983382,61996290,61998173,62031441,62037730,62044452,62070108, 61201765,61497348,61587440,61676935,61733554,61813889,61892958,61895834,61909745,61912757,61935023,61936045,61947122,61948276,61979772,61983603,61996357,61998265,62031610,62037856,62044549,62078335, 0 ADGRL3 cmpl cmpl -1,0,1,2,1,1,1,1,0,0,0,1,1,0,0,0,2,0,2,0,0,1,
186 3204 3204 18 XM_047449975.1 chr4 + 80321264 80963750 80321434 80963612 8 80321272,80335743,80362753,80583092,80608332,80869992,80944809,80963516, 80321463,80335879,80362884,80583183,80608383,80870135,80944939,80963750, 0 CFAP299 cmpl cmpl 0,2,0,2,0,0,2,0,
187 1049 1049 19 NM_001025616.3 chr4 + 85475149 86002666 85570541 86000722 10 85475149,85570521,85721884,85923647,85942065,85972035,85974887,85977569,85994582,86000478, 85475559,85570721,85721972,85923770,85942273,85972168,85974961,85977691,85995657,86002666, 0 ARHGAP24 cmpl cmpl -1,0,0,1,1,2,0,2,1,2,
188 11673 11673 155 XM_047415964.1 chr4 - 86010404 86594074 86017227 86593945 13 86010404,86029196,86031367,86064265,86067772,86098523,86101051,86101893,86103185,86107222,86159297,86194335,86593909, 86017370,86029274,86031431,86064390,86067955,86098595,86101217,86102032,86103244,86107352,86159467,86194407,86594074, 0 MAPK10 cmpl cmpl 1,1,0,1,1,1,0,2,0,2,0,0,0,
189 2782 2782 19 XM_047415679.1 chr4 + 90127393 91605295 90308284 91599057 10 90127393,90308243,90312862,90400035,90468233,90628024,90723913,90815761,91085949,91598571, 90127831,90309608,90313047,90400129,90468354,90628232,90723991,90815845,91085994,91605295, 0 CCSER1 cmpl cmpl -1,0,1,0,1,2,0,0,0,0,
190 7471 7471 20 XM_047450133.1 chr4 + 92303965 93810456 92304656 93806873 16 92303965,92590130,93084994,93110747,93207403,93216737,93224613,93238370,93395606,93422770,93455661,93490638,93515215,93626268,93769209,93806714, 92304744,92590286,93085279,93110953,93207457,93216911,93224775,93238490,93395708,93422968,93455974,93490777,93515411,93626435,93769450,93810456, 0 GRID2 cmpl cmpl 0,1,1,1,0,0,0,0,0,0,0,1,2,0,2,0,
191 19589 19589 20 XM_011531886.4 chr4 - 97441248 98143476 97448750 98143150 14 97441248,97448739,97712698,97840772,97943896,97972279,97981158,97986885,98105952,98109192,98128427,98132444,98134346,98143041, 97441534,97448888,97712814,97840932,97944007,97972440,97981318,97986993,98106064,98109305,98128592,98132603,98134459,98143476, 0 STPG2 cmpl cmpl -1,0,1,0,0,1,0,0,2,0,0,0,1,0,
192 742 742 22 NM_001386187.2 chr4 + 112705621 113383736 112706145 113381471 43 112705621,113174415,113196367,113199010,113232160,113236986,113240484,113242110,113249763,113255734,113258049,113258312,113264896,113274451,113277836,113278459,113282674,113287604,113288387,113292415,113293439,113302766,113311254,113317706,113318516,113330245,113333053,113335845,113336576,113339225,113341687,113343016,113345899,113348275,113350227,113360822,113363337,113365038,113367565,113369513,113373089,113373284,113381456, 112706217,113174517,113196466,113199109,113232259,113237172,113240583,113242209,113249862,113255932,113258148,113258411,113264995,113274649,113277935,113278558,113282872,113287703,113288486,113292514,113293538,113302839,113311399,113317809,113318620,113330470,113333208,113336057,113336781,113339322,113341916,113343142,113346022,113348308,113350249,113360897,113363469,113365182,113367851,113369805,113373173,113373449,113383736, 0 ANK2 cmpl cmpl 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,2,2,1,0,1,2,0,0,0,0,1,1,1,1,2,0,0,0,
193 8737 8737 3 XM_047416356.1 chr4 - 142023159 142846535 142028781 142431259 27 142023159,142082030,142086143,142108092,142112541,142122127,142123291,142124587,142145839,142160357,142173631,142193086,142208424,142208895,142237863,142260491,142270662,142305457,142314711,142402937,142405205,142429172,142431168,142462662,142725838,142754013,142846208, 142028914,142082185,142086256,142108190,142112682,142122245,142123415,142124760,142145996,142160561,142173809,142193195,142208529,142209026,142238011,142260564,142270774,142305537,142314762,142403054,142405324,142429217,142431385,142462726,142725901,142754132,142846535, 0 INPP4B cmpl cmpl 2,0,1,2,2,1,0,1,0,0,2,1,1,2,1,0,2,0,0,0,1,1,0,-1,-1,-1,-1,
194 11183 11183 3 XM_005263373.4 chr4 - 150264434 151015727 150265721 151014642 58 150264434,150277852,150282449,150285932,150302624,150310228,150315560,150321190,150325808,150349991,150415437,150435588,150436723,150467672,150471623,150487731,150490917,150588047,150590712,150597082,150599006,150683550,150735257,150761782,150798080,150806270,150808319,150817123,150828179,150831816,150844099,150844657,150848817,150849421,150850723,150851884,150867670,150868181,150870524,150871344,150872662,150893051,150896393,150897738,150900048,150905837,150906296,150908333,150908659,150914194,150915607,150916400,150916616,150921197,150928515,150928833,151014426,151015472, 150265812,150278004,150282646,150286034,150302792,150310384,150315623,150321383,150325898,150350159,150415590,150435708,150436864,150467785,150471739,150487834,150491035,150588184,150590859,150597115,150599131,150683717,150735366,150761847,150798142,150806404,150808398,150817257,150828621,150831976,150844207,150844779,150848998,150849575,150850902,150852943,150867863,150868305,150870606,150871453,150872755,150893149,150896456,150897818,150900217,150905990,150906405,150908467,150908857,150914341,150915727,150916527,150916738,150921293,150928616,150929065,151014861,151015727, 0 LRBA cmpl cmpl 2,0,1,1,1,1,1,0,0,0,0,0,0,1,2,1,0,1,1,1,2,0,2,0,1,2,1,2,1,0,0,1,0,2,0,0,2,1,0,2,2,0,0,1,0,0,2,0,0,0,0,2,0,0,1,0,0,-1,
195 6605 6605 28 NM_020116.5 chr4 - 161383896 162164000 161385746 162111396 16 161383896,161455003,161459211,161481019,161500015,161510397,161538165,161542531,161587454,161656327,161759410,161775877,161920403,162033624,162111270,162163614, 161386449,161455128,161459319,161481169,161500134,161510424,161538300,161542693,161587575,161656494,161759531,161776074,161920652,162033658,162111412,162164000, 0 FSTL5 cmpl cmpl 2,0,0,0,1,1,1,1,0,1,0,1,1,0,0,-1,
196 11701 11701 28 XM_017008335.2 chr4 - 163524297 164384019 163528747 163988599 8 163524297,163545595,163585748,163613313,163700812,163988500,164111587,164383186, 163529046,163545743,163585929,163613393,163700863,163988709,164111662,164384019, 0 MARCHF1 cmpl cmpl 1,0,2,0,0,0,-1,-1,
197 6768 6768 29 NM_001034845.3 chr4 + 171813403 173041559 171814580 173040100 13 171813403,171814411,172229655,172311613,172348522,172809360,172813539,172882789,172931160,172952036,173009177,173021475,173039932, 171813990,171814718,172229764,172311752,172348689,172809546,172813723,172882907,172931268,172952258,173009294,173021625,173041559, 0 GALNTL6 cmpl cmpl -1,0,0,1,2,1,1,2,0,0,0,0,0,
198 20213 20213 30 XM_047415944.1 chr4 + 181447612 182803024 182324020 182800351 30 181447612,181739486,181867751,182041663,182323945,182600923,182628650,182653770,182673004,182679665,182680247,182680542,182681813,182688165,182714086,182728964,182730199,182730877,182736807,182738400,182743169,182751799,182753449,182754384,182773471,182774917,182789092,182792273,182796636,182799595, 181447772,181739649,181867832,182041743,182324252,182601161,182628889,182653893,182673219,182679876,182680349,182680737,182682014,182688351,182714233,182729181,182730319,182731139,182737075,182738544,182743419,182752032,182753604,182755259,182773647,182775153,182789389,182793885,182796767,182803024, 0 TENM3 cmpl cmpl -1,-1,-1,-1,0,1,2,1,1,0,1,1,1,1,1,1,2,2,0,1,1,2,1,0,2,1,0,0,1,0,
199 4205 4205 10 XM_005248251.4 chr5 - 10971835 11904446 10973452 11903853 23 10971835,10981772,10988110,10992550,11017973,11022768,11082695,11083880,11098574,11110857,11117449,11159575,11199447,11236690,11346371,11364695,11384664,11397030,11411535,11412034,11564943,11732135,11903816, 10973713,10981846,10988242,10992677,11018058,11022979,11082846,11083955,11098748,11111043,11117567,11159759,11199661,11236823,11346627,11364890,11385229,11397203,11411652,11412069,11565056,11732272,11904446, 0 CTNND2 cmpl cmpl 0,1,1,0,2,1,0,0,0,0,2,1,0,2,1,1,0,1,1,2,0,1,0,
200 2949 2949 11 NM_001349558.2 chr5 - 19471295 20575713 19473225 19838986 16 19471295,19483300,19502991,19520656,19543868,19571578,19591056,19612433,19721346,19746941,19838758,19981059,19991872,20255443,20338091,20575461, 19473716,19483552,19503109,19520778,19544005,19571832,19591244,19612601,19721466,19747236,19839242,19981178,19992014,20255505,20338239,20575713, 0 CDH18 cmpl cmpl 1,1,0,1,2,0,1,1,1,0,0,-1,-1,-1,-1,-1,
201 2944 2944 11 XM_047416602.1 chr5 - 21750672 22853344 21751736 22078676 17 21750672,21755590,21760557,21764977,21783357,21802166,21816944,21842160,21854670,21975090,22078445,22172340,22212497,22405256,22505269,22810616,22853057, 21752236,21755842,21760675,21765099,21783494,21802420,21817132,21842328,21854790,21975385,22078862,22172409,22212643,22405351,22505364,22810709,22853344, 0 CDH12 cmpl cmpl 1,1,0,1,2,0,1,1,1,0,0,-1,-1,-1,-1,-1,-1,
202 14958 14958 16 XM_024446110.2 chr5 - 58969037 60522128 58974663 60185598 18 58969037,58975656,58976349,58977190,58988492,58989754,58990803,58991831,58993371,59038858,59180594,59185188,59193499,59215776,59988487,60147747,60185556,60522050, 58975080,58975839,58976472,58977345,58988592,58989919,58990902,58992004,58993465,59038971,59180644,59185262,59193536,59215968,59988717,60147894,60185687,60522128, 0 PDE4D cmpl cmpl 0,0,0,1,0,0,0,1,0,1,2,0,2,2,0,0,0,-1,
203 11745 11745 0 NM_001393525.1 chr5 + 66596392 67169593 66596655 67167051 28 66596392,66759708,66788669,66899950,67054403,67090161,67095596,67100434,67102535,67104365,67110097,67114086,67118681,67121016,67130209,67131812,67133513,67134522,67136562,67142114,67142420,67144668,67145143,67152636,67153457,67160455,67162606,67163146, 66597018,66759862,66788794,66899982,67054492,67090231,67095675,67100592,67102611,67104575,67110199,67114219,67118749,67121102,67130418,67131951,67133646,67134688,67136664,67142237,67142533,67144796,67145379,67152866,67153580,67160592,67162788,67169593, 0 MAST4 cmpl cmpl 0,0,1,0,2,1,2,0,2,0,0,0,1,0,2,1,2,0,1,1,1,0,2,1,0,0,2,1,
204 390 390 159 XM_017009967.2 chr5 + 90558796 91164437 90558895 91163900 89 90558796,90614834,90617803,90622596,90625129,90627210,90628561,90629209,90635113,90637724,90642635,90642855,90643802,90644705,90645967,90647497,90651603,90652345,90653208,90657904,90672545,90674053,90675242,90676079,90679548,90681314,90683585,90685779,90689860,90690796,90692604,90693889,90696936,90703664,90704388,90705378,90706230,90708815,90710980,90711183,90712286,90716466,90720047,90720934,90724831,90725085,90725548,90728668,90729641,90745045,90745590,90750550,90753573,90754982,90756453,90756978,90759408,90763304,90774185,90776452,90777904,90778426,90778864,90781429,90783123,90783837,90788070,90789701,90790872,90802738,90805283,90807601,90810232,90815618,90823424,90828943,90840577,90848636,90853283,90854061,90855740,90863756,90965414,90985343,91072446,91102218,91150029,91153220,91163781, 90558917,90615019,90617953,90622701,90625243,90627776,90628832,90629539,90635290,90637948,90642762,90643041,90643983,90644869,90646091,90647764,90651730,90652563,90653952,90658278,90672722,90674234,90675445,90676209,90679629,90681454,90684195,90685995,90690076,90691041,90692786,90694701,90697146,90703795,90704488,90705579,90706394,90708909,90711059,90711322,90712428,90716729,90720223,90721059,90724989,90725232,90725656,90728933,90729764,90745265,90745795,90750697,90753829,90755185,90756630,90757161,90759588,90763469,90774303,90776576,90778043,90778609,90779097,90781578,90783325,90784057,90788310,90789851,90791346,90802882,90805458,90807737,90811338,90815736,90823596,90829186,90840985,90848821,90853533,90854201,90855901,90863857,90965531,90985522,91072604,91102340,91150221,91153398,91164437, 0 ADGRV1 cmpl cmpl 0,1,0,0,0,0,2,0,0,0,2,0,0,1,0,1,1,2,1,1,0,0,1,0,1,1,0,1,1,1,0,2,1,1,0,1,1,0,1,2,0,1,0,2,1,0,0,0,1,1,2,0,0,1,0,0,0,0,0,1,2,0,0,2,1,2,0,0,0,0,0,1,2,1,2,0,0,0,2,0,2,1,0,0,2,1,0,0,1,
205 11854 11854 163 NM_024717.7 chr5 - 94703689 95285094 94707495 95284575 23 94703689,94708511,94710817,94714776,94779109,94799012,94868332,94870416,94870871,94871314,94873138,94888878,94894648,94909250,94912805,94917895,94923961,94931952,94940083,94942347,94953218,95017366,95283855, 94707567,94708609,94710927,94714886,94779163,94799132,94868452,94870491,94870973,94871417,94873241,94888972,94894835,94909381,94912976,94917973,94924021,94931991,94940195,94942427,94953361,95017484,95285094, 0 MCTP1 cmpl cmpl 0,1,2,0,0,0,0,0,0,2,1,0,2,0,0,0,0,0,2,0,1,0,0,
206 2462 2462 20 NM_001423255.1 chr5 + 95961428 96774683 96722677 96771679 31 95961428,96379565,96675538,96695835,96722638,96727488,96729152,96729611,96730779,96736171,96737848,96740037,96741265,96741493,96742654,96746341,96747344,96748517,96750586,96754059,96754657,96757443,96757582,96762273,96765220,96766052,96767437,96767906,96770530,96771643,96772639, 95961586,96379652,96675601,96695907,96722698,96727530,96729209,96729725,96730860,96736240,96737947,96740118,96741358,96741580,96742756,96746425,96747392,96748613,96750682,96754161,96754741,96757494,96757654,96762372,96765325,96766145,96767482,96767999,96770602,96771702,96774683, 0 CAST cmpl cmpl -1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,
207 6175 6175 21 NM_001163315.3 chr5 - 107859034 108382098 107861719 108381691 9 107859034,107881036,108020924,108186116,108224120,108348398,108364737,108367830,108380698, 107861860,107881179,108021001,108186247,108224228,108348530,108364995,108367953,108382098, 0 FBXL17 cmpl cmpl 0,1,2,0,0,0,0,0,0,
208 6604 6604 200 XM_011543283.2 chr5 - 133196454 133842067 133199094 133603983 16 133196454,133201932,133210190,133217228,133220747,133224189,133225149,133225657,133233416,133249409,133312653,133316458,133400737,133567185,133603857,133841951, 133199797,133202042,133210298,133217378,133220866,133224216,133225284,133225819,133233537,133249576,133312777,133316652,133400986,133567219,133603993,133842067, 0 FSTL4 cmpl cmpl 2,0,0,0,1,1,1,1,0,1,0,1,1,0,0,-1,
209 19287 19287 25 NM_004598.4 chr5 - 136975297 137499326 136978653 137498558 11 136975297,136979331,136985139,136988421,136992483,137067714,137112434,137140579,137267009,137498372,137499178, 136978844,136979469,136985202,136988643,136992600,137067829,137112561,137140694,137267055,137498558,137499326, 0 SPOCK1 cmpl cmpl 1,1,1,1,1,0,2,1,0,0,-1,
210 18143 18143 27 XM_047417519.1 chr5 + 155727831 156767788 156329576 156759390 11 155727831,155870343,156123855,156329533,156344488,156508600,156589230,156594931,156647463,156757580,156759216, 155728990,155870424,156124019,156329579,156344677,156508702,156589318,156595051,156647536,156757704,156767788, 0 SGCD cmpl cmpl -1,-1,-1,0,0,0,0,1,1,2,0,
211 20212 20212 3 XM_047417419.1 chr5 + 166979028 168264157 167284837 168262810 29 166979028,167073241,167284763,167375197,167952587,167992943,168047426,168062059,168090573,168098025,168118291,168124849,168126753,168162610,168190336,168195175,168198852,168199863,168203688,168204371,168215039,168216767,168218124,168226087,168227894,168244419,168246756,168260282,168262048, 166979523,167073356,167285063,167375473,167952822,167993182,168047549,168062265,168090769,168098127,168118486,168125050,168126966,168162757,168190547,168195295,168199114,168200131,168203832,168204621,168215272,168216922,168218999,168226263,168228130,168244716,168248371,168260413,168264157, 0 TENM2 cmpl cmpl -1,-1,0,1,1,2,1,1,0,1,1,1,1,1,1,2,2,0,1,1,2,1,0,2,1,0,0,1,0,
212 18780 18780 29 NM_001271946.2 chr5 - 168661739 169301139 168666453 169300709 36 168661739,168669782,168671197,168673176,168683965,168685686,168686978,168692606,168696291,168700581,168707975,168710894,168712282,168722255,168722932,168724415,168748301,168749471,168752954,168753863,168760861,168762538,168772780,168774234,168785906,168789559,168795506,168806445,168817299,168823259,168844583,168883264,169193478,169244704,169251387,169300512, 168666689,168669991,168671483,168673331,168684096,168685927,168687116,168692700,168696431,168700679,168708121,168711058,168712354,168722327,168723004,168724484,168748434,168749635,168753098,168754007,168760936,168762689,168772944,168774378,168785978,168789631,168795578,168806587,168817463,168823331,168844655,168883336,169193550,169244776,169251459,169301139, 0 SLIT3 cmpl cmpl 1,2,1,2,0,2,2,1,2,0,1,2,2,2,2,2,1,2,2,2,2,1,2,2,2,2,2,1,2,2,2,2,2,2,2,0,
213 7075 7075 9 NM_001500.4 chr6 - 1623805 2245605 1624168 2245422 11 1623805,1624471,1726415,1742467,1930102,1959866,1960773,2115770,2117468,2124686,2245320, 1624231,1624540,1726512,1742586,1930230,1959971,1960966,2115880,2117556,2124731,2245605, 0 GMDS cmpl cmpl 0,0,2,0,1,1,0,1,0,0,0,
214 15141 15141 85 NM_001322308.3 chr6 + 12716766 13287837 12718744 13287078 14 12716766,12718698,12749643,13053364,13160203,13182518,13205814,13227815,13230036,13272859,13278267,13283421,13286145,13287062, 12716896,12718847,12749790,13053529,13160284,13182686,13206136,13228063,13230193,13272915,13278329,13283562,13286222,13287837, 0 PHACTR1 cmpl cmpl -1,0,1,1,1,1,1,2,1,2,1,0,0,2,
215 3004 3004 11 XM_011514718.1 chr6 + 20534456 21232404 20546350 21231039 15 20534456,20535350,20546345,20548592,20649292,20739518,20758594,20781144,20846074,20955418,21000226,21065047,21198020,21201109,21230847, 20534574,20535394,20546523,20548705,20649377,20739615,20758643,20781265,20846178,20955585,21000372,21065228,21198104,21201274,21232404, 0 CDKAL1 cmpl cmpl -1,-1,0,2,1,2,0,1,2,1,0,2,0,0,0,
216 15616 15616 14 NM_001318876.2 chr6 + 43517088 44461400 43517109 44461379 11 43517088,43517305,43519332,43519705,43520065,43520274,43520624,43520931,43529248,44441889,44461319, 43517178,43517377,43519440,43519838,43520185,43520427,43520774,43521048,43529271,44441913,44461400, 0 POLR1C cmpl cmpl 0,0,0,0,1,1,1,1,1,0,0,
217 19680 19680 14 NM_181356.3 chr6 - 44826725 45377934 44829815 45322916 13 44826725,44932652,44953309,44954494,44961752,45003652,45014800,45020545,45105921,45321795,45322878,45365200,45377767, 44829857,44932763,44953417,44954607,44961828,45003792,45014891,45020632,45106006,45321891,45322967,45365301,45377934, 0 SUPT3H cmpl cmpl 0,0,0,1,0,1,0,0,2,2,0,-1,-1,
218 9203 9203 16 NM_001350622.2 chr6 - 61679960 62286225 61680962 62285948 10 61679960,61697194,61732681,61816954,61894634,61901243,61978065,62047877,62177184,62285857, 61681060,61697253,61732764,61817005,61894833,61901371,61978212,62047994,62177312,62286225, 0 KHDRBS2 cmpl cmpl 1,2,0,0,2,0,0,0,1,0,
219 5841 5841 16 NM_001292009.2 chr6 - 63719979 65707226 63720595 65495410 44 63719979,63726518,63741912,63762460,63778005,63788104,63789057,63806189,63864185,63984382,63999074,64066337,64081855,64230591,64306969,64388689,64436173,64439161,64590222,64593116,64617417,64626120,64813377,64821644,64822650,64886696,64902112,64902403,64912483,64945792,64997581,65057613,65295862,65334979,65344037,65353457,65384385,65402477,65405173,65490593,65494662,65495858,65639777,65707134, 63721797,63726680,63741975,63762633,63778180,63788249,63789224,63806372,63864358,63984603,63999183,64066491,64082002,64230824,64307082,64388840,64436265,64439352,64591989,64593309,64617533,64626245,64813577,64821723,64822822,64886842,64902220,64902500,64912743,64945914,64997703,65057727,65296119,65335146,65344177,65353617,65384500,65402605,65405367,65490707,65495607,65495993,65639892,65707226, 0 EYS cmpl cmpl 1,1,1,2,1,0,1,1,2,0,2,1,1,2,0,2,0,1,1,0,1,2,0,2,1,2,2,1,2,0,1,1,2,0,1,0,2,0,1,1,0,-1,-1,-1,
220 367 367 17 NM_001704.3 chr6 + 68635281 69389506 68638675 69388891 32 68635281,68637390,68638660,68930558,68936518,68943829,68956023,68956644,68974762,68975233,68993767,69014037,69018390,69048184,69049270,69062933,69075994,69233289,69235031,69239123,69324871,69327819,69330505,69332922,69338915,69339332,69354232,69355820,69360868,69372405,69382830,69388702, 68636000,68637562,68639432,68930669,68936680,68943994,68956188,68956809,68974864,68975340,68993962,69014106,69018499,69048334,69049346,69063036,69076038,69233416,69235135,69239226,69325022,69327889,69330572,69333008,69339014,69339504,69354328,69355860,69361512,69372441,69382935,69389506, 0 ADGRB3 cmpl cmpl -1,-1,0,1,1,1,1,1,1,1,0,0,0,1,1,2,0,2,0,2,0,1,2,0,2,2,0,0,1,0,0,0,
221 9132 9132 142 XM_047419077.1 chr6 + 72622063 73198853 72622189 73195414 12 72622063,73003907,73041935,73077321,73077761,73111307,73120482,73133420,73169745,73190572,73192564,73194451, 72622587,73003998,73042062,73077497,73077887,73111403,73120577,73133641,73169854,73190704,73192691,73198853, 0 KCNQ5 cmpl cmpl 0,2,0,1,0,0,0,2,1,2,2,0,
222 7475 7475 21 NM_021956.5 chr6 + 101393707 102070083 101399277 102068511 17 101393707,101398984,101621948,101626379,101676622,101682552,101686179,101799647,101802330,101818369,101859286,101889639,101924600,101928414,102035340,102055329,102068346, 101393837,101399392,101622116,101626637,101676804,101682606,101686353,101799791,101802438,101818483,101859493,101889863,101924719,101928632,102035566,102055580,102070083, 0 GRIK2 cmpl cmpl -1,0,1,1,1,0,0,0,0,0,0,0,2,1,0,1,0,
223 13268 13268 23 XM_017010318.3 chr6 + 123803864 124825640 123804200 124823229 6 123803864,124283004,124658185,124791338,124818386,124823219, 123804254,124283142,124658386,124791399,124818468,124825640, 0 NKAIN2 cmpl cmpl 0,0,0,0,1,2,
224 16473 16473 195 NM_001291981.2 chr6 - 127968784 128520599 127970226 128520358 33 127968784,127973021,127973663,127976656,127976922,127981115,127982830,127983241,127985720,127990768,127991293,127992672,127995248,127995461,127996900,127998719,128001195,128003196,128005083,128009129,128064757,128067518,128078812,128082436,128083714,128089689,128184431,128218921,128240034,128242520,128322038,128397565,128520258, 127970280,127973157,127973827,127976782,127977054,127981289,127982980,127983377,127985875,127990885,127991391,127992709,127995266,127995538,127996988,127998904,128001207,128003232,128005244,128009268,128064794,128067792,128078918,128082638,128083824,128089992,128184725,128219096,128240150,128242602,128322310,128397688,128520599, 0 PTPRK cmpl cmpl 0,2,0,0,0,0,0,2,0,0,1,0,0,1,0,1,1,1,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,
225 10051 10051 24 NM_001079823.2 chr6 + 128883137 129516566 128883245 129516347 64 128883137,129049917,129059783,129098172,129143900,129146958,129148978,129154504,129165575,129177705,129190204,129192679,129250111,129252083,129260710,129267105,129270623,129280060,129287846,129291613,129297684,129300735,129312860,129314654,129315475,129315761,129316037,129320537,129328277,129342342,129349297,129353163,129366218,129369891,129383121,129391490,129393044,129401223,129402323,129403820,129427751,129438645,129440815,129443062,129445666,129452987,129454154,129456334,129460199,129464289,129465144,129473213,129478692,129481262,129486473,129491900,129492314,129502658,129503090,129505199,129507488,129512362,129514372,129516189, 128883357,129050088,129059896,129098415,129144080,129147048,129149096,129154683,129165675,129177866,129190345,129192853,129250213,129252295,129260822,129267219,129270751,129280147,129288058,129291720,129297865,129300872,129313097,129314798,129315655,129315950,129316171,129320655,129328412,129342467,129349384,129353357,129366361,129369990,129383233,129391653,129393255,129401340,129402487,129403959,129427854,129438762,129440998,129443068,129445821,129453131,129454288,129456494,129460324,129464452,129465289,129473352,129478813,129481439,129486622,129492077,129492483,129502771,129503280,129505355,129507642,129512493,129514595,129516566, 0 LAMA2 cmpl cmpl 0,1,1,0,0,0,0,1,0,1,0,0,0,0,2,0,0,2,2,1,0,1,0,0,0,0,0,2,0,0,2,2,1,0,0,1,2,0,0,2,0,1,1,1,1,0,0,2,0,2,0,1,2,0,0,2,2,0,2,0,0,1,0,1,
226 21962 21962 26 NM_007124.3 chr6 + 144285334 144853034 144291828 144850997 75 144285334,144291736,144403122,144421877,144423548,144423985,144426286,144428777,144429580,144435934,144437564,144438744,144440351,144444280,144447210,144447601,144448599,144451369,144453781,144458769,144459173,144461196,144462653,144473719,144474603,144479811,144482208,144485384,144487547,144488672,144490070,144490928,144493300,144499256,144510943,144513908,144514649,144516228,144516810,144521979,144523015,144531051,144533084,144537581,144539293,144542794,144548639,144550964,144554687,144557156,144577098,144678405,144700086,144730356,144748245,144751805,144754719,144757928,144771906,144774289,144781921,144789193,144793833,144797823,144803035,144820881,144827347,144827610,144828789,144835779,144836300,144839172,144840739,144846804,144850988, 144285821,144291907,144403184,144421970,144423626,144424078,144426459,144428893,144429741,144436138,144437746,144438895,144440471,144444382,144447318,144447781,144448769,144451493,144453869,144459011,144459354,144461342,144462866,144473833,144474759,144479982,144482388,144485519,144487697,144488834,144490199,144491102,144493456,144499427,144511123,144514037,144514820,144516387,144516948,144522171,144523188,144531202,144533260,144537717,144539443,144542870,144548854,144551082,144554893,144557311,144577288,144678578,144700243,144730486,144748514,144751952,144754798,144757989,144771968,144774364,144782123,144789279,144793991,144797990,144803147,144821018,144827386,144827676,144828855,144835938,144836541,144839284,144840832,144846827,144853034, 0 UTRN cmpl cmpl -1,0,1,0,0,0,0,2,1,0,0,2,0,0,0,0,0,2,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,2,0,0,1,0,1,0,2,0,2,0,1,0,0,1,2,1,1,2,1,0,2,0,2,2,2,2,2,0,1,1,0,
227 16072 16072 28 NM_004562.3 chr6 - 161347416 162727766 161350098 162727668 12 161347416,161360087,161386793,161548853,161569354,161785771,161973301,162054090,162201130,162262524,162443309,162727661, 161350211,161360205,161386877,161549003,161569416,161785908,161973417,162054174,162201252,162262765,162443473,162727766, 0 PRKN cmpl cmpl 1,0,0,0,1,2,0,0,1,0,1,0,
228 14617 14617 228 NM_001080378.2 chr6 + 162727131 163315500 162728235 163314987 6 162727131,162728159,162814146,163062149,163089258,163314826, 162727279,162728391,162814281,163062321,163089408,163315500, 0 PACRG cmpl cmpl -1,0,0,0,1,1,
229 14946 14946 28 XM_017010194.3 chr6 - 165327288 165988052 165333121 165910865 24 165327288,165336122,165339277,165343390,165379193,165388297,165392645,165395180,165396316,165413500,165416188,165418634,165428657,165430286,165431421,165432973,165435236,165448927,165450241,165482314,165543439,165711018,165910807,165986107, 165333127,165336215,165339358,165343502,165379366,165388453,165392796,165395264,165396459,165413687,165416281,165418777,165428709,165430345,165431472,165433129,165435377,165448977,165450362,165482343,165543568,165711153,165910932,165988052, 0 PDE10A cmpl cmpl 0,0,0,2,0,0,2,2,0,2,2,0,2,0,0,0,0,1,0,1,1,1,0,-1,
230 16474 16474 73 NM_001291981.2 chr6_KI270801v1_alt - 313982 869933 315424 869692 33 313982,318219,318861,321854,322120,326313,328028,328439,330918,335966,336491,337870,340446,340659,342098,343917,346393,348394,350281,358462,414091,416852,428146,431770,433048,439023,533765,568255,589368,591854,671372,746899,869592, 315478,318355,319025,321980,322252,326487,328178,328575,331073,336083,336589,337907,340464,340736,342186,344102,346405,348430,350442,358601,414128,417126,428252,431972,433158,439326,534059,568430,589484,591936,671644,747022,869933, 0 PTPRK cmpl cmpl 0,2,0,0,0,0,0,2,0,0,1,0,0,1,0,1,1,1,2,1,0,2,1,0,1,1,1,0,1,0,1,1,0,
231 17898 17898 9 NM_152744.4 chr7 + 3301251 4269000 3301586 4265384 45 3301251,3619079,3639003,3641957,3821449,3950922,3951729,3958930,3962656,3967317,3969256,3971465,3974368,3987185,4010965,4012094,4017170,4049347,4051637,4067837,4076997,4079462,4110662,4113288,4114036,4127380,4129907,4132324,4145721,4149261,4158447,4161785,4174221,4175774,4178484,4205878,4208098,4210024,4220108,4221238,4233254,4237646,4241792,4245675,4265123, 3301884,3619239,3639110,3642105,3821583,3951034,3951920,3959014,3962851,3967434,3969424,3971568,3974545,3987322,4011113,4012235,4017352,4049463,4051830,4067936,4077189,4079584,4110772,4113439,4114274,4127496,4130097,4132423,4145916,4149463,4158551,4161856,4174357,4175834,4178586,4205994,4208285,4210162,4220270,4221364,4233419,4237784,4241913,4245805,4269000, 0 SDK1 cmpl cmpl 0,1,2,1,2,1,2,1,1,1,1,1,2,2,1,2,2,1,0,1,1,1,0,2,0,1,0,1,1,1,2,1,0,1,1,1,0,1,1,1,1,1,1,2,0,
232 4755 4755 10 XM_011515154.3 chr7 - 14145048 14974858 14149130 14841263 26 14145048,14176838,14178030,14338514,14345300,14478160,14574211,14580861,14583051,14607433,14613339,14621377,14630235,14672928,14682552,14682752,14685244,14694074,14698094,14701680,14718541,14736040,14753927,14757654,14841193,14974695, 14149238,14176899,14178151,14338710,14345391,14478225,14574372,14580951,14583137,14607508,14613413,14621494,14630271,14673027,14682669,14682841,14685362,14694194,14698169,14701730,14718685,14736194,14753948,14757731,14841450,14974858, 0 DGKB cmpl cmpl 0,2,1,0,2,0,1,1,2,2,0,0,0,0,0,1,0,0,0,1,1,0,0,1,0,-1,
233 7833 7833 11 NM_001321868.2 chr7 + 18086824 19002416 18162324 18996062 26 18086824,18162228,18496261,18585280,18590344,18591515,18593907,18634626,18644670,18647784,18648465,18666212,18727579,18749004,18762156,18767105,18793344,18829160,18829460,18835466,18835899,18874477,18935808,18954145,18975805,18996022, 18087213,18162349,18496324,18585522,18590486,18591642,18594029,18634742,18644793,18647998,18648683,18666476,18727757,18749138,18762277,18767155,18793452,18829216,18829548,18835586,18835997,18874596,18935942,18954230,18975953,19002416, 0 HDAC9 cmpl cmpl -1,0,1,1,0,1,2,1,0,0,1,0,0,1,0,1,0,0,2,0,0,2,1,0,1,2,
234 3972 3972 12 NM_182899.5 chr7 + 28299320 28825894 28494929 28819279 10 28299320,28494905,28507615,28570364,28718752,28724221,28804198,28809186,28818070,28819115, 28299441,28494999,28507737,28570537,28718879,28724332,28804522,28809414,28818179,28825894, 0 CREB5 cmpl cmpl -1,0,1,0,2,0,0,0,0,1,
235 14951 14951 103 NM_001322059.2 chr7 - 31616776 32428224 31790245 32428131 18 31783509,31809030,31815923,31823072,31824866,31828291,31837179,31837869,31847967,31850640,31864941,31873291,31877969,31878995,31880746,32169784,32209488,32427821, 31790259,31809108,31816154,31823248,31824987,31828373,31837300,31837971,31848096,31850741,31865082,31873408,31878036,31879178,31880860,32169956,32209539,32428224, 0 PDE1C cmpl cmpl 1,1,1,2,1,0,2,2,2,0,0,0,2,2,2,1,1,0,
236 5490 5490 108 XM_011515654.3 chr7 - 36852905 37449326 36855550 37342690 23 36852905,36861658,36870392,36878009,36887559,36894853,37013298,37096618,37133129,37211385,37213334,37216644,37222614,37224878,37233094,37244355,37259180,37271831,37314849,37315919,37342612,37428790,37448859, 36855751,36861736,36870475,36878117,36887672,36895017,37013435,37096727,37133234,37211517,37213457,37216695,37222693,37225030,37233194,37244391,37259350,37271882,37314922,37315960,37342763,37429756,37449326, 0 ELMO1 cmpl cmpl 0,0,1,1,2,0,1,0,0,0,0,0,2,0,2,2,0,0,2,0,0,-1,-1,
237 19646 19646 111 XM_047420843.1 chr7 + 40135004 40882597 40135020 40881766 14 40135004,40180946,40181954,40188494,40189543,40194939,40237634,40274512,40316759,40449286,40459100,40496283,40749433,40881680, 40135120,40180998,40182028,40188580,40189594,40195060,40237726,40274656,40316855,40449358,40459198,40496386,40749497,40882597, 0 SUGCT cmpl cmpl 0,1,2,1,0,0,1,0,0,0,0,2,0,1,
238 1486 1486 17 XM_047420162.1 chr7 + 69598474 70793506 69599653 70790996 16 69598474,69899285,70118131,70134535,70435751,70698568,70762869,70764754,70766113,70771548,70777102,70781614,70784941,70785954,70787208,70789747, 69599962,69899498,70118233,70134571,70435781,70698620,70763341,70765005,70766334,70771644,70777174,70781756,70785019,70786038,70787431,70793506, 0 AUTS2 cmpl cmpl 0,0,0,0,0,0,1,2,1,0,0,0,1,1,1,2,
239 6756 6756 17 NM_022479.3 chr7 + 71132143 71713599 71132802 71712146 11 71132143,71335549,71388234,71415888,71420907,71571284,71665410,71669971,71677210,71710760,71712017, 71133040,71335733,71388401,71416063,71421105,71571402,71665596,71670109,71677306,71710928,71713599, 0 GALNT17 cmpl cmpl 0,1,2,1,2,2,0,0,0,0,0,
240 2354 2354 17 XM_017012677.2 chr7 - 71779490 72504279 71787774 72504113 6 71779490,71810335,72023656,72106150,72278685,72504111, 71787902,71810492,72023769,72106294,72278810,72504279, 0 CALN1 cmpl cmpl 1,0,1,1,2,0,
241 11575 11575 18 XM_017012840.3 chr7 - 78017054 79453667 78019314 79453320 25 78017054,78026067,78065573,78078946,78125693,78127196,78132888,78135020,78160024,78167915,78178010,78185628,78194873,78201161,78255942,78343777,78345443,78345921,78369155,78489760,78501576,78521429,78627119,79007089,79453019, 78019976,78026104,78065662,78079085,78125837,78127416,78133060,78135206,78160273,78168108,78178102,78185670,78195063,78201193,78256581,78343960,78345572,78346043,78369213,78489840,78501787,78521645,78627239,79007206,79453667, 0 MAGI2 cmpl cmpl 1,0,1,0,0,2,1,1,1,0,1,1,0,1,1,1,1,2,1,2,1,1,1,1,0,
242 17964 17964 153 XM_047419751.1 chr7 - 83955776 84492725 83961370 84194586 21 83955776,83963204,83977131,83981320,83985435,84001954,84005338,84007352,84011021,84011182,84014208,84046323,84060464,84110469,84129122,84134793,84194474,84295041,84307206,84371823,84492459, 83961826,83963347,83977196,83981478,83985477,84002046,84005558,84007497,84011091,84011297,84014351,84046443,84060558,84110589,84129185,84134951,84194668,84295131,84307292,84371900,84492725, 0 SEMA3A cmpl cmpl 0,1,2,0,0,1,0,2,1,0,1,1,0,0,0,1,0,-1,-1,-1,-1,
243 23192 23192 19 NM_181646.5 chr7 + 88759699 89338528 88759976 89337032 4 88759699,89218154,89327343,89333362, 88760084,89218295,89327474,89338528, 0 ZNF804B cmpl cmpl 0,0,0,2,
244 2981 2981 159 NM_001287135.2 chr7 + 90596320 91210590 90596627 91118180 15 90596320,90604217,90726566,90747680,90790572,90863174,90899290,90917600,90955696,90984147,91045896,91079431,91112541,91118064,91207164, 90596718,90604249,90726812,90747775,90790652,90863269,90899353,90917724,90955817,90984241,91045960,91079480,91112681,91118208,91210590, 0 CDK14 cmpl cmpl 0,1,0,0,2,1,0,0,1,2,0,1,2,1,-1,
245 10240 10240 21 NM_199000.3 chr7 + 104328602 104908561 104328779 104906215 3 104328602,104736674,104906186, 104329224,104736911,104908561, 0 LHFPL3 cmpl cmpl 0,1,1,
246 8697 8697 22 XM_047420927.1 chr7 - 110662643 111562492 110663711 111521447 7 110662643,110963499,111417258,111487237,111521312,111532517,111561850, 110663721,110963565,111417342,111487341,111521449,111532585,111562492, 0 IMMP2L cmpl cmpl 2,2,2,0,0,-1,-1,
247 2329 2329 23 XM_017012796.3 chr7 - 122318410 122886460 122320164 122663539 33 122318410,122325476,122345573,122360787,122360929,122379367,122386294,122387025,122388582,122393195,122393440,122407539,122414067,122416060,122436359,122438340,122441511,122451373,122471374,122474380,122480851,122490080,122491311,122513248,122554549,122581178,122615180,122621480,122629247,122663236,122736954,122885393,122885998, 122320338,122325581,122345681,122360820,122361013,122379442,122386309,122387173,122388738,122393315,122393582,122407696,122414076,122416164,122436380,122438464,122441575,122451475,122471562,122474517,122480860,122490281,122491420,122513315,122554689,122581290,122615299,122621717,122629328,122663569,122737068,122885445,122886460, 0 CADPS2 cmpl cmpl 0,0,0,0,0,0,0,2,2,2,1,0,0,1,1,0,2,2,0,1,1,1,0,2,0,2,0,0,0,0,-1,-1,-1,
248 7507 7507 24 NM_001371083.1 chr7 - 126438597 127252941 126439118 127243204 12 126438597,126446125,126532951,126609361,126769864,126902541,126903971,126904547,127106495,127242694,127248219,127252796, 126439168,126446372,126533887,126609498,126770065,126902679,126904126,126904683,127106712,127243515,127248323,127252941, 0 GRM8 cmpl cmpl 1,0,0,1,1,1,2,1,0,0,-1,-1,
249 15509 15509 199 XM_047421017.1 chr7 - 132123339 132648688 132130478 132508693 33 132123339,132133048,132140598,132145118,132146509,132147899,132148542,132159472,132164141,132165133,132168303,132174777,132179686,132180585,132181380,132182096,132185298,132187470,132194061,132198484,132202645,132203322,132210942,132223526,132226160,132227450,132228345,132241065,132298090,132489291,132507505,132565464,132576421, 132130574,132133199,132140811,132145288,132146700,132147999,132148646,132159632,132164288,132165200,132168572,132174920,132179921,132180732,132181620,132182190,132185463,132187607,132194179,132198636,132202836,132203419,132211143,132223641,132226260,132227604,132228469,132241166,132298222,132489474,132508779,132565647,132576470, 0 PLXNA4 cmpl cmpl 0,2,2,0,1,0,1,0,0,2,0,1,0,0,0,2,2,0,2,0,1,0,0,2,1,0,2,0,0,0,0,-1,-1,
250 5814 5814 200 NM_021807.4 chr7 + 133253077 134065761 133253101 134064528 18 133253077,133274981,133288921,133305876,133317283,133356329,133374827,133475327,133480049,133630044,133817324,133895598,133917582,133937890,133997491,134004911,134007675,134064290, 133253187,133275171,133289116,133306061,133317390,133356573,133375002,133475473,133480138,133630141,133817544,133895735,133917738,133938069,133997633,134005090,134007835,134065761, 0 EXOC4 cmpl cmpl 0,2,0,0,2,1,2,0,2,1,2,0,2,2,1,2,1,2,
251 3707 3707 26 NM_014141.6 chr7 + 146116800 148420998 146116876 148415616 24 146116800,146774270,146839710,147043906,147108146,147120978,147128692,147132244,147300140,147395608,147485934,147562137,147639105,147903564,147977861,148118117,148147490,148172241,148217287,148229645,148267032,148383648,148409390,148415416, 146116973,146774381,146839904,147044054,147108350,147121163,147128836,147132509,147300290,147395780,147486041,147562257,147639306,147903721,147977989,148118288,148147709,148172478,148217524,148229779,148267126,148383888,148409471,148420998, 0 CNTNAP2 cmpl cmpl 0,1,1,0,1,1,0,0,1,1,2,1,1,1,2,1,1,1,1,1,0,1,1,1,
252 5068 5068 27 NM_001364498.2 chr7 + 153748132 154894285 153748948 154892480 27 153748132,153748754,154446213,154474938,154540531,154566841,154637820,154669359,154727766,154769416,154772844,154794078,154795844,154801354,154803863,154804916,154806993,154853779,154867994,154872623,154875905,154880887,154885632,154887675,154889271,154889456,154892333, 153748319,153749008,154446328,154475037,154540626,154566916,154637873,154669441,154727887,154769571,154772942,154794202,154795883,154801462,154803955,154804964,154807112,154853827,154868093,154872693,154876100,154880942,154885744,154887734,154889344,154889530,154894285, 0 DPP6 cmpl cmpl -1,0,0,1,1,0,0,2,0,1,0,2,0,0,0,2,2,1,1,1,2,2,0,1,0,1,0,
253 16477 16477 27 NM_002847.5 chr7 - 157539055 158587823 157540713 158587669 23 157539055,157548945,157568901,157571439,157576612,157578020,157595237,157604001,157621361,157656356,157682724,157898672,158081297,158110828,158133676,158136654,158138293,158166930,158192326,158205170,158316818,158489734,158587557, 157540785,157549019,157568966,157571493,157576779,157578140,157595315,157604075,157621509,157656551,157682937,157898737,158081377,158110915,158134059,158136695,158138515,158167291,158192495,158205273,158316932,158489785,158587823, 0 PTPRN2 cmpl cmpl 0,1,2,2,0,0,0,1,0,0,0,1,2,2,0,1,1,0,2,1,1,1,0,
254 4866 4866 9 NM_001346810.2 chr8 + 737627 1708476 737807 1701406 15 737627,907911,1258850,1501365,1548625,1565682,1626739,1632826,1668328,1669742,1676532,1678213,1691534,1697146,1701187, 737825,907966,1258883,1501431,1549683,1565894,1626887,1633046,1668678,1669784,1676618,1678629,1691626,1697299,1708476, 0 DLGAP2 cmpl cmpl 0,0,1,1,1,0,2,0,1,0,0,2,1,0,0,
255 4078 4078 9 NM_033225.6 chr8 - 2935360 4994914 2938584 4994416 70 2935360,2942471,2949298,2950230,2951113,2954223,2955588,2957695,2961140,2962465,2963221,2965774,2966569,2973116,2974450,2978611,2998010,2999957,3018476,3029318,3052461,3087096,3091515,3096848,3106527,3107717,3108602,3110157,3118398,3142464,3151396,3157896,3162158,3181109,3187868,3188886,3189911,3199713,3201611,3205503,3214496,3219254,3223728,3230039,3284143,3307694,3308311,3343293,3347991,3359151,3367031,3369253,3387493,3396193,3399390,3406026,3407898,3409422,3468711,3493622,3574944,3586135,3616709,3708413,3753929,3997902,4031904,4419952,4637341,4994331, 2938744,2942604,2949386,2950343,2951275,2954268,2955768,2957807,2961214,2962639,2963395,2965954,2966746,2973299,2974624,2978800,2998184,3000131,3018650,3029513,3052647,3087285,3091662,3097037,3106641,3107798,3108748,3110335,3118587,3142674,3151513,3157966,3162277,3181214,3187965,3189011,3190115,3199809,3201725,3205620,3214691,3219442,3223867,3230231,3284346,3307821,3308503,3343450,3348161,3359340,3367247,3369370,3387682,3396381,3399529,3406221,3408225,3409605,3468824,3493726,3575066,3586260,3616797,3708491,3754042,3998110,4032099,4420065,4637558,4994914, 0 CSMD1 cmpl cmpl 2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,2,1,1,2,1,0,
256 18146 18146 10 NM_139167.4 chr8 - 14084844 15238431 14090442 15237623 8 14084844,14102375,14108162,14164579,14237591,14324102,14554731,15237584, 14090637,14102499,14108235,14164702,14237679,14324204,14554926,15238431, 0 SGCZ cmpl cmpl 0,2,1,1,0,0,0,0,
257 16276 16276 11 NM_001412866.1 chr8 - 18527302 19084805 18535742 19084529 17 18527302,18556208,18572527,18575127,18600363,18632612,18655641,18735234,18765448,18799294,18801269,18804521,18804703,18867673,18871625,18936033,19084205, 18535958,18556352,18572672,18575285,18600434,18632806,18655685,18735315,18765538,18799353,18801382,18804602,18804898,18868069,18872733,18936142,19084805, 0 PSD3 cmpl cmpl 0,0,2,0,1,2,0,0,0,1,2,2,2,2,1,0,0,
258 13576 13576 12 NM_001322202.2 chr8 + 31639244 32774046 32754445 32764402 9 31639244,32595827,32605561,32727948,32754371,32756402,32759305,32760199,32763747, 31639431,32596005,32605683,32728078,32754474,32756529,32759436,32760406,32774046, 0 NRG1 cmpl cmpl -1,-1,-1,-1,0,2,0,2,2,
259 21803 21803 13 XM_047421381.1 chr8 + 35235474 35796540 35235784 35790563 15 35235474,35549291,35568097,35595553,35683546,35686544,35722209,35726151,35731011,35748526,35750581,35759319,35766901,35774298,35790358, 35235887,35549510,35568241,35595657,35683727,35686709,35722356,35726529,35731096,35748695,35750809,35759469,35767066,35774477,35796540, 0 UNC5D cmpl cmpl 0,1,1,1,0,1,1,1,1,2,0,0,0,0,2,
260 18992 18992 1 NM_001287813.3 chr8 + 49909795 50796692 50394238 50792829 20 49909795,49910891,50172560,50394211,50402209,50438542,50449667,50450555,50450687,50502777,50530176,50536677,50553049,50590878,50656908,50658591,50704599,50708885,50752000,50792670, 49909904,49911044,50172635,50394265,50402344,50438599,50449725,50450599,50450729,50502880,50530259,50536808,50553179,50590917,50657025,50658663,50704752,50708978,50752111,50796692, 0 SNTG1 cmpl cmpl -1,-1,-1,0,0,0,0,1,0,0,1,0,2,0,0,0,0,0,0,0,
261 3606 3606 131 XM_024447079.2 chr8 + 60964847 61501629 61299827 61499542 9 60964847,60966169,61131769,61292317,61299676,61376604,61454140,61458306,61499454, 60965361,60966237,61131860,61292454,61300282,61376779,61454251,61458542,61501629, 0 CLVS1 cmpl cmpl -1,-1,-1,-1,0,2,0,0,2,
262 13269 13269 16 XM_017013359.2 chr8 + 62248853 62999652 62249073 62999334 6 62248853,62579538,62589713,62746931,62918452,62999230, 62249127,62579676,62589794,62747129,62918513,62999652, 0 NKAIN3 cmpl cmpl 0,0,0,0,0,1,
263 16716 16716 153 XM_024447066.2 chr8 + 84182786 84921844 84529321 84920911 8 84182786,84529298,84774578,84849979,84862295,84873283,84887603,84920893, 84182944,84529577,84774654,84850027,84862453,84873397,84887776,84921844, 0 RALYL cmpl cmpl -1,0,1,2,2,1,1,0,
264 3636 3636 19 XM_017013149.2 chr8 + 86866414 87428652 86866495 87428637 11 86866438,86887541,86905080,86939595,87205992,87236918,87284677,87286538,87351684,87353635,87428545, 86866583,86887611,86905194,86939754,87206138,87237112,87284815,87286671,87351794,87353786,87428652, 0 CNBD1 cmpl cmpl 0,1,2,2,2,1,0,0,1,0,1,
265 19557 19557 20 XM_017013756.2 chr8 - 98387878 98942610 98434253 98942470 13 98429935,98437102,98526741,98547968,98579663,98596031,98706466,98707146,98749275,98767242,98774738,98883646,98942377, 98434318,98437208,98526917,98548161,98579789,98596169,98706634,98707311,98749390,98767371,98774819,98883834,98942610, 0 STK3 cmpl cmpl 1,0,1,0,0,0,0,0,2,2,2,0,0,
266 22072 22072 20 NM_017890.5 chr8 + 99013273 99877580 99013788 99875666 62 99013273,99013759,99038422,99096311,99102952,99111097,99115699,99121176,99134631,99135014,99135595,99136664,99142973,99147840,99156548,99170038,99192875,99274197,99275080,99384207,99391556,99431536,99442400,99467413,99481598,99501686,99502835,99507769,99511103,99520898,99556449,99575657,99577489,99641810,99661353,99699524,99717170,99720344,99720862,99766773,99776774,99778681,99784314,99809374,99817539,99818450,99818712,99819411,99819920,99821293,99823831,99832368,99835196,99835538,99848775,99853450,99859303,99861775,99868288,99870784,99871447,99875417, 99013347,99013935,99038566,99096432,99103120,99111279,99115874,99121445,99134727,99135137,99135733,99136752,99143165,99148010,99156743,99170163,99193057,99274332,99275254,99384317,99391704,99431664,99442635,99467634,99481802,99501858,99502950,99507911,99511512,99521010,99556653,99575784,99577633,99642498,99661491,99699932,99717373,99720552,99721047,99766970,99776956,99779031,99784476,99809530,99817803,99818534,99818888,99819582,99820122,99821482,99823978,99832652,99835324,99835738,99848894,99854256,99859480,99861946,99868465,99870887,99871697,99877580, 0 VPS13B cmpl cmpl -1,0,0,0,1,1,0,1,0,0,0,0,1,1,0,0,2,1,1,1,0,1,0,1,0,0,1,2,0,1,2,2,0,0,1,1,1,0,1,0,2,1,0,0,0,0,0,2,2,0,0,0,2,1,0,2,1,1,1,1,2,0,
267 17130 17130 21 NM_001348497.2 chr8 + 103500609 104256094 103500886 104251820 23 103500609,103697085,103766226,103885297,103910320,103912052,103915494,103916413,103918440,103921671,103931262,103936550,103942772,103961064,103975349,103989304,104014505,104015423,104244915,104248700,104249486,104251023,104251601, 103501062,103697296,103766537,103886223,103910529,103912172,103915594,103916537,103918487,103921784,103931393,103936722,103942926,103961133,103975506,103989421,104014615,104015456,104245057,104248813,104249588,104251163,104256094, 0 RIMS2 cmpl cmpl 0,2,0,2,1,0,0,1,2,1,0,2,0,1,1,2,2,1,1,2,1,1,0,
268 4080 4080 22 NM_198123.2 chr8 - 112222927 113436939 112224770 113436854 71 112222927,112228755,112231544,112234364,112237189,112241719,112244393,112247019,112254252,112255253,112263638,112265410,112281173,112287063,112289364,112291509,112292536,112295832,112301792,112304720,112306006,112310977,112313905,112314428,112318836,112319900,112335328,112336651,112337542,112341476,112346096,112351174,112352415,112380351,112383566,112390663,112406523,112408317,112408918,112472590,112492488,112503789,112506690,112517033,112550670,112552593,112556762,112573500,112587065,112636816,112638695,112645108,112650160,112656153,112666276,112682441,112685405,112689867,112800161,112829685,112859144,112921626,112947789,112954683,112975836,113019066,113098755,113173721,113278591,113314570,113436676, 112224930,112228891,112231632,112234477,112237348,112241785,112244573,112247131,112254326,112255427,112263812,112265590,112281350,112287246,112289538,112291695,112292710,112296006,112301966,112304915,112306192,112311166,112314052,112314617,112318950,112319981,112335474,112336829,112337731,112341686,112346213,112351244,112352534,112380456,112383663,112390788,112406727,112408413,112409032,112472707,112492683,112503977,112506829,112517225,112550873,112552720,112556954,112573657,112587235,112637005,112638911,112645225,112650349,112656341,112666415,112682636,112685732,112690050,112800274,112829789,112859266,112921751,112947877,112954761,112976148,113019179,113098963,113173916,113278704,113314793,113436939, 0 CSMD3 cmpl cmpl 2,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,0,1,1,0,1,1,1,1,1,1,2,1,1,2,1,1,0,1,1,1,1,1,2,1,1,1,1,2,0,1,2,1,1,1,2,1,1,2,1,0,
269 21106 21106 206 NM_031466.8 chr8 - 139727724 140458579 139731060 140451373 23 139727724,139731978,139885878,139910146,139988725,140023936,140221458,140252776,140275657,140283888,140287607,140290992,140300468,140311247,140360049,140370963,140397619,140405576,140426614,140435111,140439051,140450789,140458280, 139731228,139732202,139885969,139910300,139988836,140024079,140221583,140252929,140275821,140284021,140287734,140291078,140300614,140311374,140360193,140371180,140397745,140405698,140426641,140435240,140439197,140451383,140458579, 0 TRAPPC9 cmpl cmpl 0,1,0,2,2,0,1,1,2,1,0,1,2,1,1,0,0,1,1,1,2,0,-1,
270 7037 7037 9 XM_047422890.1 chr9 - 3824126 4490465 3828271 4348261 12 3824126,3829309,3856008,3879426,3898690,3932359,3937027,4117767,4125733,4347080,4348231,4489627, 3828408,3829492,3856184,3879595,3898835,3932470,3937189,4118881,4125941,4347183,4348412,4490465, 0 GLIS3 cmpl cmpl 1,1,2,1,0,0,0,2,1,0,0,-1,
271 16467 16467 1 NM_002839.4 chr9 - 8314245 10613002 8317873 8733843 46 8314245,8319830,8331581,8338921,8340342,8341089,8341692,8375935,8376606,8389231,8404536,8436591,8449724,8460410,8465465,8470994,8484118,8485226,8485761,8492861,8497241,8499646,8500753,8504260,8507300,8517847,8521276,8523512,8524924,8526626,8527344,8528590,8633316,8636698,8733779,9018696,9183303,9397448,9574731,9734532,9766809,9938506,10033717,10340962,10612397,10612687, 8317942,8319966,8331736,8339047,8340469,8341268,8341978,8376090,8376726,8389407,8404660,8436689,8449837,8460571,8465675,8471085,8484378,8485324,8486349,8492979,8497268,8499840,8501059,8504405,8507434,8518429,8521546,8523524,8525035,8526644,8527353,8528779,8633458,8636844,8733946,9018735,9183363,9397482,9574781,9734571,9766851,9938610,10033790,10341017,10612505,10613002, 0 PTPRD cmpl cmpl 0,2,0,0,2,0,2,0,0,1,0,1,2,0,0,2,0,1,1,0,0,1,1,0,1,1,1,1,1,1,1,1,0,1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
272 326 326 11 XM_017015312.3 chr9 + 17906632 18910950 17906826 18908548 29 17906632,18163861,18504828,18533246,18574029,18622242,18635942,18639253,18657638,18661934,18680311,18681811,18684715,18706746,18721535,18753297,18770601,18775742,18776780,18795396,18817108,18826283,18829842,18887830,18889567,18892388,18905781,18906691,18908441, 17906922,18163981,18504956,18533292,18574266,18622369,18636017,18639411,18657750,18662073,18680516,18681959,18684800,18707048,18721665,18753508,18770781,18775896,18777906,18795524,18817237,18826463,18829977,18888043,18889748,18892596,18905891,18906912,18910950, 0 ADAMTSL1 cmpl cmpl 0,0,0,2,0,0,1,1,0,1,2,0,1,2,1,2,0,0,1,2,1,1,1,1,1,2,0,2,1,
273 18445 18445 11 XM_017014592.2 chr9 - 19507454 20307892 19516152 19786866 15 19507454,19520893,19528048,19550136,19573350,19576923,19597228,19619583,19622260,19785936,19849648,19891130,20004249,20301225,20307652, 19516402,19521060,19528138,19550268,19573469,19577022,19597279,19619692,19622299,19787019,19849787,19891228,20004387,20301364,20307892, 0 SLC24A2 cmpl cmpl 2,0,0,0,1,1,1,0,0,0,-1,-1,-1,-1,-1,
274 10335 10335 12 XM_047422812.1 chr9 - 27937616 29213601 27948850 27950671 8 27937616,28295207,28372835,28475939,28670199,28913791,28947817,29212921, 27950706,28295366,28372868,28476025,28670280,28913874,28947914,29213601, 0 LINGO2 cmpl cmpl 0,-1,-1,-1,-1,-1,-1,-1,
275 21314 21314 17 NM_001366142.2 chr9 - 70529059 71446971 70535428 71446835 27 70529059,70537121,70549541,70552843,70553159,70591030,70598418,70603341,70610608,70615907,70618866,70620075,70621243,70625190,70625481,70635210,70639059,70640559,70681505,70761600,70784104,70827846,70843002,70846377,70862907,70864431,71446652, 70535451,70537405,70549674,70553043,70553310,70591205,70598670,70603470,70610749,70616075,70619095,70620365,70621273,70625331,70625517,70635261,70639194,70640660,70681578,70761724,70784279,70828018,70843127,70846591,70863112,70864511,71446971, 0 TRPM3 cmpl cmpl 1,2,1,2,1,0,0,0,0,0,2,0,0,0,0,0,0,1,0,2,1,0,1,0,2,0,0,
276 14665 14665 22 XM_047423419.1 chr9 + 109640786 110172512 109780488 110168421 8 109780197,109867490,109880550,109923734,109925060,110015953,110136126,110168398, 109780533,109867571,109880681,109923849,109925082,110016039,110138539,110172512, 0 PALM2AKAP2 cmpl cmpl 0,0,0,2,0,1,0,1,
277 1289 1289 184 NM_001365068.1 chr9 - 116423111 117415057 116425850 117414938 23 116423111,116440608,116442452,116487358,116618323,116620309,116651527,116725770,116728991,116733398,116805631,116820616,116863582,116975207,116976113,116976700,117008091,117039818,117096043,117141325,117214357,117291325,117414496, 116426088,116440792,116442553,116487500,116618472,116620443,116651793,116725950,116729096,116733523,116805820,116820783,116863733,116975345,116976188,116976785,117008259,117039965,117096151,117141478,117214742,117291513,117415057, 0 ASTN2 cmpl cmpl 2,1,2,1,2,0,1,1,1,2,2,0,2,2,2,1,1,1,1,1,0,1,0,
278 4709 4709 23 NM_001352964.2 chr9 - 123379657 123930126 123381431 123929905 24 123379657,123383654,123387729,123403401,123411775,123440359,123450692,123452275,123454738,123457347,123457792,123557569,123583168,123609435,123630375,123652012,123667025,123671290,123676719,123757702,123769513,123792586,123878950,123929888, 123382625,123383913,123387858,123403490,123411829,123440491,123450749,123452347,123454779,123457435,123457897,123557695,123583270,123609481,123630476,123652123,123667079,123671371,123676789,123757822,123769563,123792630,123879021,123930126, 0 DENND1A cmpl cmpl 0,2,2,0,0,0,0,0,1,0,0,0,0,2,0,0,0,0,2,2,0,1,2,0,
279 1070 1070 10 NM_013427.3 chrX - 11137543 11665920 11138862 11664828 13 11137543,11142232,11143979,11156528,11169504,11178099,11179301,11182062,11186235,11188727,11196924,11254547,11664240, 11139530,11142313,11144248,11156626,11169684,11178248,11179452,11182118,11186431,11188984,11196996,11254707,11665920, 0 ARHGAP6 cmpl cmpl 1,1,2,0,0,1,0,1,0,1,1,0,0,
280 6580 6580 10 NM_001368395.3 chrX + 11822438 12724523 11865188 12721858 19 11822438,11865085,11877894,12498679,12609720,12614778,12674862,12683482,12686096,12690194,12694334,12701873,12704358,12706825,12707468,12710398,12716068,12717500,12720533, 11822715,11865216,11878018,12498796,12609881,12614881,12674908,12683587,12686204,12690326,12694454,12702010,12704485,12706915,12707651,12710537,12717133,12718790,12724523, 0 FRMPD4 cmpl cmpl -1,0,1,2,2,1,2,0,0,0,0,0,2,0,0,0,1,1,1,
281 8637 8637 12 NM_014271.4 chrX + 28587445 29956718 28789343 29955820 11 28587445,28789319,29282937,29396257,29399154,29668429,29917463,29919948,29941650,29954521,29955101, 28588047,28789425,29283217,29396444,29399308,29668504,29917596,29920094,29941794,29954692,29956718, 0 IL1RAPL1 cmpl cmpl -1,0,1,2,0,1,1,2,1,1,1,
282 4894 4894 12 NM_000109.4 chrX - 31119221 33339388 31121918 33339265 79 31119221,31126641,31134101,31146290,31147274,31169442,31172347,31173538,31177931,31178668,31180369,31182737,31203960,31206581,31209497,31223046,31260954,31323597,31348555,31444480,31478105,31478982,31496787,31507280,31627672,31657989,31679374,31729630,31773959,31819974,31836717,31875187,31929595,31932079,31968338,32216915,32287528,32310081,32342099,32343133,32345942,32348405,32362787,32364581,32365019,32380509,32386309,32389500,32390070,32411751,32438240,32441179,32448455,32454661,32463438,32464585,32468497,32472163,32484918,32491276,32501754,32518007,32545158,32565701,32573529,32573744,32595756,32614302,32644131,32644963,32697869,32699111,32809492,32816467,32823294,32844782,32849727,33020138,33339258, 31121930,31126673,31134194,31146414,31147518,31169601,31172413,31173604,31177970,31178805,31180481,31182904,31204118,31206667,31209699,31223121,31261016,31323658,31348634,31444627,31478374,31479103,31496944,31507453,31627862,31658144,31679586,31729748,31774192,31820083,31836819,31875373,31929745,31932227,31968514,32217063,32287701,32310276,32342282,32343286,32346080,32348528,32362958,32364710,32365199,32380680,32386465,32389674,32390181,32411913,32438390,32441314,32448638,32454832,32463594,32464699,32468710,32472309,32485099,32491518,32501842,32518131,32545334,32565881,32573637,32573846,32595876,32614453,32644313,32645152,32697998,32699293,32809611,32816640,32823387,32844860,32849820,33020200,33339388, 0 DMD cmpl cmpl 0,1,1,0,2,2,2,2,2,0,2,0,1,2,1,1,2,1,0,0,1,0,2,0,2,0,1,0,1,0,0,0,0,2,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,2,0,0,0,0,0,2,0,0,0,1,2,0,0,0,0,1,0,
283 4421 4421 155 XM_017029255.2 chrX + 86148450 86832602 86148620 86832155 11 86148450,86514278,86651035,86695020,86714547,86739746,86812855,86813129,86814687,86816033,86832105, 86149108,86514391,86651167,86695179,86714720,86739882,86813004,86813277,86814834,86816099,86832602, 0 DACH2 cmpl cmpl 0,2,1,1,1,0,1,0,1,1,1,
284 14785 14785 2 XM_011530914.3 chrX + 91779374 92623230 91835504 92618940 8 91779374,91835460,91876780,92201374,92263113,92387734,92468298,92618263, 91779684,91836044,91879273,92201455,92263143,92387933,92468322,92623230, 0 PCDH11X cmpl cmpl -1,0,0,0,0,0,1,1,
285 4821 4821 20 NM_006729.5 chrX + 96684841 97604997 96685058 97599317 27 96684841,96735757,96738585,96758153,96881578,96912327,96912482,96916437,96918508,96930732,96937232,96939265,96942017,96945526,96948934,96957827,96965092,97072940,97075166,97099693,97114725,97141664,97247714,97348115,97383908,97429649,97599252, 96685190,96735790,96738762,96758258,96881718,96912402,96912552,96916574,96918617,96930843,96937351,96939382,96942136,96945591,96949039,96958148,96965207,97073042,97075261,97099795,97114965,97141794,97247839,97348280,97384044,97429745,97604997, 0 DIAPH2 cmpl cmpl 0,0,0,0,0,2,2,0,2,0,0,2,2,1,0,0,0,1,1,0,0,0,1,0,0,1,1,
286 8638 8638 21 NM_017416.2 chrX + 104566198 105767829 104658913 105767661 11 104566198,104658894,105195474,105233817,105267387,105484312,105717366,105740545,105748959,105755176,105766963, 104567051,104658995,105195748,105234004,105267541,105484387,105717496,105740691,105749103,105755347,105767829, 0 IL1RAPL2 cmpl cmpl -1,0,1,2,0,1,1,2,1,1,1,
287 20211 20211 23 XM_017029213.3 chrX - 124375902 125204312 124380535 124963753 35 124375902,124382669,124383633,124385676,124392051,124405030,124406316,124420310,124422271,124453336,124470724,124481731,124487208,124497015,124503559,124520516,124523363,124529863,124546873,124561670,124563748,124565374,124641790,124645142,124646708,124651913,124653583,124671682,124705012,124736956,124894295,124895980,124963536,125185642,125203799, 124381294,124382812,124384854,124386064,124392348,124405266,124406489,124420821,124422638,124453491,124470823,124481964,124487229,124497265,124503703,124520784,124523625,124529983,124547090,124561817,124563772,124565560,124641991,124645337,124646810,124652124,124653783,124671835,124705251,124737197,124894352,124896241,124963817,125185709,125204312, 0 TENM1 cmpl cmpl 0,1,1,0,0,1,2,1,0,1,1,2,2,1,1,0,2,2,1,1,1,1,1,1,1,0,1,1,2,1,1,1,0,-1,-1,
288 6323 6323 205 NM_001139501.2 chrX - 138614726 139205023 138632849 138857641 8 138614726,138635456,138702983,138708817,138857511,138990507,139204058,139204920, 138632986,138635655,138703087,138708928,138857679,138990617,139204271,139205023, 0 FGF13 cmpl cmpl 1,0,1,1,0,-1,-1,-1,
289 14786 14786 9 XM_017030080.2 chrY + 5000295 5742228 5032696 5737942 10 5000295,5030898,5031214,5031905,5032669,5056888,5098214,5501056,5581774,5737271, 5000605,5031067,5031346,5032011,5032728,5057459,5100707,5501255,5581798,5742228, 0 PCDH11Y cmpl cmpl -1,-1,-1,-1,0,2,0,0,1,1,

98
nextflow.config Normal file
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manifest {
name = 'digital patients'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/pipelines/digitalpatients'
description = 'generative digital patients and multi-omics pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
}
// docker {
// enabled = true
// temp = 'auto'
// }
// process {
// withLabel: 'gpu_process' {
// containerOptions = '--gpus all --rm'
// }
//
// withLabel: 'cpu_process' {
// containerOptions = '--rm'
// }
// }
def sharedPod = [
[env: 'NXF_DEBUG', value: '0'],
[label: 'omic-app', value: 'digitalpatients'],
[imagePullSecret: 'gitlab-registry-secret'],
[volumeClaim: 'avatar-new', mountPath: '/mnt/Avatar/'],
]
profiles {
docker {
docker.enabled = true
process {
executor = 'local'
withLabel: 'gpu_process' {
maxForks = 1 // Only one GPU task at a time on single GPU system
containerOptions = '--gpus all --rm'
}
withLabel: 'cpu_process' {
containerOptions = '--rm'
}
}
}
k8s {
process {
executor = 'k8s'
namespace = 'bioinformatics'
debug = true
pod = sharedPod
withLabel: 'gpu_process' {
pod = sharedPod + [
[nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
]
}
}
workDir = "/mnt/dreamdock-data/digital-patient-data/work"
k8s {
serviceAccount = 'nextflow-sa'
namespace = 'bioinformatics'
storageClaimName = 'dreamdock-data'
storageMountPath = '/mnt/dreamdock-data'
pullPolicy = 'IfNotPresent'
cleanup = true // delete pods after Ctrl+C or finished?
// cleanup = false // delete pods after Ctrl+C or finished?
// RUN AS DIFFERENT USERS
// securityContext = [fsGroup: 1000]
// securityContext = [
// runAsUser: 1000,
// fsGroup: 1000,
// runAsNonRoot: true
// ]
}
// Use container image
// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
}
}

325
params.json Normal file
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@@ -0,0 +1,325 @@
{
"params": {
"// SYNTHEA PARAMETERS": {},
"n_pat": {
"type": "integer",
"description": "Number of patients to generate (must be >= 2)",
"default": 2,
"required": true,
"pipeline_io": "parameter",
"var_name": "params.n_pat",
"examples": [2, 10, 100],
"pattern": "^[0-9]+$",
"validation": {
"min": 2
},
"notes": "Minimum of 2 patients required (one male, one female)"
},
"percent_male": {
"type": "number",
"description": "Percentage of male patients (between 0-1)",
"default": 0.5,
"required": true,
"pipeline_io": "parameter",
"var_name": "params.percent_male",
"examples": [0.0, 0.5, 1.0],
"pattern": "^0(\\.\\d+)?|1(\\.0)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"notes": "Value must be between 0 and 1 inclusive"
},
"imputed_store": {
"type": "folder",
"description": "Path to imputed UKBB data",
"default": "/mnt/Avatar/imputed/ukbb/imputed",
"required": true,
"pipeline_io": "input",
"var_name": "params.imputed_store",
"examples": [
"/mnt/Avatar/imputed/ukbb/imputed",
"/rosalind/ukbb/imputed"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing imputed UKBB data"
},
"pheno_store": {
"type": "file",
"description": "Path to phenotype data file",
"default": "/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv",
"required": true,
"pipeline_io": "input",
"var_name": "params.pheno_store",
"examples": [
"/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv"
],
"pattern": ".*\\.csv$",
"validation": {},
"notes": "CSV file containing filtered UKBB phenotype data"
},
"disease": {
"type": "string",
"description": "Disease or condition to simulate",
"default": "schizophrenia",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.disease",
"examples": [
"schizophrenia",
"healthy",
"leukaemia",
"Purpura and other haemorrhagic conditions"
],
"pattern": ".*",
"enum": [
"schizophrenia",
"healthy",
"leukaemia",
"Purpura and other haemorrhagic conditions"
],
"validation": {},
"notes": "Use 'healthy' for healthy individuals or specify a disease condition"
},
"healthy_dir": {
"type": "folder",
"description": "Path to healthy patient data directory",
"default": "/Workspace/next/registry/pipelines/digital_patient",
"required": true,
"pipeline_io": "input",
"var_name": "params.healthy_dir",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient",
"/mnt/Avatar/digital_patient"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing data for healthy patient generation"
},
"outdir": {
"type": "folder",
"description": "Output directory for results",
"default": "/mnt/omic-next-apis/wes/digital_patients",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": [
"/mnt/OmicNAS/dd/digital_patient",
"/path/to/custom/output"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where all pipeline results will be stored"
},
"// BORZOI PARAMETERS": {},
"container_borzoi": {
"type": "string",
"description": "Borzoi container image",
"default": "borzoi:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_borzoi",
"examples": [
"borzoi:latest",
"borzoi:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for Borzoi module"
},
"containerOptions": {
"type": "string",
"description": "Container runtime options",
"default": "--gpus all --rm -v /mnt:/mnt",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions",
"examples": [
"--gpus all --rm -v /mnt:/mnt",
"--rm -v /data:/data"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for GPU usage and volume mounts"
},
"project_name": {
"type": "string",
"description": "Project identifier",
"default": "test",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.project_name",
"examples": [
"test",
"production",
"schizophrenia_study"
],
"pattern": ".*",
"validation": {},
"notes": "Identifier for the digital patient project"
},
"mane": {
"type": "file",
"description": "Path to MANE reference file",
"default": "/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv",
"required": true,
"pipeline_io": "input",
"var_name": "params.mane",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv"
],
"pattern": ".*\\.tsv$",
"validation": {},
"notes": "MANE transcripts reference file in TSV format"
},
"// VCF2PROT PARAMETERS": {},
"container_vcf2prot": {
"type": "string",
"description": "VCF2PROT container image",
"default": "vcf2prot:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_vcf2prot",
"examples": [
"vcf2prot:latest",
"vcf2prot:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for VCF2PROT module"
},
"// RNA2PROTEINEXPRESSION PARAMETERS": {},
"container_rna2protexpression": {
"type": "string",
"description": "RNA2PROTEINEXPRESSION container image",
"default": "rna2protexpression:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_rna2protexpression",
"examples": [
"rna2protexpression:latest",
"rna2protexpression:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for RNA2PROTEINEXPRESSION module"
},
"containerOptions_rna2protexpression": {
"type": "string",
"description": "Container options for RNA2PROTEINEXPRESSION",
"default": "--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions_rna2protexpression",
"examples": [
"--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for RNA2PROTEINEXPRESSION with GPU and database volume mounts"
},
"// CORTO PARAMETERS": {},
"container_corto": {
"type": "string",
"description": "CORTO container image",
"default": "corto:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_corto",
"examples": [
"corto:latest",
"corto:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for CORTO module"
},
"regulon": {
"type": "file",
"description": "Path to regulon RDA file",
"default": "/Workspace/next/registry/pipelines/digital_patient/regulon.rda",
"required": true,
"pipeline_io": "input",
"var_name": "params.regulon",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/regulon.rda"
],
"pattern": ".*\\.rda$",
"validation": {},
"notes": "Regulon data file in RDA format for CORTO module"
},
"// CIBERSORT PARAMETERS": {},
"cibersortx_username": {
"type": "string",
"description": "CIBERSORTx username for authentication",
"default": "gabriel.richman.2009@anderson.ucla.edu",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.cibersortx_username",
"examples": [
"gabriel.richman.2009@anderson.ucla.edu"
],
"pattern": "^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\\.[a-zA-Z]{2,}$",
"validation": {},
"notes": "Username (email) for CIBERSORTx authentication"
},
"cibersortx_token": {
"type": "string",
"description": "CIBERSORTx authentication token",
"default": "b5b39e563fb947df4cfd4843d40fdb99",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.cibersortx_token",
"examples": [
"b5b39e563fb947df4cfd4843d40fdb99"
],
"pattern": "^[a-f0-9]{32}$",
"validation": {},
"notes": "Authentication token for CIBERSORTx API access"
},
"container_ecotyper": {
"type": "string",
"description": "ECOTyper container image",
"default": "ecotyper:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_ecotyper",
"examples": [
"ecotyper:latest",
"ecotyper:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for ECOTyper module"
},
"signature_matrix": {
"type": "file",
"description": "Path to signature matrix file",
"default": "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt",
"required": true,
"pipeline_io": "input",
"var_name": "params.signature_matrix",
"examples": [
"/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
],
"pattern": ".*\\.txt$",
"validation": {},
"notes": "Signature matrix file for CIBERSORTx analysis"
},
"ecotyper_outdir": {
"type": "folder",
"description": "Output directory for ECOTyper results",
"default": "/mnt/omic-next-apis/wes/digital-patients/ecotyper",
"required": true,
"pipeline_io": "output",
"var_name": "params.ecotyper_outdir",
"examples": [
"/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where ECOTyper results will be stored"
}
}
}

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@@ -0,0 +1,229 @@
,Unnamed: 0,#NCBI_GeneID,Ensembl_Gene,HGNC_ID,symbol,name,RefSeq_nuc,RefSeq_prot,Ensembl_nuc,Ensembl_prot,MANE_status,GRCh38_chr,chr_start,chr_end,chr_strand,chrom
8141,8141,GeneID:23261,ENSG00000171735.21,HGNC:18806,CAMTA1,calmodulin binding transcription activator 1,NM_015215.4,NP_056030.1,ENST00000303635.12,ENSP00000306522.6,MANE Select,NC_000001.11,6785454,7769706,+,chr1
14385,14385,GeneID:114784,ENSG00000121904.19,HGNC:19290,CSMD2,CUB and Sushi multiple domains 2,NM_001281956.2,NP_001268885.1,ENST00000373381.9,ENSP00000362479.4,MANE Select,NC_000001.11,33513998,34165230,-,chr1
13673,13673,GeneID:84871,ENSG00000186094.18,HGNC:25892,AGBL4,AGBL carboxypeptidase 4,NM_032785.4,NP_116174.3,ENST00000371839.6,ENSP00000360905.1,MANE Select,NC_000001.11,48532854,50023954,-,chr1
7622,7622,GeneID:11124,ENSG00000185104.21,HGNC:3578,FAF1,Fas associated factor 1,NM_007051.3,NP_008982.1,ENST00000396153.7,ENSP00000379457.2,MANE Select,NC_000001.11,50437028,50960267,-,chr1
3420,3420,GeneID:5142,ENSG00000184588.18,HGNC:8781,PDE4B,phosphodiesterase 4B,NM_002600.4,NP_002591.2,ENST00000341517.9,ENSP00000342637.4,MANE Select,NC_000001.11,65792895,66374574,+,chr1
11534,11534,GeneID:57554,ENSG00000033122.21,HGNC:18531,LRRC7,leucine rich repeat containing 7,NM_001370785.2,NP_001357714.1,ENST00000651989.2,ENSP00000498937.2,MANE Select,NC_000001.11,69567922,70144364,+,chr1
16804,16804,GeneID:257194,ENSG00000172260.15,HGNC:17302,NEGR1,neuronal growth regulator 1,NM_173808.3,NP_776169.2,ENST00000357731.10,ENSP00000350364.4,MANE Select,NC_000001.11,71395943,72282539,-,chr1
16775,16775,GeneID:256435,ENSG00000184005.12,HGNC:19343,ST6GALNAC3,"ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3",NM_152996.4,NP_694541.2,ENST00000328299.4,ENSP00000329214.3,MANE Select,NC_000001.11,76074746,76634603,+,chr1
1263,1263,GeneID:1806,ENSG00000188641.14,HGNC:3012,DPYD,dihydropyrimidine dehydrogenase,NM_000110.4,NP_000101.2,ENST00000370192.8,ENSP00000359211.3,MANE Select,NC_000001.11,97077743,97921034,-,chr1
8692,8692,GeneID:26052,ENSG00000197959.15,HGNC:29125,DNM3,dynamin 3,NM_015569.5,NP_056384.2,ENST00000627582.3,ENSP00000486701.1,MANE Select,NC_000001.11,171841498,172412717,+,chr1
6668,6668,GeneID:9910,ENSG00000152061.24,HGNC:24663,RABGAP1L,RAB GTPase activating protein 1 like,NM_001366446.1,NP_001353375.1,ENST00000681986.1,ENSP00000507884.1,MANE Select,NC_000001.11,174159520,174995308,+,chr1
5070,5070,GeneID:7399,ENSG00000042781.14,HGNC:12601,USH2A,usherin,NM_206933.4,NP_996816.3,ENST00000307340.8,ENSP00000305941.3,MANE Select,NC_000001.11,215622891,216423448,-,chr1
4221,4221,GeneID:6262,ENSG00000198626.19,HGNC:10484,RYR2,ryanodine receptor 2,NM_001035.3,NP_001026.2,ENST00000366574.7,ENSP00000355533.2,MANE Select,NC_000001.11,237042184,237833988,+,chr1
811,811,GeneID:1131,ENSG00000133019.12,HGNC:1952,CHRM3,cholinergic receptor muscarinic 3,NM_001375978.1,NP_001362907.1,ENST00000676153.1,ENSP00000502667.1,MANE Select,NC_000001.11,239386568,239915450,+,chr1
4071,4071,GeneID:6000,ENSG00000182901.18,HGNC:10003,RGS7,regulator of G protein signaling 7,NM_001364886.1,NP_001351815.1,ENST00000440928.6,ENSP00000404399.2,MANE Select,NC_000001.11,240775514,241357205,-,chr1
10459,10459,GeneID:55083,ENSG00000162849.16,HGNC:25484,KIF26B,kinesin family member 26B,NM_018012.4,NP_060482.2,ENST00000407071.7,ENSP00000385545.2,MANE Select,NC_000001.11,245154985,245709432,+,chr1
12068,12068,GeneID:64754,ENSG00000185420.19,HGNC:15513,SMYD3,SET and MYND domain containing 3,NM_001167740.2,NP_001161212.1,ENST00000490107.6,ENSP00000419184.2,MANE Select,NC_000001.11,245749347,246507279,-,chr1
67,67,GeneID:105,ENSG00000185736.16,HGNC:227,ADARB2,adenosine deaminase RNA specific B2 (inactive),NM_018702.4,NP_061172.1,ENST00000381312.6,ENSP00000370713.1,MANE Select,NC_000010.11,1177313,1737525,-,chr10
10839,10839,GeneID:55691,ENSG00000151474.23,HGNC:25491,FRMD4A,FERM domain containing 4A,NM_018027.5,NP_060497.3,ENST00000357447.7,ENSP00000350032.2,MANE Select,NC_000010.11,13643706,14330924,-,chr10
17391,17391,GeneID:340895,ENSG00000204740.11,HGNC:24331,MALRD1,MAM and LDL receptor class A domain containing 1,NM_001142308.3,NP_001135780.2,ENST00000454679.7,ENSP00000412763.3,MANE Select,NC_000010.11,19048801,19734478,+,chr10
11129,11129,GeneID:56288,ENSG00000148498.17,HGNC:16051,PARD3,par-3 family cell polarity regulator,NM_001184785.2,NP_001171714.1,ENST00000374788.8,ENSP00000363920.3,MANE Select,NC_000010.11,34109561,34815296,-,chr10
3761,3761,GeneID:5592,ENSG00000185532.20,HGNC:9414,PRKG1,protein kinase cGMP-dependent 1,NM_006258.4,NP_006249.1,ENST00000373980.11,ENSP00000363092.5,MANE Select,NC_000010.11,51074487,52298350,+,chr10
12195,12195,GeneID:65217,ENSG00000150275.20,HGNC:14674,PCDH15,protocadherin related 15,NM_001384140.1,NP_001371069.1,ENST00000644397.2,ENSP00000495195.1,MANE Select,NC_000010.11,53802771,54801231,-,chr10
12194,12194,GeneID:65217,ENSG00000150275.20,HGNC:14674,PCDH15,protocadherin related 15,NM_033056.4,NP_149045.3,ENST00000320301.11,ENSP00000322604.6,MANE Plus Clinical,NC_000010.11,53821099,54801231,-,chr10
9209,9209,GeneID:29119,ENSG00000183230.18,HGNC:2511,CTNNA3,catenin alpha 3,NM_013266.4,NP_037398.2,ENST00000433211.7,ENSP00000389714.1,MANE Select,NC_000010.11,65912523,67696195,-,chr10
89,89,GeneID:132,ENSG00000156110.15,HGNC:257,ADK,adenosine kinase,NM_006721.4,NP_006712.2,ENST00000539909.6,ENSP00000443965.2,MANE Select,NC_000010.11,74151221,74709290,+,chr10
13265,13265,GeneID:83938,ENSG00000148655.16,HGNC:23405,LRMDA,leucine rich melanocyte differentiation associated,NM_001305581.2,NP_001292510.1,ENST00000611255.5,ENSP00000480240.1,MANE Select,NC_000010.11,75431624,76560168,+,chr10
2556,2556,GeneID:3778,ENSG00000156113.25,HGNC:6284,KCNMA1,potassium calcium-activated channel subfamily M alpha 1,NM_001161352.2,NP_001154824.1,ENST00000286628.14,ENSP00000286628.8,MANE Select,NC_000010.11,76884882,77637808,-,chr10
7315,7315,GeneID:10718,ENSG00000185737.13,HGNC:7999,NRG3,neuregulin 3,NM_001010848.4,NP_001010848.2,ENST00000372141.7,ENSP00000361214.2,MANE Select,NC_000010.11,81875194,82987178,+,chr10
1955,1955,GeneID:2894,ENSG00000182771.19,HGNC:4575,GRID1,glutamate ionotropic receptor delta type subunit 1,NM_017551.3,NP_060021.1,ENST00000327946.12,ENSP00000330148.7,MANE Select,NC_000010.11,85599552,86366795,-,chr10
11810,11810,GeneID:60495,ENSG00000172987.14,HGNC:18374,HPSE2,heparanase 2 (inactive),NM_021828.5,NP_068600.4,ENST00000370552.8,ENSP00000359583.3,MANE Select,NC_000010.11,98457077,99235852,-,chr10
7919,7919,GeneID:22986,ENSG00000156395.14,HGNC:16699,SORCS3,sortilin related VPS10 domain containing receptor 3,NM_014978.3,NP_055793.1,ENST00000369701.8,ENSP00000358715.3,MANE Select,NC_000010.11,104641290,105265242,+,chr10
14404,14404,GeneID:114815,ENSG00000108018.17,HGNC:16697,SORCS1,sortilin related VPS10 domain containing receptor 1,NM_052918.5,NP_443150.3,ENST00000263054.11,ENSP00000263054.5,MANE Select,NC_000010.11,106573663,107164706,-,chr10
8676,8676,GeneID:26033,ENSG00000107518.18,HGNC:29063,ATRNL1,attractin like 1,NM_207303.4,NP_997186.1,ENST00000355044.8,ENSP00000347152.3,MANE Select,NC_000010.11,115093365,115948999,+,chr10
1251,1251,GeneID:1793,ENSG00000150760.13,HGNC:2987,DOCK1,dedicator of cytokinesis 1,NM_001290223.2,NP_001277152.2,ENST00000623213.2,ENSP00000485033.1,MANE Select,NC_000010.11,126905428,127452516,+,chr10
3152,3152,GeneID:4745,ENSG00000165973.19,HGNC:7750,NELL1,neural EGFL like 1,NM_006157.5,NP_006148.2,ENST00000357134.10,ENSP00000349654.5,MANE Select,NC_000011.10,20669586,21575686,+,chr11
17268,17268,GeneID:338645,ENSG00000187398.12,HGNC:23206,LUZP2,leucine zipper protein 2,NM_001009909.4,NP_001009909.2,ENST00000336930.11,ENSP00000336817.6,MANE Select,NC_000011.10,24497053,25082638,+,chr11
11635,11635,GeneID:57689,ENSG00000148948.8,HGNC:29317,LRRC4C,leucine rich repeat containing 4C,NM_001258419.2,NP_001245348.1,ENST00000528697.6,ENSP00000437132.1,MANE Select,NC_000011.10,40114209,41459652,-,chr11
7899,7899,GeneID:22941,ENSG00000162105.21,HGNC:14295,SHANK2,SH3 and multiple ankyrin repeat domains 2,NM_012309.5,NP_036441.2,ENST00000601538.6,ENSP00000469689.2,MANE Select,NC_000011.10,70467854,71252577,-,chr11
8661,8661,GeneID:26011,ENSG00000149256.16,HGNC:29945,TENM4,teneurin transmembrane protein 4,NM_001098816.3,NP_001092286.2,ENST00000278550.12,ENSP00000278550.7,MANE Select,NC_000011.10,78652829,79441030,-,chr11
1213,1213,GeneID:1740,ENSG00000150672.19,HGNC:2901,DLG2,discs large MAGUK scaffold protein 2,NM_001142699.3,NP_001136171.1,ENST00000376104.7,ENSP00000365272.2,MANE Select,NC_000011.10,83455173,85627344,-,chr11
1975,1975,GeneID:2915,ENSG00000168959.15,HGNC:4597,GRM5,glutamate metabotropic receptor 5,NM_001143831.3,NP_001137303.1,ENST00000305447.5,ENSP00000306138.4,MANE Select,NC_000011.10,88504642,89065982,-,chr11
14645,14645,GeneID:120114,ENSG00000165323.16,HGNC:23112,FAT3,FAT atypical cadherin 3,NM_001367949.2,NP_001354878.1,ENST00000525166.6,ENSP00000432586.2,MANE Select,NC_000011.10,92224818,92896473,+,chr11
10000,10000,GeneID:53942,ENSG00000149972.12,HGNC:2175,CNTN5,contactin 5,NM_014361.4,NP_055176.1,ENST00000524871.6,ENSP00000435637.1,MANE Select,NC_000011.10,99020949,100358885,+,chr11
13556,13556,GeneID:84623,ENSG00000149571.12,HGNC:23204,KIRREL3,kirre like nephrin family adhesion molecule 3,NM_032531.4,NP_115920.1,ENST00000525144.7,ENSP00000435466.2,MANE Select,NC_000011.10,126423358,127000770,-,chr11
9432,9432,GeneID:50863,ENSG00000182667.15,HGNC:17941,NTM,neurotrimin,NM_001352005.2,NP_001338934.1,ENST00000683400.1,ENSP00000507313.1,MANE Select,NC_000011.10,131370615,132336822,+,chr11
3302,3302,GeneID:4978,ENSG00000183715.15,HGNC:8143,OPCML,opioid binding protein/cell adhesion molecule like,NM_001012393.5,NP_001012393.1,ENST00000524381.6,ENSP00000434750.1,MANE Select,NC_000011.10,132414981,133532501,-,chr11
540,540,GeneID:775,ENSG00000151067.23,HGNC:1390,CACNA1C,calcium voltage-gated channel subunit alpha1 C,NM_001167623.2,NP_001161095.1,ENST00000399603.6,ENSP00000382512.1,MANE Plus Clinical,NC_000012.12,2052987,2697950,+,chr12
541,541,GeneID:775,ENSG00000151067.23,HGNC:1390,CACNA1C,calcium voltage-gated channel subunit alpha1 C,NM_000719.7,NP_000710.5,ENST00000399655.6,ENSP00000382563.1,MANE Select,NC_000012.12,2052987,2697950,+,chr12
13373,13373,GeneID:84216,ENSG00000139173.10,HGNC:25308,TMEM117,transmembrane protein 117,NM_032256.3,NP_115632.1,ENST00000266534.8,ENSP00000266534.3,MANE Select,NC_000012.12,43836081,44389758,+,chr12
4697,4697,GeneID:6857,ENSG00000067715.15,HGNC:11509,SYT1,synaptotagmin 1,NM_005639.3,NP_005630.1,ENST00000261205.9,ENSP00000261205.4,MANE Select,NC_000012.12,78864774,79452008,+,chr12
11203,11203,GeneID:56899,ENSG00000185046.21,HGNC:24600,ANKS1B,ankyrin repeat and sterile alpha motif domain containing 1B,NM_001352186.2,NP_001339115.1,ENST00000683438.2,ENSP00000508105.1,MANE Select,NC_000012.12,98743974,99984936,-,chr12
14674,14674,GeneID:121256,ENSG00000151952.16,HGNC:29411,TMEM132D,transmembrane protein 132D,NM_133448.3,NP_597705.2,ENST00000422113.7,ENSP00000408581.2,MANE Select,NC_000012.12,129071726,129904025,-,chr12
9935,9935,GeneID:51761,ENSG00000132932.19,HGNC:13533,ATP8A2,ATPase phospholipid transporting 8A2,NM_016529.6,NP_057613.4,ENST00000381655.7,ENSP00000371070.2,MANE Select,NC_000013.11,25371974,26025851,+,chr13
8157,8157,GeneID:23281,ENSG00000132938.22,HGNC:20595,MTUS2,microtubule associated scaffold protein 2,NM_001033602.4,NP_001028774.3,ENST00000612955.6,ENSP00000483729.2,MANE Select,NC_000013.11,28820339,29505947,+,chr13
8908,8908,GeneID:26960,ENSG00000172915.20,HGNC:7648,NBEA,neurobeachin,NM_001385012.1,NP_001371941.1,ENST00000379939.7,ENSP00000369271.2,MANE Select,NC_000013.11,34942270,35672736,+,chr13
10447,10447,GeneID:55068,ENSG00000120658.14,HGNC:25474,ENOX1,ecto-NOX disulfide-thiol exchanger 1,NM_001347969.2,NP_001334898.1,ENST00000690772.1,ENSP00000509229.1,MANE Select,NC_000013.11,43213130,43786972,-,chr13
3393,3393,GeneID:5101,ENSG00000184226.15,HGNC:8661,PCDH9,protocadherin 9,NM_203487.3,NP_982354.1,ENST00000377865.7,ENSP00000367096.2,MANE Select,NC_000013.11,66302834,67230336,-,chr13
1587,1587,GeneID:2262,ENSG00000179399.16,HGNC:4453,GPC5,glypican 5,NM_004466.6,NP_004457.1,ENST00000377067.9,ENSP00000366267.3,MANE Select,NC_000013.11,91398621,92867237,+,chr13
6808,6808,GeneID:10082,ENSG00000183098.12,HGNC:4454,GPC6,glypican 6,NM_005708.5,NP_005699.1,ENST00000377047.9,ENSP00000366246.3,MANE Select,NC_000013.11,93226807,94408020,+,chr13
16853,16853,GeneID:266722,ENSG00000185352.10,HGNC:19134,HS6ST3,heparan sulfate 6-O-sulfotransferase 3,NM_153456.4,NP_703157.2,ENST00000376705.4,ENSP00000365895.2,MANE Select,NC_000013.11,96090107,96839562,+,chr13
18768,18768,GeneID:728215,ENSG00000204442.4,HGNC:33877,NALF1,NALCN channel auxiliary factor 1,NM_001080396.3,NP_001073865.1,ENST00000375915.4,ENSP00000365080.1,MANE Select,NC_000013.11,107163510,107867496,-,chr13
7949,7949,GeneID:23026,ENSG00000041515.16,HGNC:29822,MYO16,myosin XVI,NM_001198950.3,NP_001185879.1,ENST00000457511.7,ENSP00000401633.3,MANE Select,NC_000013.11,108629611,109208005,+,chr13
11902,11902,GeneID:64067,ENSG00000151322.20,HGNC:19311,NPAS3,neuronal PAS domain protein 3,NM_001164749.2,NP_001158221.1,ENST00000356141.9,ENSP00000348460.4,MANE Select,NC_000014.9,32938879,33804173,+,chr14
15945,15945,GeneID:161357,ENSG00000139915.22,HGNC:19835,MDGA2,MAM domain containing glycosylphosphatidylinositol anchor 2,NM_001113498.3,NP_001106970.4,ENST00000399232.8,ENSP00000382178.4,MANE Select,NC_000014.9,46840092,47675605,-,chr14
6946,6946,GeneID:10243,ENSG00000171723.16,HGNC:15465,GPHN,gephyrin,NM_020806.5,NP_065857.1,ENST00000478722.6,ENSP00000417901.1,MANE Select,NC_000014.9,66508147,67181803,+,chr14
3981,3981,GeneID:5890,ENSG00000182185.19,HGNC:9822,RAD51B,RAD51 paralog B,NM_133510.4,NP_598194.1,ENST00000471583.6,ENSP00000418859.1,MANE Select,NC_000014.9,67819779,68478093,+,chr14
6421,6421,GeneID:9628,ENSG00000182732.18,HGNC:10002,RGS6,regulator of G protein signaling 6,NM_001204424.2,NP_001191353.1,ENST00000553525.6,ENSP00000451030.1,MANE Select,NC_000014.9,71932429,72566530,+,chr14
6220,6220,GeneID:9369,ENSG00000021645.20,HGNC:8010,NRXN3,neurexin 3,NM_001330195.2,NP_001317124.1,ENST00000335750.7,ENSP00000338349.7,MANE Select,NC_000014.9,78170373,79868291,+,chr14
1713,1713,GeneID:2567,ENSG00000182256.13,HGNC:4088,GABRG3,gamma-aminobutyric acid type A receptor subunit gamma3,NM_033223.5,NP_150092.2,ENST00000615808.5,ENSP00000479113.1,MANE Select,NC_000015.10,26971181,27541984,+,chr15
4222,4222,GeneID:6263,ENSG00000198838.15,HGNC:10485,RYR3,ryanodine receptor 3,NM_001036.6,NP_001027.3,ENST00000634891.2,ENSP00000489262.1,MANE Select,NC_000015.10,33310967,33866102,+,chr15
18310,18310,GeneID:440279,ENSG00000137766.18,HGNC:23149,UNC13C,unc-13 homolog C,NM_001080534.3,NP_001074003.1,ENST00000260323.16,ENSP00000260323.11,MANE Select,NC_000015.10,53978441,54628605,+,chr15
4107,4107,GeneID:6095,ENSG00000069667.16,HGNC:10258,RORA,RAR related orphan receptor A,NM_134261.3,NP_599023.1,ENST00000335670.11,ENSP00000335087.6,MANE Select,NC_000015.10,60488284,61229302,-,chr15
12646,12646,GeneID:79875,ENSG00000187720.15,HGNC:25835,THSD4,thrombospondin type 1 domain containing 4,NM_024817.3,NP_079093.2,ENST00000261862.8,ENSP00000261862.8,MANE Select,NC_000015.10,71115471,71783383,+,chr15
9367,9367,GeneID:49855,ENSG00000140386.13,HGNC:13081,SCAPER,S-phase cyclin A associated protein in the ER,NM_020843.4,NP_065894.2,ENST00000563290.6,ENSP00000454973.1,MANE Select,NC_000015.10,76347904,76905340,-,chr15
14748,14748,GeneID:123624,ENSG00000273540.5,HGNC:26504,AGBL1,AGBL carboxypeptidase 1,NM_001386094.1,NP_001373023.1,ENST00000614907.3,ENSP00000490608.2,MANE Select,NC_000015.10,86079871,86916156,+,chr15
10183,10183,GeneID:54715,ENSG00000078328.23,HGNC:18222,RBFOX1,RNA binding fox-1 homolog 1,NM_018723.4,NP_061193.2,ENST00000550418.6,ENSP00000450031.1,MANE Select,NC_000016.10,6019024,7713340,+,chr16
14117,14117,GeneID:92017,ENSG00000048471.14,HGNC:30542,SNX29,sorting nexin 29,NM_032167.5,NP_115543.3,ENST00000566228.6,ENSP00000456480.1,MANE Select,NC_000016.10,11976734,12574287,+,chr16
9924,9924,GeneID:51741,ENSG00000186153.19,HGNC:12799,WWOX,WW domain containing oxidoreductase,NM_016373.4,NP_057457.1,ENST00000566780.6,ENSP00000457230.1,MANE Select,NC_000016.10,78099654,79212667,+,chr16
728,728,GeneID:1012,ENSG00000140945.17,HGNC:1753,CDH13,cadherin 13,NM_001257.5,NP_001248.1,ENST00000567109.6,ENSP00000479395.1,MANE Select,NC_000016.10,82626969,83800640,+,chr16
11231,11231,GeneID:56934,ENSG00000154975.14,HGNC:1369,CA10,carbonic anhydrase 10,NM_020178.5,NP_064563.1,ENST00000451037.7,ENSP00000405388.2,MANE Select,NC_000017.11,51630320,52158714,-,chr17
10248,10248,GeneID:54828,ENSG00000141376.24,HGNC:14347,BCAS3,BCAS3 microtubule associated cell migration factor,NM_017679.5,NP_060149.3,ENST00000407086.8,ENSP00000385323.2,MANE Select,NC_000017.11,60677851,61392831,+,chr17
16293,16293,GeneID:201134,ENSG00000154240.18,HGNC:28514,CEP112,centrosomal protein 112,NM_001199165.4,NP_001186094.1,ENST00000535342.7,ENSP00000442784.2,MANE Select,NC_000017.11,65635537,66192133,-,chr17
6124,6124,GeneID:9229,ENSG00000170579.19,HGNC:2905,DLGAP1,DLG associated protein 1,NM_004746.4,NP_004737.2,ENST00000315677.8,ENSP00000316377.3,MANE Select,NC_000018.10,3496032,4455307,-,chr18
3920,3920,GeneID:5797,ENSG00000173482.17,HGNC:9675,PTPRM,protein tyrosine phosphatase receptor type M,NM_001105244.2,NP_001098714.1,ENST00000580170.6,ENSP00000463325.1,MANE Select,NC_000018.10,7567316,8406856,+,chr18
1152,1152,GeneID:1630,ENSG00000187323.13,HGNC:2701,DCC,DCC netrin 1 receptor,NM_005215.4,NP_005206.2,ENST00000442544.7,ENSP00000389140.2,MANE Select,NC_000018.10,52340197,53535899,+,chr18
7962,7962,GeneID:23040,ENSG00000186487.21,HGNC:7623,MYT1L,myelin transcription factor 1 like,NM_001303052.2,NP_001289981.1,ENST00000647738.2,ENSP00000497479.2,MANE Select,NC_000002.12,1789113,2331275,-,chr2
163,163,GeneID:238,ENSG00000171094.18,HGNC:427,ALK,ALK receptor tyrosine kinase,NM_004304.5,NP_004295.2,ENST00000389048.8,ENSP00000373700.3,MANE Select,NC_000002.12,29192774,29921586,-,chr2
3750,3750,GeneID:5581,ENSG00000171132.14,HGNC:9401,PRKCE,protein kinase C epsilon,NM_005400.3,NP_005391.1,ENST00000306156.8,ENSP00000306124.3,MANE Select,NC_000002.12,45651675,46187990,+,chr2
6229,6229,GeneID:9378,ENSG00000179915.25,HGNC:8008,NRXN1,neurexin 1,NM_001330078.2,NP_001317007.1,ENST00000401669.7,ENSP00000385017.2,MANE Select,NC_000002.12,49918503,51032132,-,chr2
8117,8117,GeneID:23233,ENSG00000144036.16,HGNC:17085,EXOC6B,exocyst complex component 6B,NM_015189.3,NP_056004.1,ENST00000272427.11,ENSP00000272427.7,MANE Select,NC_000002.12,72175984,72826033,-,chr2
12756,12756,GeneID:80059,ENSG00000176204.14,HGNC:19411,LRRTM4,leucine rich repeat transmembrane neuronal 4,NM_001134745.3,NP_001128217.1,ENST00000409884.6,ENSP00000387297.1,MANE Select,NC_000002.12,76747685,77522376,-,chr2
1062,1062,GeneID:1496,ENSG00000066032.19,HGNC:2510,CTNNA2,catenin alpha 2,NM_001282597.3,NP_001269526.1,ENST00000402739.9,ENSP00000384638.4,MANE Select,NC_000002.12,79513051,80648780,+,chr2
2648,2648,GeneID:3899,ENSG00000144218.21,HGNC:6473,AFF3,ALF transcription elongation factor 3,NM_001386135.1,NP_001373064.1,ENST00000672756.2,ENSP00000500419.1,MANE Select,NC_000002.12,99545419,100142590,-,chr2
11595,11595,GeneID:57628,ENSG00000175497.17,HGNC:20823,DPP10,dipeptidyl peptidase like 10,NM_020868.6,NP_065919.3,ENST00000410059.6,ENSP00000386565.1,MANE Select,NC_000002.12,114442641,115845780,+,chr2
15024,15024,GeneID:129684,ENSG00000155052.15,HGNC:18748,CNTNAP5,contactin associated protein family member 5,NM_001367498.1,NP_001354427.1,ENST00000682447.1,ENSP00000508115.1,MANE Select,NC_000002.12,124025287,124921219,+,chr2
17475,17475,GeneID:344148,ENSG00000176771.18,HGNC:29847,NCKAP5,NCK associated protein 5,NM_207363.3,NP_997246.2,ENST00000409261.6,ENSP00000387128.1,MANE Select,NC_000002.12,132671788,133568463,-,chr2
12907,12907,GeneID:80731,ENSG00000144229.13,HGNC:29348,THSD7B,thrombospondin type 1 domain containing 7B,NM_001316349.2,NP_001303278.1,ENST00000409968.6,ENSP00000387145.1,MANE Select,NC_000002.12,136765545,137677718,+,chr2
9964,9964,GeneID:53353,ENSG00000168702.18,HGNC:6693,LRP1B,LDL receptor related protein 1B,NM_018557.3,NP_061027.2,ENST00000389484.8,ENSP00000374135.3,MANE Select,NC_000002.12,140231423,142131016,-,chr2
10964,10964,GeneID:55843,ENSG00000075884.14,HGNC:21030,ARHGAP15,Rho GTPase activating protein 15,NM_018460.4,NP_060930.3,ENST00000295095.11,ENSP00000295095.6,MANE Select,NC_000002.12,143129419,143768352,+,chr2
14403,14403,GeneID:114805,ENSG00000144278.15,HGNC:23242,GALNT13,polypeptide N-acetylgalactosaminyltransferase 13,NM_052917.4,NP_443149.2,ENST00000392825.8,ENSP00000376570.3,MANE Select,NC_000002.12,153871922,154453979,+,chr2
5750,5750,GeneID:8708,ENSG00000172318.6,HGNC:916,B3GALT1,"beta-1,3-galactosyltransferase 1",NM_020981.4,NP_066191.1,ENST00000392690.4,ENSP00000376456.2,MANE Select,NC_000002.12,167293001,167874045,+,chr2
14586,14586,GeneID:117583,ENSG00000116117.20,HGNC:14446,PARD3B,par-3 family cell polarity regulator beta,NM_001302769.2,NP_001289698.1,ENST00000406610.7,ENSP00000385848.2,MANE Select,NC_000002.12,204545475,205620162,+,chr2
1447,1447,GeneID:2066,ENSG00000178568.16,HGNC:3432,ERBB4,erb-b2 receptor tyrosine kinase 4,NM_005235.3,NP_005226.1,ENST00000342788.9,ENSP00000342235.4,MANE Select,NC_000002.12,211375717,212538802,-,chr2
12417,12417,GeneID:79582,ENSG00000144451.20,HGNC:23225,SPAG16,sperm associated antigen 16,NM_024532.5,NP_078808.3,ENST00000331683.10,ENSP00000332592.5,MANE Select,NC_000002.12,213284464,214410501,+,chr2
14558,14558,GeneID:116987,ENSG00000157985.20,HGNC:16922,AGAP1,"ArfGAP with GTPase domain, ankyrin repeat and PH domain 1",NM_001037131.3,NP_001032208.1,ENST00000304032.13,ENSP00000307634.7,MANE Select,NC_000002.12,235494043,236131793,+,chr2
8120,8120,GeneID:23236,ENSG00000182621.19,HGNC:15917,PLCB1,phospholipase C beta 1,NM_015192.4,NP_056007.1,ENST00000338037.11,ENSP00000338185.6,MANE Select,NC_000020.11,8132266,8884900,+,chr20
15336,15336,GeneID:140733,ENSG00000172264.19,HGNC:16126,MACROD2,mono-ADP ribosylhydrolase 2,NM_001351661.2,NP_001338590.1,ENST00000684519.1,ENSP00000507484.1,MANE Select,NC_000020.11,13995516,16053197,+,chr20
7620,7620,GeneID:11122,ENSG00000196090.14,HGNC:9682,PTPRT,protein tyrosine phosphatase receptor type T,NM_007050.6,NP_008981.4,ENST00000373187.6,ENSP00000362283.1,MANE Select,NC_000020.11,42072756,43189906,-,chr20
14987,14987,GeneID:128553,ENSG00000182463.17,HGNC:13010,TSHZ2,teashirt zinc finger homeobox 2,NM_173485.6,NP_775756.3,ENST00000371497.10,ENSP00000360552.3,MANE Select,NC_000020.11,52972358,53495330,+,chr20
719,719,GeneID:1002,ENSG00000179242.16,HGNC:1763,CDH4,cadherin 4,NM_001794.5,NP_001785.2,ENST00000614565.5,ENSP00000484928.1,MANE Select,NC_000020.11,61252261,61940617,+,chr20
3101,3101,GeneID:4685,ENSG00000154654.15,HGNC:7657,NCAM2,neural cell adhesion molecule 2,NM_004540.5,NP_004531.2,ENST00000400546.6,ENSP00000383392.1,MANE Select,NC_000021.9,20998409,21543329,+,chr21
1281,1281,GeneID:1826,ENSG00000171587.15,HGNC:3039,DSCAM,DS cell adhesion molecule,NM_001389.5,NP_001380.2,ENST00000400454.6,ENSP00000383303.1,MANE Select,NC_000021.9,40010999,40847158,-,chr21
8194,8194,GeneID:23331,ENSG00000100154.15,HGNC:29179,TTC28,tetratricopeptide repeat domain 28,NM_001145418.2,NP_001138890.1,ENST00000397906.7,ENSP00000381003.2,MANE Select,NC_000022.11,27978014,28679840,-,chr22
5416,5416,GeneID:8224,ENSG00000185666.16,HGNC:11496,SYN3,synapsin III,NM_003490.4,NP_003481.3,ENST00000358763.7,ENSP00000351614.2,MANE Select,NC_000022.11,32507820,33058381,-,chr22
6116,6116,GeneID:9215,ENSG00000133424.22,HGNC:6511,LARGE1,LARGE xylosyl- and glucuronyltransferase 1,NM_133642.5,NP_598397.1,ENST00000397394.8,ENSP00000380549.2,MANE Select,NC_000022.11,33272509,33920476,-,chr22
15759,15759,GeneID:152330,ENSG00000144619.15,HGNC:2174,CNTN4,contactin 4,NM_175607.3,NP_783200.1,ENST00000418658.6,ENSP00000396010.1,MANE Select,NC_000003.12,2098866,3057959,+,chr3
1977,1977,GeneID:2917,ENSG00000196277.17,HGNC:4599,GRM7,glutamate metabotropic receptor 7,NM_000844.4,NP_000835.1,ENST00000357716.9,ENSP00000350348.4,MANE Select,NC_000003.12,6861115,7741533,+,chr3
6555,6555,GeneID:9779,ENSG00000131374.15,HGNC:19166,TBC1D5,TBC1 domain family member 5,NM_001349074.2,NP_001336003.1,ENST00000696125.1,ENSP00000512418.1,MANE Select,NC_000003.12,17157168,17742631,-,chr3
9071,9071,GeneID:27303,ENSG00000144642.22,HGNC:13427,RBMS3,RNA binding motif single stranded interacting protein 3,NM_001003793.3,NP_001003793.1,ENST00000383767.7,ENSP00000373277.2,MANE Select,NC_000003.12,29281071,30010386,+,chr3
10385,10385,GeneID:54986,ENSG00000168038.11,HGNC:15784,ULK4,unc-51 like kinase 4,NM_017886.4,NP_060356.2,ENST00000301831.9,ENSP00000301831.4,MANE Select,NC_000003.12,41246599,41962103,-,chr3
1253,1253,GeneID:1795,ENSG00000088538.13,HGNC:2989,DOCK3,dedicator of cytokinesis 3,NM_004947.5,NP_004938.1,ENST00000266037.10,ENSP00000266037.8,MANE Select,NC_000003.12,50674927,51384198,+,chr3
10932,10932,GeneID:55799,ENSG00000157445.16,HGNC:15460,CACNA2D3,calcium voltage-gated channel auxiliary subunit alpha2delta 3,NM_018398.3,NP_060868.2,ENST00000474759.6,ENSP00000419101.1,MANE Select,NC_000003.12,54122552,55074557,+,chr3
8698,8698,GeneID:26059,ENSG00000187672.15,HGNC:31922,ERC2,ELKS/RAB6-interacting/CAST family member 2,NM_015576.3,NP_056391.1,ENST00000288221.11,ENSP00000288221.6,MANE Select,NC_000003.12,55508311,56468467,-,chr3
1595,1595,GeneID:2272,ENSG00000189283.11,HGNC:3701,FHIT,fragile histidine triad diadenosine triphosphatase,NM_002012.4,NP_002003.1,ENST00000492590.6,ENSP00000418582.1,MANE Select,NC_000003.12,59747277,61251452,-,chr3
3916,3916,GeneID:5793,ENSG00000144724.20,HGNC:9671,PTPRG,protein tyrosine phosphatase receptor type G,NM_002841.4,NP_002832.3,ENST00000474889.6,ENSP00000418112.1,MANE Select,NC_000003.12,61561571,62297609,+,chr3
6121,6121,GeneID:9223,ENSG00000151276.24,HGNC:946,MAGI1,"membrane associated guanylate kinase, WW and PDZ domain containing 1",NM_001033057.2,NP_001028229.1,ENST00000402939.7,ENSP00000385450.2,MANE Select,NC_000003.12,65353526,66038918,-,chr3
18262,18262,GeneID:407738,ENSG00000183662.12,HGNC:21587,TAFA1,TAFA chemokine like family member 1,NM_213609.4,NP_998774.2,ENST00000478136.6,ENSP00000418575.1,MANE Select,NC_000003.12,68004247,68545621,+,chr3
8957,8957,GeneID:27086,ENSG00000114861.24,HGNC:3823,FOXP1,forkhead box P1,NM_001349338.3,NP_001336267.1,ENST00000649528.3,ENSP00000497369.1,MANE Select,NC_000003.12,70954708,71583728,-,chr3
4104,4104,GeneID:6092,ENSG00000185008.19,HGNC:10250,ROBO2,roundabout guidance receptor 2,NM_001395656.1,NP_001382585.1,ENST00000696593.1,ENSP00000512738.1,MANE Select,NC_000003.12,77040099,77649964,+,chr3
4103,4103,GeneID:6091,ENSG00000169855.21,HGNC:10249,ROBO1,roundabout guidance receptor 1,NM_002941.4,NP_002932.1,ENST00000464233.6,ENSP00000420321.1,MANE Select,NC_000003.12,78597239,79767998,-,chr3
16659,16659,GeneID:253559,ENSG00000175161.14,HGNC:29849,CADM2,cell adhesion molecule 2,NM_001167675.2,NP_001161147.1,ENST00000383699.8,ENSP00000373200.3,MANE Select,NC_000003.12,84958989,86074429,+,chr3
17100,17100,GeneID:285220,ENSG00000080224.18,HGNC:19296,EPHA6,EPH receptor A6,NM_001080448.3,NP_001073917.2,ENST00000389672.10,ENSP00000374323.5,MANE Select,NC_000003.12,96814594,97761532,+,chr3
8736,8736,GeneID:26137,ENSG00000181722.18,HGNC:13503,ZBTB20,zinc finger and BTB domain containing 20,NM_001348800.3,NP_001335729.1,ENST00000675478.1,ENSP00000501561.1,MANE Select,NC_000003.12,114314500,115147288,-,chr3
2743,2743,GeneID:4045,ENSG00000185565.13,HGNC:6705,LSAMP,limbic system associated membrane protein,NM_002338.5,NP_002329.2,ENST00000490035.7,ENSP00000419000.1,MANE Select,NC_000003.12,115802374,116445487,-,chr3
5957,5957,GeneID:8997,ENSG00000160145.16,HGNC:4814,KALRN,kalirin RhoGEF kinase,NM_001388419.1,NP_001375348.1,ENST00000682506.1,ENSP00000508359.1,MANE Select,NC_000003.12,124033369,124726325,+,chr3
11910,11910,GeneID:64084,ENSG00000158258.16,HGNC:17448,CLSTN2,calsyntenin 2,NM_022131.3,NP_071414.2,ENST00000458420.7,ENSP00000402460.2,MANE Select,NC_000003.12,139935185,140577397,+,chr3
17098,17098,GeneID:285195,ENSG00000181804.15,HGNC:20653,SLC9A9,solute carrier family 9 member A9,NM_173653.4,NP_775924.1,ENST00000316549.11,ENSP00000320246.6,MANE Select,NC_000003.12,143265222,143848468,-,chr3
9309,9309,GeneID:29970,ENSG00000151967.19,HGNC:15678,SCHIP1,schwannomin interacting protein 1,NM_014575.4,NP_055390.1,ENST00000638749.2,ENSP00000491030.1,MANE Select,NC_000003.12,159273244,159897359,+,chr3
1482,1482,GeneID:2122,ENSG00000085276.19,HGNC:3498,MECOM,MDS1 and EVI1 complex locus,NM_004991.4,NP_004982.2,ENST00000651503.2,ENSP00000498411.1,MANE Select,NC_000003.12,169083507,169663712,-,chr3
7839,7839,GeneID:22871,ENSG00000169760.18,HGNC:14291,NLGN1,neuroligin 1,NM_001365925.2,NP_001352854.1,ENST00000695368.1,ENSP00000511841.1,MANE Select,NC_000003.12,173397744,174294372,+,chr3
16707,16707,GeneID:254827,ENSG00000177694.16,HGNC:23219,NAALADL2,N-acetylated alpha-linked acidic dipeptidase like 2,NM_207015.3,NP_996898.2,ENST00000454872.6,ENSP00000404705.1,MANE Select,NC_000003.12,174859334,175810548,+,chr3
2733,2733,GeneID:4026,ENSG00000145012.15,HGNC:6679,LPP,LIM domain containing preferred translocation partner in lipoma,NM_001375462.1,NP_001362391.1,ENST00000617246.5,ENSP00000478901.1,MANE Select,NC_000003.12,188154157,188890671,+,chr3
1582,1582,GeneID:2257,ENSG00000114279.15,HGNC:3668,FGF12,fibroblast growth factor 12,NM_004113.6,NP_004104.3,ENST00000445105.7,ENSP00000393686.1,MANE Select,NC_000003.12,192139390,192727541,-,chr3
11519,11519,GeneID:57537,ENSG00000184985.17,HGNC:16698,SORCS2,sortilin related VPS10 domain containing receptor 2,NM_020777.3,NP_065828.2,ENST00000507866.6,ENSP00000422185.2,MANE Select,NC_000004.12,7192538,7742827,+,chr4
12879,12879,GeneID:80333,ENSG00000185774.17,HGNC:30083,KCNIP4,potassium voltage-gated channel interacting protein 4,NM_025221.6,NP_079497.2,ENST00000382152.7,ENSP00000371587.2,MANE Select,NC_000004.12,20728606,21948772,-,chr4
8159,8159,GeneID:23284,ENSG00000150471.17,HGNC:20974,ADGRL3,adhesion G protein-coupled receptor L3,NM_001387552.1,NP_001374481.1,ENST00000683033.1,ENSP00000507980.1,MANE Select,NC_000004.12,61200326,62078335,+,chr4
16722,16722,GeneID:255119,ENSG00000197826.13,HGNC:28554,CFAP299,cilia and flagella associated protein 299,NM_152770.3,NP_689983.2,ENST00000358105.8,ENSP00000350818.3,MANE Select,NC_000004.12,80335730,80963750,+,chr4
13132,13132,GeneID:83478,ENSG00000138639.18,HGNC:25361,ARHGAP24,Rho GTPase activating protein 24,NM_001025616.3,NP_001020787.2,ENST00000395184.6,ENSP00000378611.1,MANE Select,NC_000004.12,85475150,86002666,+,chr4
18184,18184,GeneID:401145,ENSG00000184305.16,HGNC:29349,CCSER1,coiled-coil serine rich protein 1,NM_001145065.2,NP_001138537.1,ENST00000509176.6,ENSP00000425040.1,MANE Select,NC_000004.12,90127394,91605295,+,chr4
1956,1956,GeneID:2895,ENSG00000152208.13,HGNC:4576,GRID2,glutamate ionotropic receptor delta type subunit 2,NM_001510.4,NP_001501.2,ENST00000282020.9,ENSP00000282020.4,MANE Select,NC_000004.12,92303966,93774566,+,chr4
17131,17131,GeneID:285555,ENSG00000163116.10,HGNC:28712,STPG2,sperm tail PG-rich repeat containing 2,NM_174952.3,NP_777612.1,ENST00000295268.4,ENSP00000295268.3,MANE Select,NC_000004.12,97558872,98143476,-,chr4
5837,5837,GeneID:8821,ENSG00000109452.13,HGNC:6075,INPP4B,inositol polyphosphate-4-phosphatase type II B,NM_001101669.3,NP_001095139.1,ENST00000262992.9,ENSP00000262992.4,MANE Select,NC_000004.12,142023160,142846301,-,chr4
705,705,GeneID:987,ENSG00000198589.15,HGNC:1742,LRBA,LPS responsive beige-like anchor protein,NM_001364905.1,NP_001351834.1,ENST00000651943.2,ENSP00000498582.2,MANE Select,NC_000004.12,150264435,151015284,-,chr4
11190,11190,GeneID:56884,ENSG00000168843.14,HGNC:21386,FSTL5,follistatin like 5,NM_020116.5,NP_064501.2,ENST00000306100.10,ENSP00000305334.4,MANE Select,NC_000004.12,161383897,162164000,-,chr4
10412,10412,GeneID:55016,ENSG00000145416.14,HGNC:26077,MARCHF1,membrane associated ring-CH-type finger 1,NM_001394959.1,NP_001381888.1,ENST00000514618.6,ENSP00000421322.1,MANE Select,NC_000004.12,163524718,164384019,-,chr4
18404,18404,GeneID:442117,ENSG00000174473.17,HGNC:33844,GALNTL6,polypeptide N-acetylgalactosaminyltransferase like 6,NM_001034845.3,NP_001030017.2,ENST00000506823.6,ENSP00000423313.1,MANE Select,NC_000004.12,171813404,173041559,+,chr4
10858,10858,GeneID:55714,ENSG00000218336.9,HGNC:29944,TENM3,teneurin transmembrane protein 3,NM_001080477.4,NP_001073946.1,ENST00000511685.6,ENSP00000424226.1,MANE Select,NC_000004.12,182243402,182803024,+,chr4
1066,1066,GeneID:1501,ENSG00000169862.21,HGNC:2516,CTNND2,catenin delta 2,NM_001332.4,NP_001323.1,ENST00000304623.13,ENSP00000307134.8,MANE Select,NC_000005.10,10971836,11904446,-,chr5
727,727,GeneID:1010,ENSG00000154162.15,HGNC:1751,CDH12,cadherin 12,NM_004061.5,NP_004052.2,ENST00000382254.6,ENSP00000371689.1,MANE Select,NC_000005.10,21750673,22853344,-,chr5
3422,3422,GeneID:5144,ENSG00000113448.21,HGNC:8783,PDE4D,phosphodiesterase 4D,NM_001104631.2,NP_001098101.1,ENST00000340635.11,ENSP00000345502.6,MANE Select,NC_000005.10,58969038,59893726,-,chr5
17704,17704,GeneID:375449,ENSG00000069020.19,HGNC:19037,MAST4,microtubule associated serine/threonine kinase family member 4,NM_001164664.2,NP_001158136.1,ENST00000403625.7,ENSP00000385727.1,MANE Select,NC_000005.10,66596393,67169593,+,chr5
13291,13291,GeneID:84059,ENSG00000164199.18,HGNC:17416,ADGRV1,adhesion G protein-coupled receptor V1,NM_032119.4,NP_115495.3,ENST00000405460.9,ENSP00000384582.2,MANE Select,NC_000005.10,90558797,91164437,+,chr5
12563,12563,GeneID:79772,ENSG00000175471.20,HGNC:26183,MCTP1,multiple C2 and transmembrane domain containing 1,NM_024717.7,NP_078993.4,ENST00000515393.6,ENSP00000424126.1,MANE Select,NC_000005.10,94703690,95285094,-,chr5
12114,12114,GeneID:64839,ENSG00000145743.18,HGNC:13615,FBXL17,F-box and leucine rich repeat protein 17,NM_001163315.3,NP_001156787.2,ENST00000542267.7,ENSP00000437464.2,MANE Select,NC_000005.10,107859035,108382098,-,chr5
4572,4572,GeneID:6695,ENSG00000152377.15,HGNC:11251,SPOCK1,"SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1",NM_004598.4,NP_004589.1,ENST00000394945.6,ENSP00000378401.1,MANE Select,NC_000005.10,136975298,137499326,-,chr5
11447,11447,GeneID:57451,ENSG00000145934.17,HGNC:29943,TENM2,teneurin transmembrane protein 2,NM_001395460.1,NP_001382389.1,ENST00000518659.6,ENSP00000429430.1,MANE Select,NC_000005.10,166979029,168264157,+,chr5
4480,4480,GeneID:6586,ENSG00000184347.16,HGNC:11087,SLIT3,slit guidance ligand 3,NM_003062.4,NP_003053.2,ENST00000519560.6,ENSP00000430333.2,MANE Select,NC_000005.10,168661740,169301139,-,chr5
1839,1839,GeneID:2762,ENSG00000112699.11,HGNC:4369,GMDS,"GDP-mannose 4,6-dehydratase",NM_001500.4,NP_001491.1,ENST00000380815.5,ENSP00000370194.4,MANE Select,NC_000006.12,1623806,2245605,-,chr6
16547,16547,GeneID:221692,ENSG00000112137.19,HGNC:20990,PHACTR1,phosphatase and actin regulator 1,NM_030948.6,NP_112210.1,ENST00000332995.12,ENSP00000329880.8,MANE Select,NC_000006.12,12716767,13287837,+,chr6
10312,10312,GeneID:54901,ENSG00000145996.11,HGNC:21050,CDKAL1,CDK5 regulatory subunit associated protein 1 like 1,NM_017774.3,NP_060244.2,ENST00000274695.8,ENSP00000274695.4,MANE Select,NC_000006.12,20534457,21232404,+,chr6
5564,5564,GeneID:8464,ENSG00000196284.18,HGNC:11466,SUPT3H,"SPT3 homolog, SAGA and STAGA complex component",NM_003599.4,NP_003590.1,ENST00000371459.6,ENSP00000360514.1,MANE Select,NC_000006.12,44826726,45377934,-,chr6
16340,16340,GeneID:202559,ENSG00000112232.10,HGNC:18114,KHDRBS2,"KH RNA binding domain containing, signal transduction associated 2",NM_152688.4,NP_689901.2,ENST00000281156.5,ENSP00000281156.3,MANE Select,NC_000006.12,61679961,62286225,-,chr6
17510,17510,GeneID:346007,ENSG00000188107.15,HGNC:21555,EYS,eyes shut homolog,NM_001142800.2,NP_001136272.1,ENST00000503581.6,ENSP00000424243.1,MANE Select,NC_000006.12,63719980,65707226,-,chr6
393,393,GeneID:577,ENSG00000135298.15,HGNC:945,ADGRB3,adhesion G protein-coupled receptor B3,NM_001704.3,NP_001695.2,ENST00000370598.6,ENSP00000359630.1,MANE Select,NC_000006.12,68635282,69389506,+,chr6
11143,11143,GeneID:56479,ENSG00000185760.18,HGNC:6299,KCNQ5,potassium voltage-gated channel subfamily Q member 5,NM_019842.4,NP_062816.2,ENST00000370398.6,ENSP00000359425.1,MANE Select,NC_000006.12,72622064,73198853,+,chr6
1959,1959,GeneID:2898,ENSG00000164418.22,HGNC:4580,GRIK2,glutamate ionotropic receptor kainate type subunit 2,NM_021956.5,NP_068775.1,ENST00000369134.9,ENSP00000358130.6,MANE Select,NC_000006.12,101393708,102070083,+,chr6
15816,15816,GeneID:154215,ENSG00000188580.16,HGNC:16443,NKAIN2,sodium/potassium transporting ATPase interacting 2,NM_001040214.3,NP_001035304.1,ENST00000368417.6,ENSP00000357402.1,MANE Select,NC_000006.12,123803865,124825640,+,chr6
3919,3919,GeneID:5796,ENSG00000152894.15,HGNC:9674,PTPRK,protein tyrosine phosphatase receptor type K,NM_002844.4,NP_002835.2,ENST00000368226.9,ENSP00000357209.4,MANE Select,NC_000006.12,127968785,128520599,-,chr6
2653,2653,GeneID:3908,ENSG00000196569.14,HGNC:6482,LAMA2,laminin subunit alpha 2,NM_000426.4,NP_000417.3,ENST00000421865.3,ENSP00000400365.2,MANE Select,NC_000006.12,128883138,129516566,+,chr6
5072,5072,GeneID:7402,ENSG00000152818.20,HGNC:12635,UTRN,utrophin,NM_007124.3,NP_009055.2,ENST00000367545.8,ENSP00000356515.3,MANE Select,NC_000006.12,144285335,144853034,+,chr6
3368,3368,GeneID:5071,ENSG00000185345.25,HGNC:8607,PRKN,parkin RBR E3 ubiquitin protein ligase,NM_004562.3,NP_004553.2,ENST00000366898.6,ENSP00000355865.1,MANE Select,NC_000006.12,161347417,162727766,-,chr6
15178,15178,GeneID:135138,ENSG00000112530.13,HGNC:19152,PACRG,parkin coregulated,NM_001080379.2,NP_001073848.1,ENST00000366888.7,ENSP00000355854.2,MANE Select,NC_000006.12,162727974,163315500,+,chr6
16561,16561,GeneID:221935,ENSG00000146555.20,HGNC:19307,SDK1,sidekick cell adhesion molecule 1,NM_152744.4,NP_689957.3,ENST00000404826.7,ENSP00000385899.2,MANE Select,NC_000007.14,3301252,4269000,+,chr7
1135,1135,GeneID:1607,ENSG00000136267.14,HGNC:2850,DGKB,diacylglycerol kinase beta,NM_001350709.2,NP_001337638.1,ENST00000402815.6,ENSP00000384909.1,MANE Select,NC_000007.14,14145049,14902751,-,chr7
6610,6610,GeneID:9844,ENSG00000155849.16,HGNC:16286,ELMO1,engulfment and cell motility 1,NM_014800.11,NP_055615.8,ENST00000310758.9,ENSP00000312185.4,MANE Select,NC_000007.14,36852906,37448864,-,chr7
12571,12571,GeneID:79783,ENSG00000175600.16,HGNC:16001,SUGCT,succinyl-CoA:glutarate-CoA transferase,NM_001193313.2,NP_001180242.2,ENST00000335693.9,ENSP00000338475.5,MANE Select,NC_000007.14,40135005,40860763,+,chr7
8693,8693,GeneID:26053,ENSG00000158321.19,HGNC:14262,AUTS2,activator of transcription and developmental regulator AUTS2,NM_015570.4,NP_056385.1,ENST00000342771.10,ENSP00000344087.4,MANE Select,NC_000007.14,69598475,70793506,+,chr7
12012,12012,GeneID:64409,ENSG00000185274.13,HGNC:16347,GALNT17,polypeptide N-acetylgalactosaminyltransferase 17,NM_022479.3,NP_071924.1,ENST00000333538.10,ENSP00000329654.5,MANE Select,NC_000007.14,71132144,71713599,+,chr7
13188,13188,GeneID:83698,ENSG00000183166.12,HGNC:13248,CALN1,calneuron 1,NM_031468.4,NP_113656.2,ENST00000395275.7,ENSP00000378690.2,MANE Select,NC_000007.14,71779491,72412338,-,chr7
6627,6627,GeneID:9863,ENSG00000187391.23,HGNC:18957,MAGI2,"membrane associated guanylate kinase, WW and PDZ domain containing 2",NM_012301.4,NP_036433.2,ENST00000354212.9,ENSP00000346151.4,MANE Select,NC_000007.14,78017055,79453667,-,chr7
16419,16419,GeneID:219578,ENSG00000182348.7,HGNC:21958,ZNF804B,zinc finger protein 804B,NM_181646.5,NP_857597.1,ENST00000333190.5,ENSP00000329638.4,MANE Select,NC_000007.14,88759700,89338528,+,chr7
3485,3485,GeneID:5218,ENSG00000058091.17,HGNC:8883,CDK14,cyclin dependent kinase 14,NM_001287135.2,NP_001274064.1,ENST00000380050.8,ENSP00000369390.3,MANE Select,NC_000007.14,90596321,91210590,+,chr7
17711,17711,GeneID:375612,ENSG00000187416.13,HGNC:6589,LHFPL3,LHFPL tetraspan subfamily member 3,NM_199000.3,NP_945351.1,ENST00000424859.7,ENSP00000393128.2,MANE Select,NC_000007.14,104328603,104908561,+,chr7
13270,13270,GeneID:83943,ENSG00000184903.10,HGNC:14598,IMMP2L,inner mitochondrial membrane peptidase subunit 2,NM_032549.4,NP_115938.1,ENST00000405709.7,ENSP00000384966.2,MANE Select,NC_000007.14,110662644,111562492,-,chr7
14243,14243,GeneID:93664,ENSG00000081803.17,HGNC:16018,CADPS2,calcium dependent secretion activator 2,NM_017954.11,NP_060424.9,ENST00000449022.7,ENSP00000398481.2,MANE Select,NC_000007.14,122318411,122886460,-,chr7
1978,1978,GeneID:2918,ENSG00000179603.19,HGNC:4600,GRM8,glutamate metabotropic receptor 8,NM_000845.3,NP_000836.2,ENST00000339582.7,ENSP00000344173.2,MANE Select,NC_000007.14,126438598,127252941,-,chr7
11794,11794,GeneID:60412,ENSG00000131558.15,HGNC:30389,EXOC4,exocyst complex component 4,NM_021807.4,NP_068579.3,ENST00000253861.5,ENSP00000253861.4,MANE Select,NC_000007.14,133253078,134065761,+,chr7
8687,8687,GeneID:26047,ENSG00000174469.23,HGNC:13830,CNTNAP2,contactin associated protein 2,NM_014141.6,NP_054860.1,ENST00000361727.8,ENSP00000354778.3,MANE Select,NC_000007.14,146116801,148420998,+,chr7
1261,1261,GeneID:1804,ENSG00000130226.18,HGNC:3010,DPP6,dipeptidyl peptidase like 6,NM_130797.4,NP_570629.2,ENST00000377770.8,ENSP00000367001.3,MANE Select,NC_000007.14,154052398,154894285,+,chr7
3922,3922,GeneID:5799,ENSG00000155093.20,HGNC:9677,PTPRN2,protein tyrosine phosphatase receptor type N2,NM_002847.5,NP_002838.2,ENST00000389418.9,ENSP00000374069.4,MANE Select,NC_000007.14,157539056,158587823,-,chr7
6123,6123,GeneID:9228,ENSG00000198010.13,HGNC:2906,DLGAP2,DLG associated protein 2,NM_001346810.2,NP_001333739.1,ENST00000637795.2,ENSP00000489774.1,MANE Select,NC_000008.11,737628,1708476,+,chr8
12033,12033,GeneID:64478,ENSG00000183117.20,HGNC:14026,CSMD1,CUB and Sushi multiple domains 1,NM_033225.6,NP_150094.5,ENST00000635120.2,ENSP00000489225.1,MANE Select,NC_000008.11,2935361,4994914,-,chr8
15225,15225,GeneID:137868,ENSG00000185053.14,HGNC:14075,SGCZ,sarcoglycan zeta,NM_139167.4,NP_631906.2,ENST00000382080.6,ENSP00000371512.1,MANE Select,NC_000008.11,14084845,15238431,-,chr8
15230,15230,GeneID:137970,ENSG00000156687.11,HGNC:18634,UNC5D,unc-5 netrin receptor D,NM_080872.4,NP_543148.2,ENST00000404895.7,ENSP00000385143.2,MANE Select,NC_000008.11,35235475,35796540,+,chr8
10032,10032,GeneID:54212,ENSG00000147481.17,HGNC:13740,SNTG1,syntrophin gamma 1,NM_018967.5,NP_061840.1,ENST00000642720.2,ENSP00000493900.1,MANE Select,NC_000008.11,49911407,50796692,+,chr8
17175,17175,GeneID:286183,ENSG00000185942.13,HGNC:26829,NKAIN3,sodium/potassium transporting ATPase interacting 3,NM_001304533.3,NP_001291462.1,ENST00000623646.3,ENSP00000501908.1,MANE Select,NC_000008.11,62248854,62984904,+,chr8
15233,15233,GeneID:138046,ENSG00000184672.12,HGNC:27036,RALYL,RALY RNA binding protein like,NM_173848.7,NP_776247.3,ENST00000521268.6,ENSP00000430367.1,MANE Select,NC_000008.11,84183274,84921844,+,chr8
15853,15853,GeneID:157680,ENSG00000132549.20,HGNC:2183,VPS13B,vacuolar protein sorting 13 homolog B,NM_017890.5,NP_060360.3,ENST00000358544.7,ENSP00000351346.2,MANE Plus Clinical,NC_000008.11,99013274,99877580,+,chr8
15852,15852,GeneID:157680,ENSG00000132549.20,HGNC:2183,VPS13B,vacuolar protein sorting 13 homolog B,NM_152564.5,NP_689777.3,ENST00000357162.7,ENSP00000349685.2,MANE Select,NC_000008.11,99013274,99877580,+,chr8
6483,6483,GeneID:9699,ENSG00000176406.25,HGNC:17283,RIMS2,regulating synaptic membrane exocytosis 2,NM_001348484.3,NP_001335413.1,ENST00000696799.1,ENSP00000512879.1,MANE Select,NC_000008.11,103500610,104254430,+,chr8
14389,14389,GeneID:114788,ENSG00000164796.18,HGNC:19291,CSMD3,CUB and Sushi multiple domains 3,NM_198123.2,NP_937756.1,ENST00000297405.10,ENSP00000297405.5,MANE Select,NC_000008.11,112222928,113436939,-,chr8
13186,13186,GeneID:83696,ENSG00000167632.18,HGNC:30832,TRAPPC9,trafficking protein particle complex subunit 9,NM_001160372.4,NP_001153844.1,ENST00000438773.4,ENSP00000405060.3,MANE Select,NC_000008.11,139727725,140457744,-,chr8
3912,3912,GeneID:5789,ENSG00000153707.19,HGNC:9668,PTPRD,protein tyrosine phosphatase receptor type D,NM_002839.4,NP_002830.1,ENST00000381196.9,ENSP00000370593.3,MANE Select,NC_000009.12,8314246,10613002,-,chr9
15866,15866,GeneID:158038,ENSG00000174482.11,HGNC:21207,LINGO2,leucine rich repeat and Ig domain containing 2,NM_001258282.3,NP_001245211.1,ENST00000698399.1,ENSP00000513694.1,MANE Select,NC_000009.12,27937617,29213601,-,chr9
12753,12753,GeneID:80036,ENSG00000083067.27,HGNC:17992,TRPM3,transient receptor potential cation channel subfamily M member 3,NM_001366145.2,NP_001353074.1,ENST00000677713.2,ENSP00000503830.2,MANE Select,NC_000009.12,70529060,71121621,-,chr9
8128,8128,GeneID:23245,ENSG00000148219.18,HGNC:17021,ASTN2,astrotactin 2,NM_001365068.1,NP_001351997.1,ENST00000313400.9,ENSP00000314038.4,MANE Select,NC_000009.12,116423112,117415057,-,chr9
11650,11650,GeneID:57706,ENSG00000119522.18,HGNC:29324,DENND1A,DENN domain containing 1A,NM_001352964.2,NP_001339893.1,ENST00000394215.7,ENSP00000377763.4,MANE Select,NC_000009.12,123379658,123930126,-,chr9
283,283,GeneID:395,ENSG00000047648.23,HGNC:676,ARHGAP6,Rho GTPase activating protein 6,NM_013427.3,NP_038286.2,ENST00000337414.9,ENSP00000338967.4,MANE Select,NC_000023.11,11137544,11665920,-,chrX
6537,6537,GeneID:9758,ENSG00000169933.17,HGNC:29007,FRMPD4,FERM and PDZ domain containing 4,NM_001368397.1,NP_001355326.1,ENST00000675598.1,ENSP00000502607.1,MANE Select,NC_000023.11,12138473,12724523,+,chrX
7636,7636,GeneID:11141,ENSG00000169306.11,HGNC:5996,IL1RAPL1,interleukin 1 receptor accessory protein like 1,NM_014271.4,NP_055086.1,ENST00000378993.6,ENSP00000368278.1,MANE Select,NC_000023.11,28587446,29956718,+,chrX
1224,1224,GeneID:1756,ENSG00000198947.18,HGNC:2928,DMD,dystrophin,NM_004006.3,NP_003997.2,ENST00000357033.9,ENSP00000354923.3,MANE Select,NC_000023.11,31119222,33211549,-,chrX
14563,14563,GeneID:117154,ENSG00000126733.22,HGNC:16814,DACH2,dachshund family transcription factor 2,NM_053281.3,NP_444511.1,ENST00000373125.9,ENSP00000362217.4,MANE Select,NC_000023.11,86148451,86832602,+,chrX
9081,9081,GeneID:27328,ENSG00000102290.23,HGNC:8656,PCDH11X,protocadherin 11 X-linked,NM_032968.5,NP_116750.1,ENST00000682573.1,ENSP00000507225.1,MANE Select,NC_000023.11,91779375,92623230,+,chrX
1204,1204,GeneID:1730,ENSG00000147202.19,HGNC:2877,DIAPH2,diaphanous related formin 2,NM_006729.5,NP_006720.1,ENST00000324765.13,ENSP00000321348.8,MANE Select,NC_000023.11,96684842,97604997,+,chrX
8808,8808,GeneID:26280,ENSG00000189108.14,HGNC:5997,IL1RAPL2,interleukin 1 receptor accessory protein like 2,NM_017416.2,NP_059112.1,ENST00000372582.6,ENSP00000361663.1,MANE Select,NC_000023.11,104566199,105767829,+,chrX
6889,6889,GeneID:10178,ENSG00000009694.14,HGNC:8117,TENM1,teneurin transmembrane protein 1,NM_001163278.2,NP_001156750.1,ENST00000422452.4,ENSP00000403954.4,MANE Select,NC_000023.11,124375903,125204312,-,chrX
13107,13107,GeneID:83259,ENSG00000099715.15,HGNC:15813,PCDH11Y,protocadherin 11 Y-linked,NM_001395587.1,NP_001382516.1,ENST00000698851.1,ENSP00000513983.1,MANE Select,NC_000024.10,5000296,5742224,+,chrY
1 Unnamed: 0 #NCBI_GeneID Ensembl_Gene HGNC_ID symbol name RefSeq_nuc RefSeq_prot Ensembl_nuc Ensembl_prot MANE_status GRCh38_chr chr_start chr_end chr_strand chrom
2 8141 8141 GeneID:23261 ENSG00000171735.21 HGNC:18806 CAMTA1 calmodulin binding transcription activator 1 NM_015215.4 NP_056030.1 ENST00000303635.12 ENSP00000306522.6 MANE Select NC_000001.11 6785454 7769706 + chr1
3 14385 14385 GeneID:114784 ENSG00000121904.19 HGNC:19290 CSMD2 CUB and Sushi multiple domains 2 NM_001281956.2 NP_001268885.1 ENST00000373381.9 ENSP00000362479.4 MANE Select NC_000001.11 33513998 34165230 - chr1
4 13673 13673 GeneID:84871 ENSG00000186094.18 HGNC:25892 AGBL4 AGBL carboxypeptidase 4 NM_032785.4 NP_116174.3 ENST00000371839.6 ENSP00000360905.1 MANE Select NC_000001.11 48532854 50023954 - chr1
5 7622 7622 GeneID:11124 ENSG00000185104.21 HGNC:3578 FAF1 Fas associated factor 1 NM_007051.3 NP_008982.1 ENST00000396153.7 ENSP00000379457.2 MANE Select NC_000001.11 50437028 50960267 - chr1
6 3420 3420 GeneID:5142 ENSG00000184588.18 HGNC:8781 PDE4B phosphodiesterase 4B NM_002600.4 NP_002591.2 ENST00000341517.9 ENSP00000342637.4 MANE Select NC_000001.11 65792895 66374574 + chr1
7 11534 11534 GeneID:57554 ENSG00000033122.21 HGNC:18531 LRRC7 leucine rich repeat containing 7 NM_001370785.2 NP_001357714.1 ENST00000651989.2 ENSP00000498937.2 MANE Select NC_000001.11 69567922 70144364 + chr1
8 16804 16804 GeneID:257194 ENSG00000172260.15 HGNC:17302 NEGR1 neuronal growth regulator 1 NM_173808.3 NP_776169.2 ENST00000357731.10 ENSP00000350364.4 MANE Select NC_000001.11 71395943 72282539 - chr1
9 16775 16775 GeneID:256435 ENSG00000184005.12 HGNC:19343 ST6GALNAC3 ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 NM_152996.4 NP_694541.2 ENST00000328299.4 ENSP00000329214.3 MANE Select NC_000001.11 76074746 76634603 + chr1
10 1263 1263 GeneID:1806 ENSG00000188641.14 HGNC:3012 DPYD dihydropyrimidine dehydrogenase NM_000110.4 NP_000101.2 ENST00000370192.8 ENSP00000359211.3 MANE Select NC_000001.11 97077743 97921034 - chr1
11 8692 8692 GeneID:26052 ENSG00000197959.15 HGNC:29125 DNM3 dynamin 3 NM_015569.5 NP_056384.2 ENST00000627582.3 ENSP00000486701.1 MANE Select NC_000001.11 171841498 172412717 + chr1
12 6668 6668 GeneID:9910 ENSG00000152061.24 HGNC:24663 RABGAP1L RAB GTPase activating protein 1 like NM_001366446.1 NP_001353375.1 ENST00000681986.1 ENSP00000507884.1 MANE Select NC_000001.11 174159520 174995308 + chr1
13 5070 5070 GeneID:7399 ENSG00000042781.14 HGNC:12601 USH2A usherin NM_206933.4 NP_996816.3 ENST00000307340.8 ENSP00000305941.3 MANE Select NC_000001.11 215622891 216423448 - chr1
14 4221 4221 GeneID:6262 ENSG00000198626.19 HGNC:10484 RYR2 ryanodine receptor 2 NM_001035.3 NP_001026.2 ENST00000366574.7 ENSP00000355533.2 MANE Select NC_000001.11 237042184 237833988 + chr1
15 811 811 GeneID:1131 ENSG00000133019.12 HGNC:1952 CHRM3 cholinergic receptor muscarinic 3 NM_001375978.1 NP_001362907.1 ENST00000676153.1 ENSP00000502667.1 MANE Select NC_000001.11 239386568 239915450 + chr1
16 4071 4071 GeneID:6000 ENSG00000182901.18 HGNC:10003 RGS7 regulator of G protein signaling 7 NM_001364886.1 NP_001351815.1 ENST00000440928.6 ENSP00000404399.2 MANE Select NC_000001.11 240775514 241357205 - chr1
17 10459 10459 GeneID:55083 ENSG00000162849.16 HGNC:25484 KIF26B kinesin family member 26B NM_018012.4 NP_060482.2 ENST00000407071.7 ENSP00000385545.2 MANE Select NC_000001.11 245154985 245709432 + chr1
18 12068 12068 GeneID:64754 ENSG00000185420.19 HGNC:15513 SMYD3 SET and MYND domain containing 3 NM_001167740.2 NP_001161212.1 ENST00000490107.6 ENSP00000419184.2 MANE Select NC_000001.11 245749347 246507279 - chr1
19 67 67 GeneID:105 ENSG00000185736.16 HGNC:227 ADARB2 adenosine deaminase RNA specific B2 (inactive) NM_018702.4 NP_061172.1 ENST00000381312.6 ENSP00000370713.1 MANE Select NC_000010.11 1177313 1737525 - chr10
20 10839 10839 GeneID:55691 ENSG00000151474.23 HGNC:25491 FRMD4A FERM domain containing 4A NM_018027.5 NP_060497.3 ENST00000357447.7 ENSP00000350032.2 MANE Select NC_000010.11 13643706 14330924 - chr10
21 17391 17391 GeneID:340895 ENSG00000204740.11 HGNC:24331 MALRD1 MAM and LDL receptor class A domain containing 1 NM_001142308.3 NP_001135780.2 ENST00000454679.7 ENSP00000412763.3 MANE Select NC_000010.11 19048801 19734478 + chr10
22 11129 11129 GeneID:56288 ENSG00000148498.17 HGNC:16051 PARD3 par-3 family cell polarity regulator NM_001184785.2 NP_001171714.1 ENST00000374788.8 ENSP00000363920.3 MANE Select NC_000010.11 34109561 34815296 - chr10
23 3761 3761 GeneID:5592 ENSG00000185532.20 HGNC:9414 PRKG1 protein kinase cGMP-dependent 1 NM_006258.4 NP_006249.1 ENST00000373980.11 ENSP00000363092.5 MANE Select NC_000010.11 51074487 52298350 + chr10
24 12195 12195 GeneID:65217 ENSG00000150275.20 HGNC:14674 PCDH15 protocadherin related 15 NM_001384140.1 NP_001371069.1 ENST00000644397.2 ENSP00000495195.1 MANE Select NC_000010.11 53802771 54801231 - chr10
25 12194 12194 GeneID:65217 ENSG00000150275.20 HGNC:14674 PCDH15 protocadherin related 15 NM_033056.4 NP_149045.3 ENST00000320301.11 ENSP00000322604.6 MANE Plus Clinical NC_000010.11 53821099 54801231 - chr10
26 9209 9209 GeneID:29119 ENSG00000183230.18 HGNC:2511 CTNNA3 catenin alpha 3 NM_013266.4 NP_037398.2 ENST00000433211.7 ENSP00000389714.1 MANE Select NC_000010.11 65912523 67696195 - chr10
27 89 89 GeneID:132 ENSG00000156110.15 HGNC:257 ADK adenosine kinase NM_006721.4 NP_006712.2 ENST00000539909.6 ENSP00000443965.2 MANE Select NC_000010.11 74151221 74709290 + chr10
28 13265 13265 GeneID:83938 ENSG00000148655.16 HGNC:23405 LRMDA leucine rich melanocyte differentiation associated NM_001305581.2 NP_001292510.1 ENST00000611255.5 ENSP00000480240.1 MANE Select NC_000010.11 75431624 76560168 + chr10
29 2556 2556 GeneID:3778 ENSG00000156113.25 HGNC:6284 KCNMA1 potassium calcium-activated channel subfamily M alpha 1 NM_001161352.2 NP_001154824.1 ENST00000286628.14 ENSP00000286628.8 MANE Select NC_000010.11 76884882 77637808 - chr10
30 7315 7315 GeneID:10718 ENSG00000185737.13 HGNC:7999 NRG3 neuregulin 3 NM_001010848.4 NP_001010848.2 ENST00000372141.7 ENSP00000361214.2 MANE Select NC_000010.11 81875194 82987178 + chr10
31 1955 1955 GeneID:2894 ENSG00000182771.19 HGNC:4575 GRID1 glutamate ionotropic receptor delta type subunit 1 NM_017551.3 NP_060021.1 ENST00000327946.12 ENSP00000330148.7 MANE Select NC_000010.11 85599552 86366795 - chr10
32 11810 11810 GeneID:60495 ENSG00000172987.14 HGNC:18374 HPSE2 heparanase 2 (inactive) NM_021828.5 NP_068600.4 ENST00000370552.8 ENSP00000359583.3 MANE Select NC_000010.11 98457077 99235852 - chr10
33 7919 7919 GeneID:22986 ENSG00000156395.14 HGNC:16699 SORCS3 sortilin related VPS10 domain containing receptor 3 NM_014978.3 NP_055793.1 ENST00000369701.8 ENSP00000358715.3 MANE Select NC_000010.11 104641290 105265242 + chr10
34 14404 14404 GeneID:114815 ENSG00000108018.17 HGNC:16697 SORCS1 sortilin related VPS10 domain containing receptor 1 NM_052918.5 NP_443150.3 ENST00000263054.11 ENSP00000263054.5 MANE Select NC_000010.11 106573663 107164706 - chr10
35 8676 8676 GeneID:26033 ENSG00000107518.18 HGNC:29063 ATRNL1 attractin like 1 NM_207303.4 NP_997186.1 ENST00000355044.8 ENSP00000347152.3 MANE Select NC_000010.11 115093365 115948999 + chr10
36 1251 1251 GeneID:1793 ENSG00000150760.13 HGNC:2987 DOCK1 dedicator of cytokinesis 1 NM_001290223.2 NP_001277152.2 ENST00000623213.2 ENSP00000485033.1 MANE Select NC_000010.11 126905428 127452516 + chr10
37 3152 3152 GeneID:4745 ENSG00000165973.19 HGNC:7750 NELL1 neural EGFL like 1 NM_006157.5 NP_006148.2 ENST00000357134.10 ENSP00000349654.5 MANE Select NC_000011.10 20669586 21575686 + chr11
38 17268 17268 GeneID:338645 ENSG00000187398.12 HGNC:23206 LUZP2 leucine zipper protein 2 NM_001009909.4 NP_001009909.2 ENST00000336930.11 ENSP00000336817.6 MANE Select NC_000011.10 24497053 25082638 + chr11
39 11635 11635 GeneID:57689 ENSG00000148948.8 HGNC:29317 LRRC4C leucine rich repeat containing 4C NM_001258419.2 NP_001245348.1 ENST00000528697.6 ENSP00000437132.1 MANE Select NC_000011.10 40114209 41459652 - chr11
40 7899 7899 GeneID:22941 ENSG00000162105.21 HGNC:14295 SHANK2 SH3 and multiple ankyrin repeat domains 2 NM_012309.5 NP_036441.2 ENST00000601538.6 ENSP00000469689.2 MANE Select NC_000011.10 70467854 71252577 - chr11
41 8661 8661 GeneID:26011 ENSG00000149256.16 HGNC:29945 TENM4 teneurin transmembrane protein 4 NM_001098816.3 NP_001092286.2 ENST00000278550.12 ENSP00000278550.7 MANE Select NC_000011.10 78652829 79441030 - chr11
42 1213 1213 GeneID:1740 ENSG00000150672.19 HGNC:2901 DLG2 discs large MAGUK scaffold protein 2 NM_001142699.3 NP_001136171.1 ENST00000376104.7 ENSP00000365272.2 MANE Select NC_000011.10 83455173 85627344 - chr11
43 1975 1975 GeneID:2915 ENSG00000168959.15 HGNC:4597 GRM5 glutamate metabotropic receptor 5 NM_001143831.3 NP_001137303.1 ENST00000305447.5 ENSP00000306138.4 MANE Select NC_000011.10 88504642 89065982 - chr11
44 14645 14645 GeneID:120114 ENSG00000165323.16 HGNC:23112 FAT3 FAT atypical cadherin 3 NM_001367949.2 NP_001354878.1 ENST00000525166.6 ENSP00000432586.2 MANE Select NC_000011.10 92224818 92896473 + chr11
45 10000 10000 GeneID:53942 ENSG00000149972.12 HGNC:2175 CNTN5 contactin 5 NM_014361.4 NP_055176.1 ENST00000524871.6 ENSP00000435637.1 MANE Select NC_000011.10 99020949 100358885 + chr11
46 13556 13556 GeneID:84623 ENSG00000149571.12 HGNC:23204 KIRREL3 kirre like nephrin family adhesion molecule 3 NM_032531.4 NP_115920.1 ENST00000525144.7 ENSP00000435466.2 MANE Select NC_000011.10 126423358 127000770 - chr11
47 9432 9432 GeneID:50863 ENSG00000182667.15 HGNC:17941 NTM neurotrimin NM_001352005.2 NP_001338934.1 ENST00000683400.1 ENSP00000507313.1 MANE Select NC_000011.10 131370615 132336822 + chr11
48 3302 3302 GeneID:4978 ENSG00000183715.15 HGNC:8143 OPCML opioid binding protein/cell adhesion molecule like NM_001012393.5 NP_001012393.1 ENST00000524381.6 ENSP00000434750.1 MANE Select NC_000011.10 132414981 133532501 - chr11
49 540 540 GeneID:775 ENSG00000151067.23 HGNC:1390 CACNA1C calcium voltage-gated channel subunit alpha1 C NM_001167623.2 NP_001161095.1 ENST00000399603.6 ENSP00000382512.1 MANE Plus Clinical NC_000012.12 2052987 2697950 + chr12
50 541 541 GeneID:775 ENSG00000151067.23 HGNC:1390 CACNA1C calcium voltage-gated channel subunit alpha1 C NM_000719.7 NP_000710.5 ENST00000399655.6 ENSP00000382563.1 MANE Select NC_000012.12 2052987 2697950 + chr12
51 13373 13373 GeneID:84216 ENSG00000139173.10 HGNC:25308 TMEM117 transmembrane protein 117 NM_032256.3 NP_115632.1 ENST00000266534.8 ENSP00000266534.3 MANE Select NC_000012.12 43836081 44389758 + chr12
52 4697 4697 GeneID:6857 ENSG00000067715.15 HGNC:11509 SYT1 synaptotagmin 1 NM_005639.3 NP_005630.1 ENST00000261205.9 ENSP00000261205.4 MANE Select NC_000012.12 78864774 79452008 + chr12
53 11203 11203 GeneID:56899 ENSG00000185046.21 HGNC:24600 ANKS1B ankyrin repeat and sterile alpha motif domain containing 1B NM_001352186.2 NP_001339115.1 ENST00000683438.2 ENSP00000508105.1 MANE Select NC_000012.12 98743974 99984936 - chr12
54 14674 14674 GeneID:121256 ENSG00000151952.16 HGNC:29411 TMEM132D transmembrane protein 132D NM_133448.3 NP_597705.2 ENST00000422113.7 ENSP00000408581.2 MANE Select NC_000012.12 129071726 129904025 - chr12
55 9935 9935 GeneID:51761 ENSG00000132932.19 HGNC:13533 ATP8A2 ATPase phospholipid transporting 8A2 NM_016529.6 NP_057613.4 ENST00000381655.7 ENSP00000371070.2 MANE Select NC_000013.11 25371974 26025851 + chr13
56 8157 8157 GeneID:23281 ENSG00000132938.22 HGNC:20595 MTUS2 microtubule associated scaffold protein 2 NM_001033602.4 NP_001028774.3 ENST00000612955.6 ENSP00000483729.2 MANE Select NC_000013.11 28820339 29505947 + chr13
57 8908 8908 GeneID:26960 ENSG00000172915.20 HGNC:7648 NBEA neurobeachin NM_001385012.1 NP_001371941.1 ENST00000379939.7 ENSP00000369271.2 MANE Select NC_000013.11 34942270 35672736 + chr13
58 10447 10447 GeneID:55068 ENSG00000120658.14 HGNC:25474 ENOX1 ecto-NOX disulfide-thiol exchanger 1 NM_001347969.2 NP_001334898.1 ENST00000690772.1 ENSP00000509229.1 MANE Select NC_000013.11 43213130 43786972 - chr13
59 3393 3393 GeneID:5101 ENSG00000184226.15 HGNC:8661 PCDH9 protocadherin 9 NM_203487.3 NP_982354.1 ENST00000377865.7 ENSP00000367096.2 MANE Select NC_000013.11 66302834 67230336 - chr13
60 1587 1587 GeneID:2262 ENSG00000179399.16 HGNC:4453 GPC5 glypican 5 NM_004466.6 NP_004457.1 ENST00000377067.9 ENSP00000366267.3 MANE Select NC_000013.11 91398621 92867237 + chr13
61 6808 6808 GeneID:10082 ENSG00000183098.12 HGNC:4454 GPC6 glypican 6 NM_005708.5 NP_005699.1 ENST00000377047.9 ENSP00000366246.3 MANE Select NC_000013.11 93226807 94408020 + chr13
62 16853 16853 GeneID:266722 ENSG00000185352.10 HGNC:19134 HS6ST3 heparan sulfate 6-O-sulfotransferase 3 NM_153456.4 NP_703157.2 ENST00000376705.4 ENSP00000365895.2 MANE Select NC_000013.11 96090107 96839562 + chr13
63 18768 18768 GeneID:728215 ENSG00000204442.4 HGNC:33877 NALF1 NALCN channel auxiliary factor 1 NM_001080396.3 NP_001073865.1 ENST00000375915.4 ENSP00000365080.1 MANE Select NC_000013.11 107163510 107867496 - chr13
64 7949 7949 GeneID:23026 ENSG00000041515.16 HGNC:29822 MYO16 myosin XVI NM_001198950.3 NP_001185879.1 ENST00000457511.7 ENSP00000401633.3 MANE Select NC_000013.11 108629611 109208005 + chr13
65 11902 11902 GeneID:64067 ENSG00000151322.20 HGNC:19311 NPAS3 neuronal PAS domain protein 3 NM_001164749.2 NP_001158221.1 ENST00000356141.9 ENSP00000348460.4 MANE Select NC_000014.9 32938879 33804173 + chr14
66 15945 15945 GeneID:161357 ENSG00000139915.22 HGNC:19835 MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 NM_001113498.3 NP_001106970.4 ENST00000399232.8 ENSP00000382178.4 MANE Select NC_000014.9 46840092 47675605 - chr14
67 6946 6946 GeneID:10243 ENSG00000171723.16 HGNC:15465 GPHN gephyrin NM_020806.5 NP_065857.1 ENST00000478722.6 ENSP00000417901.1 MANE Select NC_000014.9 66508147 67181803 + chr14
68 3981 3981 GeneID:5890 ENSG00000182185.19 HGNC:9822 RAD51B RAD51 paralog B NM_133510.4 NP_598194.1 ENST00000471583.6 ENSP00000418859.1 MANE Select NC_000014.9 67819779 68478093 + chr14
69 6421 6421 GeneID:9628 ENSG00000182732.18 HGNC:10002 RGS6 regulator of G protein signaling 6 NM_001204424.2 NP_001191353.1 ENST00000553525.6 ENSP00000451030.1 MANE Select NC_000014.9 71932429 72566530 + chr14
70 6220 6220 GeneID:9369 ENSG00000021645.20 HGNC:8010 NRXN3 neurexin 3 NM_001330195.2 NP_001317124.1 ENST00000335750.7 ENSP00000338349.7 MANE Select NC_000014.9 78170373 79868291 + chr14
71 1713 1713 GeneID:2567 ENSG00000182256.13 HGNC:4088 GABRG3 gamma-aminobutyric acid type A receptor subunit gamma3 NM_033223.5 NP_150092.2 ENST00000615808.5 ENSP00000479113.1 MANE Select NC_000015.10 26971181 27541984 + chr15
72 4222 4222 GeneID:6263 ENSG00000198838.15 HGNC:10485 RYR3 ryanodine receptor 3 NM_001036.6 NP_001027.3 ENST00000634891.2 ENSP00000489262.1 MANE Select NC_000015.10 33310967 33866102 + chr15
73 18310 18310 GeneID:440279 ENSG00000137766.18 HGNC:23149 UNC13C unc-13 homolog C NM_001080534.3 NP_001074003.1 ENST00000260323.16 ENSP00000260323.11 MANE Select NC_000015.10 53978441 54628605 + chr15
74 4107 4107 GeneID:6095 ENSG00000069667.16 HGNC:10258 RORA RAR related orphan receptor A NM_134261.3 NP_599023.1 ENST00000335670.11 ENSP00000335087.6 MANE Select NC_000015.10 60488284 61229302 - chr15
75 12646 12646 GeneID:79875 ENSG00000187720.15 HGNC:25835 THSD4 thrombospondin type 1 domain containing 4 NM_024817.3 NP_079093.2 ENST00000261862.8 ENSP00000261862.8 MANE Select NC_000015.10 71115471 71783383 + chr15
76 9367 9367 GeneID:49855 ENSG00000140386.13 HGNC:13081 SCAPER S-phase cyclin A associated protein in the ER NM_020843.4 NP_065894.2 ENST00000563290.6 ENSP00000454973.1 MANE Select NC_000015.10 76347904 76905340 - chr15
77 14748 14748 GeneID:123624 ENSG00000273540.5 HGNC:26504 AGBL1 AGBL carboxypeptidase 1 NM_001386094.1 NP_001373023.1 ENST00000614907.3 ENSP00000490608.2 MANE Select NC_000015.10 86079871 86916156 + chr15
78 10183 10183 GeneID:54715 ENSG00000078328.23 HGNC:18222 RBFOX1 RNA binding fox-1 homolog 1 NM_018723.4 NP_061193.2 ENST00000550418.6 ENSP00000450031.1 MANE Select NC_000016.10 6019024 7713340 + chr16
79 14117 14117 GeneID:92017 ENSG00000048471.14 HGNC:30542 SNX29 sorting nexin 29 NM_032167.5 NP_115543.3 ENST00000566228.6 ENSP00000456480.1 MANE Select NC_000016.10 11976734 12574287 + chr16
80 9924 9924 GeneID:51741 ENSG00000186153.19 HGNC:12799 WWOX WW domain containing oxidoreductase NM_016373.4 NP_057457.1 ENST00000566780.6 ENSP00000457230.1 MANE Select NC_000016.10 78099654 79212667 + chr16
81 728 728 GeneID:1012 ENSG00000140945.17 HGNC:1753 CDH13 cadherin 13 NM_001257.5 NP_001248.1 ENST00000567109.6 ENSP00000479395.1 MANE Select NC_000016.10 82626969 83800640 + chr16
82 11231 11231 GeneID:56934 ENSG00000154975.14 HGNC:1369 CA10 carbonic anhydrase 10 NM_020178.5 NP_064563.1 ENST00000451037.7 ENSP00000405388.2 MANE Select NC_000017.11 51630320 52158714 - chr17
83 10248 10248 GeneID:54828 ENSG00000141376.24 HGNC:14347 BCAS3 BCAS3 microtubule associated cell migration factor NM_017679.5 NP_060149.3 ENST00000407086.8 ENSP00000385323.2 MANE Select NC_000017.11 60677851 61392831 + chr17
84 16293 16293 GeneID:201134 ENSG00000154240.18 HGNC:28514 CEP112 centrosomal protein 112 NM_001199165.4 NP_001186094.1 ENST00000535342.7 ENSP00000442784.2 MANE Select NC_000017.11 65635537 66192133 - chr17
85 6124 6124 GeneID:9229 ENSG00000170579.19 HGNC:2905 DLGAP1 DLG associated protein 1 NM_004746.4 NP_004737.2 ENST00000315677.8 ENSP00000316377.3 MANE Select NC_000018.10 3496032 4455307 - chr18
86 3920 3920 GeneID:5797 ENSG00000173482.17 HGNC:9675 PTPRM protein tyrosine phosphatase receptor type M NM_001105244.2 NP_001098714.1 ENST00000580170.6 ENSP00000463325.1 MANE Select NC_000018.10 7567316 8406856 + chr18
87 1152 1152 GeneID:1630 ENSG00000187323.13 HGNC:2701 DCC DCC netrin 1 receptor NM_005215.4 NP_005206.2 ENST00000442544.7 ENSP00000389140.2 MANE Select NC_000018.10 52340197 53535899 + chr18
88 7962 7962 GeneID:23040 ENSG00000186487.21 HGNC:7623 MYT1L myelin transcription factor 1 like NM_001303052.2 NP_001289981.1 ENST00000647738.2 ENSP00000497479.2 MANE Select NC_000002.12 1789113 2331275 - chr2
89 163 163 GeneID:238 ENSG00000171094.18 HGNC:427 ALK ALK receptor tyrosine kinase NM_004304.5 NP_004295.2 ENST00000389048.8 ENSP00000373700.3 MANE Select NC_000002.12 29192774 29921586 - chr2
90 3750 3750 GeneID:5581 ENSG00000171132.14 HGNC:9401 PRKCE protein kinase C epsilon NM_005400.3 NP_005391.1 ENST00000306156.8 ENSP00000306124.3 MANE Select NC_000002.12 45651675 46187990 + chr2
91 6229 6229 GeneID:9378 ENSG00000179915.25 HGNC:8008 NRXN1 neurexin 1 NM_001330078.2 NP_001317007.1 ENST00000401669.7 ENSP00000385017.2 MANE Select NC_000002.12 49918503 51032132 - chr2
92 8117 8117 GeneID:23233 ENSG00000144036.16 HGNC:17085 EXOC6B exocyst complex component 6B NM_015189.3 NP_056004.1 ENST00000272427.11 ENSP00000272427.7 MANE Select NC_000002.12 72175984 72826033 - chr2
93 12756 12756 GeneID:80059 ENSG00000176204.14 HGNC:19411 LRRTM4 leucine rich repeat transmembrane neuronal 4 NM_001134745.3 NP_001128217.1 ENST00000409884.6 ENSP00000387297.1 MANE Select NC_000002.12 76747685 77522376 - chr2
94 1062 1062 GeneID:1496 ENSG00000066032.19 HGNC:2510 CTNNA2 catenin alpha 2 NM_001282597.3 NP_001269526.1 ENST00000402739.9 ENSP00000384638.4 MANE Select NC_000002.12 79513051 80648780 + chr2
95 2648 2648 GeneID:3899 ENSG00000144218.21 HGNC:6473 AFF3 ALF transcription elongation factor 3 NM_001386135.1 NP_001373064.1 ENST00000672756.2 ENSP00000500419.1 MANE Select NC_000002.12 99545419 100142590 - chr2
96 11595 11595 GeneID:57628 ENSG00000175497.17 HGNC:20823 DPP10 dipeptidyl peptidase like 10 NM_020868.6 NP_065919.3 ENST00000410059.6 ENSP00000386565.1 MANE Select NC_000002.12 114442641 115845780 + chr2
97 15024 15024 GeneID:129684 ENSG00000155052.15 HGNC:18748 CNTNAP5 contactin associated protein family member 5 NM_001367498.1 NP_001354427.1 ENST00000682447.1 ENSP00000508115.1 MANE Select NC_000002.12 124025287 124921219 + chr2
98 17475 17475 GeneID:344148 ENSG00000176771.18 HGNC:29847 NCKAP5 NCK associated protein 5 NM_207363.3 NP_997246.2 ENST00000409261.6 ENSP00000387128.1 MANE Select NC_000002.12 132671788 133568463 - chr2
99 12907 12907 GeneID:80731 ENSG00000144229.13 HGNC:29348 THSD7B thrombospondin type 1 domain containing 7B NM_001316349.2 NP_001303278.1 ENST00000409968.6 ENSP00000387145.1 MANE Select NC_000002.12 136765545 137677718 + chr2
100 9964 9964 GeneID:53353 ENSG00000168702.18 HGNC:6693 LRP1B LDL receptor related protein 1B NM_018557.3 NP_061027.2 ENST00000389484.8 ENSP00000374135.3 MANE Select NC_000002.12 140231423 142131016 - chr2
101 10964 10964 GeneID:55843 ENSG00000075884.14 HGNC:21030 ARHGAP15 Rho GTPase activating protein 15 NM_018460.4 NP_060930.3 ENST00000295095.11 ENSP00000295095.6 MANE Select NC_000002.12 143129419 143768352 + chr2
102 14403 14403 GeneID:114805 ENSG00000144278.15 HGNC:23242 GALNT13 polypeptide N-acetylgalactosaminyltransferase 13 NM_052917.4 NP_443149.2 ENST00000392825.8 ENSP00000376570.3 MANE Select NC_000002.12 153871922 154453979 + chr2
103 5750 5750 GeneID:8708 ENSG00000172318.6 HGNC:916 B3GALT1 beta-1,3-galactosyltransferase 1 NM_020981.4 NP_066191.1 ENST00000392690.4 ENSP00000376456.2 MANE Select NC_000002.12 167293001 167874045 + chr2
104 14586 14586 GeneID:117583 ENSG00000116117.20 HGNC:14446 PARD3B par-3 family cell polarity regulator beta NM_001302769.2 NP_001289698.1 ENST00000406610.7 ENSP00000385848.2 MANE Select NC_000002.12 204545475 205620162 + chr2
105 1447 1447 GeneID:2066 ENSG00000178568.16 HGNC:3432 ERBB4 erb-b2 receptor tyrosine kinase 4 NM_005235.3 NP_005226.1 ENST00000342788.9 ENSP00000342235.4 MANE Select NC_000002.12 211375717 212538802 - chr2
106 12417 12417 GeneID:79582 ENSG00000144451.20 HGNC:23225 SPAG16 sperm associated antigen 16 NM_024532.5 NP_078808.3 ENST00000331683.10 ENSP00000332592.5 MANE Select NC_000002.12 213284464 214410501 + chr2
107 14558 14558 GeneID:116987 ENSG00000157985.20 HGNC:16922 AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 NM_001037131.3 NP_001032208.1 ENST00000304032.13 ENSP00000307634.7 MANE Select NC_000002.12 235494043 236131793 + chr2
108 8120 8120 GeneID:23236 ENSG00000182621.19 HGNC:15917 PLCB1 phospholipase C beta 1 NM_015192.4 NP_056007.1 ENST00000338037.11 ENSP00000338185.6 MANE Select NC_000020.11 8132266 8884900 + chr20
109 15336 15336 GeneID:140733 ENSG00000172264.19 HGNC:16126 MACROD2 mono-ADP ribosylhydrolase 2 NM_001351661.2 NP_001338590.1 ENST00000684519.1 ENSP00000507484.1 MANE Select NC_000020.11 13995516 16053197 + chr20
110 7620 7620 GeneID:11122 ENSG00000196090.14 HGNC:9682 PTPRT protein tyrosine phosphatase receptor type T NM_007050.6 NP_008981.4 ENST00000373187.6 ENSP00000362283.1 MANE Select NC_000020.11 42072756 43189906 - chr20
111 14987 14987 GeneID:128553 ENSG00000182463.17 HGNC:13010 TSHZ2 teashirt zinc finger homeobox 2 NM_173485.6 NP_775756.3 ENST00000371497.10 ENSP00000360552.3 MANE Select NC_000020.11 52972358 53495330 + chr20
112 719 719 GeneID:1002 ENSG00000179242.16 HGNC:1763 CDH4 cadherin 4 NM_001794.5 NP_001785.2 ENST00000614565.5 ENSP00000484928.1 MANE Select NC_000020.11 61252261 61940617 + chr20
113 3101 3101 GeneID:4685 ENSG00000154654.15 HGNC:7657 NCAM2 neural cell adhesion molecule 2 NM_004540.5 NP_004531.2 ENST00000400546.6 ENSP00000383392.1 MANE Select NC_000021.9 20998409 21543329 + chr21
114 1281 1281 GeneID:1826 ENSG00000171587.15 HGNC:3039 DSCAM DS cell adhesion molecule NM_001389.5 NP_001380.2 ENST00000400454.6 ENSP00000383303.1 MANE Select NC_000021.9 40010999 40847158 - chr21
115 8194 8194 GeneID:23331 ENSG00000100154.15 HGNC:29179 TTC28 tetratricopeptide repeat domain 28 NM_001145418.2 NP_001138890.1 ENST00000397906.7 ENSP00000381003.2 MANE Select NC_000022.11 27978014 28679840 - chr22
116 5416 5416 GeneID:8224 ENSG00000185666.16 HGNC:11496 SYN3 synapsin III NM_003490.4 NP_003481.3 ENST00000358763.7 ENSP00000351614.2 MANE Select NC_000022.11 32507820 33058381 - chr22
117 6116 6116 GeneID:9215 ENSG00000133424.22 HGNC:6511 LARGE1 LARGE xylosyl- and glucuronyltransferase 1 NM_133642.5 NP_598397.1 ENST00000397394.8 ENSP00000380549.2 MANE Select NC_000022.11 33272509 33920476 - chr22
118 15759 15759 GeneID:152330 ENSG00000144619.15 HGNC:2174 CNTN4 contactin 4 NM_175607.3 NP_783200.1 ENST00000418658.6 ENSP00000396010.1 MANE Select NC_000003.12 2098866 3057959 + chr3
119 1977 1977 GeneID:2917 ENSG00000196277.17 HGNC:4599 GRM7 glutamate metabotropic receptor 7 NM_000844.4 NP_000835.1 ENST00000357716.9 ENSP00000350348.4 MANE Select NC_000003.12 6861115 7741533 + chr3
120 6555 6555 GeneID:9779 ENSG00000131374.15 HGNC:19166 TBC1D5 TBC1 domain family member 5 NM_001349074.2 NP_001336003.1 ENST00000696125.1 ENSP00000512418.1 MANE Select NC_000003.12 17157168 17742631 - chr3
121 9071 9071 GeneID:27303 ENSG00000144642.22 HGNC:13427 RBMS3 RNA binding motif single stranded interacting protein 3 NM_001003793.3 NP_001003793.1 ENST00000383767.7 ENSP00000373277.2 MANE Select NC_000003.12 29281071 30010386 + chr3
122 10385 10385 GeneID:54986 ENSG00000168038.11 HGNC:15784 ULK4 unc-51 like kinase 4 NM_017886.4 NP_060356.2 ENST00000301831.9 ENSP00000301831.4 MANE Select NC_000003.12 41246599 41962103 - chr3
123 1253 1253 GeneID:1795 ENSG00000088538.13 HGNC:2989 DOCK3 dedicator of cytokinesis 3 NM_004947.5 NP_004938.1 ENST00000266037.10 ENSP00000266037.8 MANE Select NC_000003.12 50674927 51384198 + chr3
124 10932 10932 GeneID:55799 ENSG00000157445.16 HGNC:15460 CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3 NM_018398.3 NP_060868.2 ENST00000474759.6 ENSP00000419101.1 MANE Select NC_000003.12 54122552 55074557 + chr3
125 8698 8698 GeneID:26059 ENSG00000187672.15 HGNC:31922 ERC2 ELKS/RAB6-interacting/CAST family member 2 NM_015576.3 NP_056391.1 ENST00000288221.11 ENSP00000288221.6 MANE Select NC_000003.12 55508311 56468467 - chr3
126 1595 1595 GeneID:2272 ENSG00000189283.11 HGNC:3701 FHIT fragile histidine triad diadenosine triphosphatase NM_002012.4 NP_002003.1 ENST00000492590.6 ENSP00000418582.1 MANE Select NC_000003.12 59747277 61251452 - chr3
127 3916 3916 GeneID:5793 ENSG00000144724.20 HGNC:9671 PTPRG protein tyrosine phosphatase receptor type G NM_002841.4 NP_002832.3 ENST00000474889.6 ENSP00000418112.1 MANE Select NC_000003.12 61561571 62297609 + chr3
128 6121 6121 GeneID:9223 ENSG00000151276.24 HGNC:946 MAGI1 membrane associated guanylate kinase, WW and PDZ domain containing 1 NM_001033057.2 NP_001028229.1 ENST00000402939.7 ENSP00000385450.2 MANE Select NC_000003.12 65353526 66038918 - chr3
129 18262 18262 GeneID:407738 ENSG00000183662.12 HGNC:21587 TAFA1 TAFA chemokine like family member 1 NM_213609.4 NP_998774.2 ENST00000478136.6 ENSP00000418575.1 MANE Select NC_000003.12 68004247 68545621 + chr3
130 8957 8957 GeneID:27086 ENSG00000114861.24 HGNC:3823 FOXP1 forkhead box P1 NM_001349338.3 NP_001336267.1 ENST00000649528.3 ENSP00000497369.1 MANE Select NC_000003.12 70954708 71583728 - chr3
131 4104 4104 GeneID:6092 ENSG00000185008.19 HGNC:10250 ROBO2 roundabout guidance receptor 2 NM_001395656.1 NP_001382585.1 ENST00000696593.1 ENSP00000512738.1 MANE Select NC_000003.12 77040099 77649964 + chr3
132 4103 4103 GeneID:6091 ENSG00000169855.21 HGNC:10249 ROBO1 roundabout guidance receptor 1 NM_002941.4 NP_002932.1 ENST00000464233.6 ENSP00000420321.1 MANE Select NC_000003.12 78597239 79767998 - chr3
133 16659 16659 GeneID:253559 ENSG00000175161.14 HGNC:29849 CADM2 cell adhesion molecule 2 NM_001167675.2 NP_001161147.1 ENST00000383699.8 ENSP00000373200.3 MANE Select NC_000003.12 84958989 86074429 + chr3
134 17100 17100 GeneID:285220 ENSG00000080224.18 HGNC:19296 EPHA6 EPH receptor A6 NM_001080448.3 NP_001073917.2 ENST00000389672.10 ENSP00000374323.5 MANE Select NC_000003.12 96814594 97761532 + chr3
135 8736 8736 GeneID:26137 ENSG00000181722.18 HGNC:13503 ZBTB20 zinc finger and BTB domain containing 20 NM_001348800.3 NP_001335729.1 ENST00000675478.1 ENSP00000501561.1 MANE Select NC_000003.12 114314500 115147288 - chr3
136 2743 2743 GeneID:4045 ENSG00000185565.13 HGNC:6705 LSAMP limbic system associated membrane protein NM_002338.5 NP_002329.2 ENST00000490035.7 ENSP00000419000.1 MANE Select NC_000003.12 115802374 116445487 - chr3
137 5957 5957 GeneID:8997 ENSG00000160145.16 HGNC:4814 KALRN kalirin RhoGEF kinase NM_001388419.1 NP_001375348.1 ENST00000682506.1 ENSP00000508359.1 MANE Select NC_000003.12 124033369 124726325 + chr3
138 11910 11910 GeneID:64084 ENSG00000158258.16 HGNC:17448 CLSTN2 calsyntenin 2 NM_022131.3 NP_071414.2 ENST00000458420.7 ENSP00000402460.2 MANE Select NC_000003.12 139935185 140577397 + chr3
139 17098 17098 GeneID:285195 ENSG00000181804.15 HGNC:20653 SLC9A9 solute carrier family 9 member A9 NM_173653.4 NP_775924.1 ENST00000316549.11 ENSP00000320246.6 MANE Select NC_000003.12 143265222 143848468 - chr3
140 9309 9309 GeneID:29970 ENSG00000151967.19 HGNC:15678 SCHIP1 schwannomin interacting protein 1 NM_014575.4 NP_055390.1 ENST00000638749.2 ENSP00000491030.1 MANE Select NC_000003.12 159273244 159897359 + chr3
141 1482 1482 GeneID:2122 ENSG00000085276.19 HGNC:3498 MECOM MDS1 and EVI1 complex locus NM_004991.4 NP_004982.2 ENST00000651503.2 ENSP00000498411.1 MANE Select NC_000003.12 169083507 169663712 - chr3
142 7839 7839 GeneID:22871 ENSG00000169760.18 HGNC:14291 NLGN1 neuroligin 1 NM_001365925.2 NP_001352854.1 ENST00000695368.1 ENSP00000511841.1 MANE Select NC_000003.12 173397744 174294372 + chr3
143 16707 16707 GeneID:254827 ENSG00000177694.16 HGNC:23219 NAALADL2 N-acetylated alpha-linked acidic dipeptidase like 2 NM_207015.3 NP_996898.2 ENST00000454872.6 ENSP00000404705.1 MANE Select NC_000003.12 174859334 175810548 + chr3
144 2733 2733 GeneID:4026 ENSG00000145012.15 HGNC:6679 LPP LIM domain containing preferred translocation partner in lipoma NM_001375462.1 NP_001362391.1 ENST00000617246.5 ENSP00000478901.1 MANE Select NC_000003.12 188154157 188890671 + chr3
145 1582 1582 GeneID:2257 ENSG00000114279.15 HGNC:3668 FGF12 fibroblast growth factor 12 NM_004113.6 NP_004104.3 ENST00000445105.7 ENSP00000393686.1 MANE Select NC_000003.12 192139390 192727541 - chr3
146 11519 11519 GeneID:57537 ENSG00000184985.17 HGNC:16698 SORCS2 sortilin related VPS10 domain containing receptor 2 NM_020777.3 NP_065828.2 ENST00000507866.6 ENSP00000422185.2 MANE Select NC_000004.12 7192538 7742827 + chr4
147 12879 12879 GeneID:80333 ENSG00000185774.17 HGNC:30083 KCNIP4 potassium voltage-gated channel interacting protein 4 NM_025221.6 NP_079497.2 ENST00000382152.7 ENSP00000371587.2 MANE Select NC_000004.12 20728606 21948772 - chr4
148 8159 8159 GeneID:23284 ENSG00000150471.17 HGNC:20974 ADGRL3 adhesion G protein-coupled receptor L3 NM_001387552.1 NP_001374481.1 ENST00000683033.1 ENSP00000507980.1 MANE Select NC_000004.12 61200326 62078335 + chr4
149 16722 16722 GeneID:255119 ENSG00000197826.13 HGNC:28554 CFAP299 cilia and flagella associated protein 299 NM_152770.3 NP_689983.2 ENST00000358105.8 ENSP00000350818.3 MANE Select NC_000004.12 80335730 80963750 + chr4
150 13132 13132 GeneID:83478 ENSG00000138639.18 HGNC:25361 ARHGAP24 Rho GTPase activating protein 24 NM_001025616.3 NP_001020787.2 ENST00000395184.6 ENSP00000378611.1 MANE Select NC_000004.12 85475150 86002666 + chr4
151 18184 18184 GeneID:401145 ENSG00000184305.16 HGNC:29349 CCSER1 coiled-coil serine rich protein 1 NM_001145065.2 NP_001138537.1 ENST00000509176.6 ENSP00000425040.1 MANE Select NC_000004.12 90127394 91605295 + chr4
152 1956 1956 GeneID:2895 ENSG00000152208.13 HGNC:4576 GRID2 glutamate ionotropic receptor delta type subunit 2 NM_001510.4 NP_001501.2 ENST00000282020.9 ENSP00000282020.4 MANE Select NC_000004.12 92303966 93774566 + chr4
153 17131 17131 GeneID:285555 ENSG00000163116.10 HGNC:28712 STPG2 sperm tail PG-rich repeat containing 2 NM_174952.3 NP_777612.1 ENST00000295268.4 ENSP00000295268.3 MANE Select NC_000004.12 97558872 98143476 - chr4
154 5837 5837 GeneID:8821 ENSG00000109452.13 HGNC:6075 INPP4B inositol polyphosphate-4-phosphatase type II B NM_001101669.3 NP_001095139.1 ENST00000262992.9 ENSP00000262992.4 MANE Select NC_000004.12 142023160 142846301 - chr4
155 705 705 GeneID:987 ENSG00000198589.15 HGNC:1742 LRBA LPS responsive beige-like anchor protein NM_001364905.1 NP_001351834.1 ENST00000651943.2 ENSP00000498582.2 MANE Select NC_000004.12 150264435 151015284 - chr4
156 11190 11190 GeneID:56884 ENSG00000168843.14 HGNC:21386 FSTL5 follistatin like 5 NM_020116.5 NP_064501.2 ENST00000306100.10 ENSP00000305334.4 MANE Select NC_000004.12 161383897 162164000 - chr4
157 10412 10412 GeneID:55016 ENSG00000145416.14 HGNC:26077 MARCHF1 membrane associated ring-CH-type finger 1 NM_001394959.1 NP_001381888.1 ENST00000514618.6 ENSP00000421322.1 MANE Select NC_000004.12 163524718 164384019 - chr4
158 18404 18404 GeneID:442117 ENSG00000174473.17 HGNC:33844 GALNTL6 polypeptide N-acetylgalactosaminyltransferase like 6 NM_001034845.3 NP_001030017.2 ENST00000506823.6 ENSP00000423313.1 MANE Select NC_000004.12 171813404 173041559 + chr4
159 10858 10858 GeneID:55714 ENSG00000218336.9 HGNC:29944 TENM3 teneurin transmembrane protein 3 NM_001080477.4 NP_001073946.1 ENST00000511685.6 ENSP00000424226.1 MANE Select NC_000004.12 182243402 182803024 + chr4
160 1066 1066 GeneID:1501 ENSG00000169862.21 HGNC:2516 CTNND2 catenin delta 2 NM_001332.4 NP_001323.1 ENST00000304623.13 ENSP00000307134.8 MANE Select NC_000005.10 10971836 11904446 - chr5
161 727 727 GeneID:1010 ENSG00000154162.15 HGNC:1751 CDH12 cadherin 12 NM_004061.5 NP_004052.2 ENST00000382254.6 ENSP00000371689.1 MANE Select NC_000005.10 21750673 22853344 - chr5
162 3422 3422 GeneID:5144 ENSG00000113448.21 HGNC:8783 PDE4D phosphodiesterase 4D NM_001104631.2 NP_001098101.1 ENST00000340635.11 ENSP00000345502.6 MANE Select NC_000005.10 58969038 59893726 - chr5
163 17704 17704 GeneID:375449 ENSG00000069020.19 HGNC:19037 MAST4 microtubule associated serine/threonine kinase family member 4 NM_001164664.2 NP_001158136.1 ENST00000403625.7 ENSP00000385727.1 MANE Select NC_000005.10 66596393 67169593 + chr5
164 13291 13291 GeneID:84059 ENSG00000164199.18 HGNC:17416 ADGRV1 adhesion G protein-coupled receptor V1 NM_032119.4 NP_115495.3 ENST00000405460.9 ENSP00000384582.2 MANE Select NC_000005.10 90558797 91164437 + chr5
165 12563 12563 GeneID:79772 ENSG00000175471.20 HGNC:26183 MCTP1 multiple C2 and transmembrane domain containing 1 NM_024717.7 NP_078993.4 ENST00000515393.6 ENSP00000424126.1 MANE Select NC_000005.10 94703690 95285094 - chr5
166 12114 12114 GeneID:64839 ENSG00000145743.18 HGNC:13615 FBXL17 F-box and leucine rich repeat protein 17 NM_001163315.3 NP_001156787.2 ENST00000542267.7 ENSP00000437464.2 MANE Select NC_000005.10 107859035 108382098 - chr5
167 4572 4572 GeneID:6695 ENSG00000152377.15 HGNC:11251 SPOCK1 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 NM_004598.4 NP_004589.1 ENST00000394945.6 ENSP00000378401.1 MANE Select NC_000005.10 136975298 137499326 - chr5
168 11447 11447 GeneID:57451 ENSG00000145934.17 HGNC:29943 TENM2 teneurin transmembrane protein 2 NM_001395460.1 NP_001382389.1 ENST00000518659.6 ENSP00000429430.1 MANE Select NC_000005.10 166979029 168264157 + chr5
169 4480 4480 GeneID:6586 ENSG00000184347.16 HGNC:11087 SLIT3 slit guidance ligand 3 NM_003062.4 NP_003053.2 ENST00000519560.6 ENSP00000430333.2 MANE Select NC_000005.10 168661740 169301139 - chr5
170 1839 1839 GeneID:2762 ENSG00000112699.11 HGNC:4369 GMDS GDP-mannose 4,6-dehydratase NM_001500.4 NP_001491.1 ENST00000380815.5 ENSP00000370194.4 MANE Select NC_000006.12 1623806 2245605 - chr6
171 16547 16547 GeneID:221692 ENSG00000112137.19 HGNC:20990 PHACTR1 phosphatase and actin regulator 1 NM_030948.6 NP_112210.1 ENST00000332995.12 ENSP00000329880.8 MANE Select NC_000006.12 12716767 13287837 + chr6
172 10312 10312 GeneID:54901 ENSG00000145996.11 HGNC:21050 CDKAL1 CDK5 regulatory subunit associated protein 1 like 1 NM_017774.3 NP_060244.2 ENST00000274695.8 ENSP00000274695.4 MANE Select NC_000006.12 20534457 21232404 + chr6
173 5564 5564 GeneID:8464 ENSG00000196284.18 HGNC:11466 SUPT3H SPT3 homolog, SAGA and STAGA complex component NM_003599.4 NP_003590.1 ENST00000371459.6 ENSP00000360514.1 MANE Select NC_000006.12 44826726 45377934 - chr6
174 16340 16340 GeneID:202559 ENSG00000112232.10 HGNC:18114 KHDRBS2 KH RNA binding domain containing, signal transduction associated 2 NM_152688.4 NP_689901.2 ENST00000281156.5 ENSP00000281156.3 MANE Select NC_000006.12 61679961 62286225 - chr6
175 17510 17510 GeneID:346007 ENSG00000188107.15 HGNC:21555 EYS eyes shut homolog NM_001142800.2 NP_001136272.1 ENST00000503581.6 ENSP00000424243.1 MANE Select NC_000006.12 63719980 65707226 - chr6
176 393 393 GeneID:577 ENSG00000135298.15 HGNC:945 ADGRB3 adhesion G protein-coupled receptor B3 NM_001704.3 NP_001695.2 ENST00000370598.6 ENSP00000359630.1 MANE Select NC_000006.12 68635282 69389506 + chr6
177 11143 11143 GeneID:56479 ENSG00000185760.18 HGNC:6299 KCNQ5 potassium voltage-gated channel subfamily Q member 5 NM_019842.4 NP_062816.2 ENST00000370398.6 ENSP00000359425.1 MANE Select NC_000006.12 72622064 73198853 + chr6
178 1959 1959 GeneID:2898 ENSG00000164418.22 HGNC:4580 GRIK2 glutamate ionotropic receptor kainate type subunit 2 NM_021956.5 NP_068775.1 ENST00000369134.9 ENSP00000358130.6 MANE Select NC_000006.12 101393708 102070083 + chr6
179 15816 15816 GeneID:154215 ENSG00000188580.16 HGNC:16443 NKAIN2 sodium/potassium transporting ATPase interacting 2 NM_001040214.3 NP_001035304.1 ENST00000368417.6 ENSP00000357402.1 MANE Select NC_000006.12 123803865 124825640 + chr6
180 3919 3919 GeneID:5796 ENSG00000152894.15 HGNC:9674 PTPRK protein tyrosine phosphatase receptor type K NM_002844.4 NP_002835.2 ENST00000368226.9 ENSP00000357209.4 MANE Select NC_000006.12 127968785 128520599 - chr6
181 2653 2653 GeneID:3908 ENSG00000196569.14 HGNC:6482 LAMA2 laminin subunit alpha 2 NM_000426.4 NP_000417.3 ENST00000421865.3 ENSP00000400365.2 MANE Select NC_000006.12 128883138 129516566 + chr6
182 5072 5072 GeneID:7402 ENSG00000152818.20 HGNC:12635 UTRN utrophin NM_007124.3 NP_009055.2 ENST00000367545.8 ENSP00000356515.3 MANE Select NC_000006.12 144285335 144853034 + chr6
183 3368 3368 GeneID:5071 ENSG00000185345.25 HGNC:8607 PRKN parkin RBR E3 ubiquitin protein ligase NM_004562.3 NP_004553.2 ENST00000366898.6 ENSP00000355865.1 MANE Select NC_000006.12 161347417 162727766 - chr6
184 15178 15178 GeneID:135138 ENSG00000112530.13 HGNC:19152 PACRG parkin coregulated NM_001080379.2 NP_001073848.1 ENST00000366888.7 ENSP00000355854.2 MANE Select NC_000006.12 162727974 163315500 + chr6
185 16561 16561 GeneID:221935 ENSG00000146555.20 HGNC:19307 SDK1 sidekick cell adhesion molecule 1 NM_152744.4 NP_689957.3 ENST00000404826.7 ENSP00000385899.2 MANE Select NC_000007.14 3301252 4269000 + chr7
186 1135 1135 GeneID:1607 ENSG00000136267.14 HGNC:2850 DGKB diacylglycerol kinase beta NM_001350709.2 NP_001337638.1 ENST00000402815.6 ENSP00000384909.1 MANE Select NC_000007.14 14145049 14902751 - chr7
187 6610 6610 GeneID:9844 ENSG00000155849.16 HGNC:16286 ELMO1 engulfment and cell motility 1 NM_014800.11 NP_055615.8 ENST00000310758.9 ENSP00000312185.4 MANE Select NC_000007.14 36852906 37448864 - chr7
188 12571 12571 GeneID:79783 ENSG00000175600.16 HGNC:16001 SUGCT succinyl-CoA:glutarate-CoA transferase NM_001193313.2 NP_001180242.2 ENST00000335693.9 ENSP00000338475.5 MANE Select NC_000007.14 40135005 40860763 + chr7
189 8693 8693 GeneID:26053 ENSG00000158321.19 HGNC:14262 AUTS2 activator of transcription and developmental regulator AUTS2 NM_015570.4 NP_056385.1 ENST00000342771.10 ENSP00000344087.4 MANE Select NC_000007.14 69598475 70793506 + chr7
190 12012 12012 GeneID:64409 ENSG00000185274.13 HGNC:16347 GALNT17 polypeptide N-acetylgalactosaminyltransferase 17 NM_022479.3 NP_071924.1 ENST00000333538.10 ENSP00000329654.5 MANE Select NC_000007.14 71132144 71713599 + chr7
191 13188 13188 GeneID:83698 ENSG00000183166.12 HGNC:13248 CALN1 calneuron 1 NM_031468.4 NP_113656.2 ENST00000395275.7 ENSP00000378690.2 MANE Select NC_000007.14 71779491 72412338 - chr7
192 6627 6627 GeneID:9863 ENSG00000187391.23 HGNC:18957 MAGI2 membrane associated guanylate kinase, WW and PDZ domain containing 2 NM_012301.4 NP_036433.2 ENST00000354212.9 ENSP00000346151.4 MANE Select NC_000007.14 78017055 79453667 - chr7
193 16419 16419 GeneID:219578 ENSG00000182348.7 HGNC:21958 ZNF804B zinc finger protein 804B NM_181646.5 NP_857597.1 ENST00000333190.5 ENSP00000329638.4 MANE Select NC_000007.14 88759700 89338528 + chr7
194 3485 3485 GeneID:5218 ENSG00000058091.17 HGNC:8883 CDK14 cyclin dependent kinase 14 NM_001287135.2 NP_001274064.1 ENST00000380050.8 ENSP00000369390.3 MANE Select NC_000007.14 90596321 91210590 + chr7
195 17711 17711 GeneID:375612 ENSG00000187416.13 HGNC:6589 LHFPL3 LHFPL tetraspan subfamily member 3 NM_199000.3 NP_945351.1 ENST00000424859.7 ENSP00000393128.2 MANE Select NC_000007.14 104328603 104908561 + chr7
196 13270 13270 GeneID:83943 ENSG00000184903.10 HGNC:14598 IMMP2L inner mitochondrial membrane peptidase subunit 2 NM_032549.4 NP_115938.1 ENST00000405709.7 ENSP00000384966.2 MANE Select NC_000007.14 110662644 111562492 - chr7
197 14243 14243 GeneID:93664 ENSG00000081803.17 HGNC:16018 CADPS2 calcium dependent secretion activator 2 NM_017954.11 NP_060424.9 ENST00000449022.7 ENSP00000398481.2 MANE Select NC_000007.14 122318411 122886460 - chr7
198 1978 1978 GeneID:2918 ENSG00000179603.19 HGNC:4600 GRM8 glutamate metabotropic receptor 8 NM_000845.3 NP_000836.2 ENST00000339582.7 ENSP00000344173.2 MANE Select NC_000007.14 126438598 127252941 - chr7
199 11794 11794 GeneID:60412 ENSG00000131558.15 HGNC:30389 EXOC4 exocyst complex component 4 NM_021807.4 NP_068579.3 ENST00000253861.5 ENSP00000253861.4 MANE Select NC_000007.14 133253078 134065761 + chr7
200 8687 8687 GeneID:26047 ENSG00000174469.23 HGNC:13830 CNTNAP2 contactin associated protein 2 NM_014141.6 NP_054860.1 ENST00000361727.8 ENSP00000354778.3 MANE Select NC_000007.14 146116801 148420998 + chr7
201 1261 1261 GeneID:1804 ENSG00000130226.18 HGNC:3010 DPP6 dipeptidyl peptidase like 6 NM_130797.4 NP_570629.2 ENST00000377770.8 ENSP00000367001.3 MANE Select NC_000007.14 154052398 154894285 + chr7
202 3922 3922 GeneID:5799 ENSG00000155093.20 HGNC:9677 PTPRN2 protein tyrosine phosphatase receptor type N2 NM_002847.5 NP_002838.2 ENST00000389418.9 ENSP00000374069.4 MANE Select NC_000007.14 157539056 158587823 - chr7
203 6123 6123 GeneID:9228 ENSG00000198010.13 HGNC:2906 DLGAP2 DLG associated protein 2 NM_001346810.2 NP_001333739.1 ENST00000637795.2 ENSP00000489774.1 MANE Select NC_000008.11 737628 1708476 + chr8
204 12033 12033 GeneID:64478 ENSG00000183117.20 HGNC:14026 CSMD1 CUB and Sushi multiple domains 1 NM_033225.6 NP_150094.5 ENST00000635120.2 ENSP00000489225.1 MANE Select NC_000008.11 2935361 4994914 - chr8
205 15225 15225 GeneID:137868 ENSG00000185053.14 HGNC:14075 SGCZ sarcoglycan zeta NM_139167.4 NP_631906.2 ENST00000382080.6 ENSP00000371512.1 MANE Select NC_000008.11 14084845 15238431 - chr8
206 15230 15230 GeneID:137970 ENSG00000156687.11 HGNC:18634 UNC5D unc-5 netrin receptor D NM_080872.4 NP_543148.2 ENST00000404895.7 ENSP00000385143.2 MANE Select NC_000008.11 35235475 35796540 + chr8
207 10032 10032 GeneID:54212 ENSG00000147481.17 HGNC:13740 SNTG1 syntrophin gamma 1 NM_018967.5 NP_061840.1 ENST00000642720.2 ENSP00000493900.1 MANE Select NC_000008.11 49911407 50796692 + chr8
208 17175 17175 GeneID:286183 ENSG00000185942.13 HGNC:26829 NKAIN3 sodium/potassium transporting ATPase interacting 3 NM_001304533.3 NP_001291462.1 ENST00000623646.3 ENSP00000501908.1 MANE Select NC_000008.11 62248854 62984904 + chr8
209 15233 15233 GeneID:138046 ENSG00000184672.12 HGNC:27036 RALYL RALY RNA binding protein like NM_173848.7 NP_776247.3 ENST00000521268.6 ENSP00000430367.1 MANE Select NC_000008.11 84183274 84921844 + chr8
210 15853 15853 GeneID:157680 ENSG00000132549.20 HGNC:2183 VPS13B vacuolar protein sorting 13 homolog B NM_017890.5 NP_060360.3 ENST00000358544.7 ENSP00000351346.2 MANE Plus Clinical NC_000008.11 99013274 99877580 + chr8
211 15852 15852 GeneID:157680 ENSG00000132549.20 HGNC:2183 VPS13B vacuolar protein sorting 13 homolog B NM_152564.5 NP_689777.3 ENST00000357162.7 ENSP00000349685.2 MANE Select NC_000008.11 99013274 99877580 + chr8
212 6483 6483 GeneID:9699 ENSG00000176406.25 HGNC:17283 RIMS2 regulating synaptic membrane exocytosis 2 NM_001348484.3 NP_001335413.1 ENST00000696799.1 ENSP00000512879.1 MANE Select NC_000008.11 103500610 104254430 + chr8
213 14389 14389 GeneID:114788 ENSG00000164796.18 HGNC:19291 CSMD3 CUB and Sushi multiple domains 3 NM_198123.2 NP_937756.1 ENST00000297405.10 ENSP00000297405.5 MANE Select NC_000008.11 112222928 113436939 - chr8
214 13186 13186 GeneID:83696 ENSG00000167632.18 HGNC:30832 TRAPPC9 trafficking protein particle complex subunit 9 NM_001160372.4 NP_001153844.1 ENST00000438773.4 ENSP00000405060.3 MANE Select NC_000008.11 139727725 140457744 - chr8
215 3912 3912 GeneID:5789 ENSG00000153707.19 HGNC:9668 PTPRD protein tyrosine phosphatase receptor type D NM_002839.4 NP_002830.1 ENST00000381196.9 ENSP00000370593.3 MANE Select NC_000009.12 8314246 10613002 - chr9
216 15866 15866 GeneID:158038 ENSG00000174482.11 HGNC:21207 LINGO2 leucine rich repeat and Ig domain containing 2 NM_001258282.3 NP_001245211.1 ENST00000698399.1 ENSP00000513694.1 MANE Select NC_000009.12 27937617 29213601 - chr9
217 12753 12753 GeneID:80036 ENSG00000083067.27 HGNC:17992 TRPM3 transient receptor potential cation channel subfamily M member 3 NM_001366145.2 NP_001353074.1 ENST00000677713.2 ENSP00000503830.2 MANE Select NC_000009.12 70529060 71121621 - chr9
218 8128 8128 GeneID:23245 ENSG00000148219.18 HGNC:17021 ASTN2 astrotactin 2 NM_001365068.1 NP_001351997.1 ENST00000313400.9 ENSP00000314038.4 MANE Select NC_000009.12 116423112 117415057 - chr9
219 11650 11650 GeneID:57706 ENSG00000119522.18 HGNC:29324 DENND1A DENN domain containing 1A NM_001352964.2 NP_001339893.1 ENST00000394215.7 ENSP00000377763.4 MANE Select NC_000009.12 123379658 123930126 - chr9
220 283 283 GeneID:395 ENSG00000047648.23 HGNC:676 ARHGAP6 Rho GTPase activating protein 6 NM_013427.3 NP_038286.2 ENST00000337414.9 ENSP00000338967.4 MANE Select NC_000023.11 11137544 11665920 - chrX
221 6537 6537 GeneID:9758 ENSG00000169933.17 HGNC:29007 FRMPD4 FERM and PDZ domain containing 4 NM_001368397.1 NP_001355326.1 ENST00000675598.1 ENSP00000502607.1 MANE Select NC_000023.11 12138473 12724523 + chrX
222 7636 7636 GeneID:11141 ENSG00000169306.11 HGNC:5996 IL1RAPL1 interleukin 1 receptor accessory protein like 1 NM_014271.4 NP_055086.1 ENST00000378993.6 ENSP00000368278.1 MANE Select NC_000023.11 28587446 29956718 + chrX
223 1224 1224 GeneID:1756 ENSG00000198947.18 HGNC:2928 DMD dystrophin NM_004006.3 NP_003997.2 ENST00000357033.9 ENSP00000354923.3 MANE Select NC_000023.11 31119222 33211549 - chrX
224 14563 14563 GeneID:117154 ENSG00000126733.22 HGNC:16814 DACH2 dachshund family transcription factor 2 NM_053281.3 NP_444511.1 ENST00000373125.9 ENSP00000362217.4 MANE Select NC_000023.11 86148451 86832602 + chrX
225 9081 9081 GeneID:27328 ENSG00000102290.23 HGNC:8656 PCDH11X protocadherin 11 X-linked NM_032968.5 NP_116750.1 ENST00000682573.1 ENSP00000507225.1 MANE Select NC_000023.11 91779375 92623230 + chrX
226 1204 1204 GeneID:1730 ENSG00000147202.19 HGNC:2877 DIAPH2 diaphanous related formin 2 NM_006729.5 NP_006720.1 ENST00000324765.13 ENSP00000321348.8 MANE Select NC_000023.11 96684842 97604997 + chrX
227 8808 8808 GeneID:26280 ENSG00000189108.14 HGNC:5997 IL1RAPL2 interleukin 1 receptor accessory protein like 2 NM_017416.2 NP_059112.1 ENST00000372582.6 ENSP00000361663.1 MANE Select NC_000023.11 104566199 105767829 + chrX
228 6889 6889 GeneID:10178 ENSG00000009694.14 HGNC:8117 TENM1 teneurin transmembrane protein 1 NM_001163278.2 NP_001156750.1 ENST00000422452.4 ENSP00000403954.4 MANE Select NC_000023.11 124375903 125204312 - chrX
229 13107 13107 GeneID:83259 ENSG00000099715.15 HGNC:15813 PCDH11Y protocadherin 11 Y-linked NM_001395587.1 NP_001382516.1 ENST00000698851.1 ENSP00000513983.1 MANE Select NC_000024.10 5000296 5742224 + chrY

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import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, TensorDataset
from axial_attention import AxialAttention
from thefuzz import fuzz
import argparse
from joblib import load
#load data from docker container
#tissue and ensg preprocessing
tissue2number = load('/home/omic/rna2protexpresson/tissue2number.joblib')
ensg2number = load('/home/omic/rna2protexpresson/ensg2number.joblib')
#model weights
model_path = '/home/omic/rna2protexpresson/go_term_protein_expression_model.pth'
#get device
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
#get go terms
go_df_work = pd.read_csv('/home/omic/rna2protexpresson/go_df_work.csv', index_col=0)
#model
class TissueSpecificProteinExpressionModel(nn.Module):
def __init__(self, emb_dim = 64, dim_heads = 512, n_tissues = 29, n_ensg = 14601, go_size=go_df_work.shape[1]):
super(TissueSpecificProteinExpressionModel, self).__init__()
self.emb_dim = emb_dim
self.emb_ensg = nn.Embedding(n_ensg, int(emb_dim/2))
self.emb_tiss = nn.Embedding(n_tissues, emb_dim)
self.attn1 = AxialAttention(
dim = 1, # embedding dimension
dim_index = 1, # where is the embedding dimension
dim_heads = dim_heads, # dimension of each head. defaults to dim // heads if not supplied
heads = 1, # number of heads for multi-head attention
num_dimensions = 2, # number of axial dimensions (images is 2, video is 3, or more)
sum_axial_out = True # whether to sum the contributions of attention on each axis, or to run the input through them sequentially. defaults to true
)
self.attn2 = AxialAttention(dim = emb_dim*2+1, dim_index = 1, dim_heads = dim_heads, heads = 1, num_dimensions = 2, sum_axial_out = True)
self.attn3 = AxialAttention(dim = emb_dim*2+1, dim_index = 1, dim_heads = dim_heads, heads = 1, num_dimensions = 2, sum_axial_out = True)
self.con = nn.Conv2d(emb_dim*2+1, 1, 1, stride=1)
self.batch_norm1 = nn.BatchNorm2d(emb_dim*2+1)
self.batch_norm2 = nn.BatchNorm2d(emb_dim*2+1)
self.emb_go = nn.Linear(go_size, int(emb_dim/2))
def forward(self, x, emb_pos_prot, emb_pos_tissu, go_term):
#embeding go terms
emb_in_go = self.emb_go(go_term)
emb_in_go = torch.unsqueeze(torch.permute(emb_in_go, (0,2,1)),-1)
#embeding proteins
emb_in_p = self.emb_ensg(emb_pos_prot)
emb_in_p = torch.unsqueeze(torch.permute(emb_in_p, (0,2,1)),-1)
emb_in_p = torch.cat([emb_in_go,emb_in_p], dim = 1)
emb_in_p = emb_in_p.expand(x.shape[0],self.emb_dim,emb_pos_prot.shape[1],emb_pos_tissu.shape[1])
#embeding tissues
emb_in_t = self.emb_tiss(emb_pos_tissu)
emb_in_t = torch.unsqueeze(torch.permute(emb_in_t, (0,2,1)),-2)
emb_in_t = emb_in_t.expand(x.shape[0],self.emb_dim,emb_pos_prot.shape[1],emb_pos_tissu.shape[1])
#RNA expresson
x = torch.unsqueeze(x, 1)
x = self.attn1(x)
#concat protein embedding, tissue embedding and RNA expresson
x = torch.cat([x,emb_in_p, emb_in_t], dim = 1)
x = self.batch_norm1(x)
x = self.attn2(x)
x = self.batch_norm2(x)
x = self.attn3(x)
x = self.con(x)
x = torch.squeeze(x, 1)
return x
#run model from pandas dataframe
def run_model(model, X_test, goterm, scaler):
model.eval()
X_test_scaled = [scaler.fit_transform(np.array(i).reshape(i.shape[0], -1)).reshape(i.shape) for i in X_test]# np.array(X_test)
X_test_tensor = torch.FloatTensor(X_test_scaled).to(device)
X_test_tissues = [tissue2number.transform(i.columns) for i in X_test]
X_test_ensg = [ensg2number.fit_transform(i.index) for i in X_test]
X_test_tissues = torch.IntTensor(X_test_tissues).to(device)
X_test_ensg = torch.IntTensor(X_test_ensg).to(device)
X_go = torch.FloatTensor(np.array(goterm)).to(device)
test_dataset = TensorDataset(X_test_tensor, X_test_ensg, X_test_tissues, X_go)
test_loader = DataLoader(test_dataset, batch_size=1)
with torch.no_grad():
for batch_X, ensg_numb, tissue_numb, X_go in test_loader:
y_pred = model(batch_X, ensg_numb, tissue_numb, X_go).cpu().numpy()
return y_pred
def run_save_protrin_esxpression_predicition(TPM, goterm, model, scaler, tissue2number, ensg2number, split_len, name):
#set column names
TPM.columns = [i.split(':')[1] for i in TPM.columns]
#drop tissue/columns not used in model
TPM = TPM[TPM.columns.intersection(tissue2number.classes_)]
## this is done with go_df_work merge
#drop ensg/row not used in model
#TPM = TPM.loc[TPM.index.intersection(ensg2number.classes_),:]
#transform to log2 / used to train model
TPM = np.log2(TPM)
#split TPM in 5 000 chunks
pred = [run_model(model, [i], [j], scaler) for i, j in zip(np.array_split(TPM, int(np.ceil(TPM.shape[0] / split_len))), np.array_split(goterm, int(np.ceil(TPM.shape[0] / split_len))))]
#create Dataframe with tissue and ensg names
pred = pd.DataFrame(np.squeeze(np.concatenate(pred, 1)))
pred = pred.set_index(TPM.index)
pred.columns = TPM.columns
#save predicitions log2
pred.to_csv(f'{name}_Protein_Expression_log2.csv')
checkpoint = torch.load(model_path, map_location=device)
model = TissueSpecificProteinExpressionModel().to(device)
model.load_state_dict(checkpoint['model_state_dict'])
scaler = checkpoint['scaler']
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Predict protein expression from RNA expression')
parser.add_argument('--borzoi_ouput', help='Output from borzoi step', required=True)
args = parser.parse_args()
#borzoi output TPM
TPM = pd.read_csv(args.borzoi_ouput,index_col=0)
#get output name
out_name = args.borzoi_ouput.split('_TPM.csv')[0]
#get go term
X_go = pd.merge(TPM, go_df_work, left_index=True, right_index=True).iloc[:,TPM.shape[1]:]
#drop ensg/row not used in model
TPM = pd.merge(TPM, go_df_work, left_index=True, right_index=True).iloc[:,:TPM.shape[1]]
#run and save output to Protein_Expression_log2.csv
run_save_protrin_esxpression_predicition(TPM, X_go, model, scaler, tissue2number, ensg2number, 2500, out_name)

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nextflow.enable.dsl=2
// ================= IMAGES GO HERE ================================================================
params.containerOptions = '--rm' // '--gpus all --rm -v /mnt:/mnt'
params.containerOptions_synthea = "--rm --privileged --gpus all" // -v /mnt:/mnt"
params.containerOptions_borzoi = '--rm --gpus all' // '--gpus all --rm -v /mnt:/mnt'
params.container_borzoi = 'harbor.cluster.omic.ai/omic/digital-patients/borzoi:latest'
params.container_vcf2prot = "harbor.cluster.omic.ai/omic/digital-patients/vcf2prot:latest"
params.container_rna2protexpression = 'harbor.cluster.omic.ai/omic/digital-patients/rna2protexpression:latest'
params.containerOptions_rna2protexpression = '--gpus all --rm' // -v /mnt:/mnt -v /dbs:/dbs'
// params.containerOptions_rna2protexpression = '--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs'
params.container_corto = 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
params.container_ecotyper = 'harbor.cluster.omic.ai/omic/digital-patients/ecotyper:latest'
params.container_synthea = 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
// =================================================================================================
//SYNTHEA
params.n_pat = 2 //10 //number of patients to generate, must be => 2 (one male one female)
params.percent_male = 0.5 // between 0-1, percent of male patients
//params.age = '18-80' //age range of the population, expressed as age-age
//params.state = '"District of Columbia"' //'Hawaii' //'Texas' //'Georgia'
//params.city = '' //'Washington' //'' //'Honolulu' //'Houston' //'Atlanta'
// Keep both versions of disease params
params.disease = 'schizophrenia' //'schizophrenia' //'healthy' //'leukaemia' //'leukaemia' //'Purpura and other haemorrhagic conditions' //['tongue cancer', 'dementia', 'arthritis'] //'tongue cancer' //'dementia'
//params.n_var = 100
params.project_name = 'test'
//CIBERSORT
params.cibersortx_username = "gabriel.richman.2009@anderson.ucla.edu"
params.cibersortx_token = "b5b39e563fb947df4cfd4843d40fdb99"
// ====================== FILEPATHS HERE =========================================================================
params.imputed_store = '/mnt/Avatar/imputed/ukbb/imputed' //'/rosalind/ukbb/imputed'
params.pheno_store ='/mnt/dreamdock-data/digital-patient-data/data/ukbb_phenotypes_filtered.csv' // '/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv'
//CORTO
params.regulon = '/mnt/dreamdock-data/digital-patient-data/data/regulon.rda' // '/Workspace/next/registry/pipelines/digital_patient/regulon.rda'
params.healthy_dir = '/mnt/dreamdock-data/digital-patient-data/healthy' // '/Workspace/next/registry/pipelines/digital_patient' //'/mnt/Avatar/digital_patient' // data copy is here
params.synthea_support_dir = '/mnt/Avatar/dd/synthea/supporting-data/'
//BORZOI
params.mane = '/mnt/dreamdock-data/digital-patient-data/data/MANE.GRCh38.v1.3.update.tsv' // '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
//CIBERSORT
params.signature_matrix = '/mnt/dreamdock-data/digital-patient-data/data/LM22_sourceGEP_ensg.txt' // "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
params.outdir = '/mnt/dreamdock-data/digital-patient-data/out' // '/mnt/OmicNAS/dd/digital_patient/new'
// params.outdir = '/data/digital-patients-data' // '/mnt/OmicNAS/dd/digital_patient/new'
params.ecotyper_outdir = "${params.outdir}/ecotyper"
// ====================== FILTERING PARAMETERS ====================================================================
// Enable/disable filtering
params.enable_filtering = true
// Filtering thresholds based on Gabe's requirements
params.top_n_variants = 500
params.top_n_genes = 1000
params.transcriptome_log2fc_threshold = 1.5
params.top_n_proteins = 500
params.top_n_immune_cells = 20
params.top_n_metabolites = 50
params.metabolome_pvalue_threshold = 0.05
// ===============================================================================================================
//SYNTHEA
include {get_disease_stats_no_patients} from './main_synthea.nf'
include {generate_m_variants_cudf} from './main_synthea.nf'
include {generate_f_variants_cudf} from './main_synthea.nf'
include {make_vcfs} from './main_synthea.nf'
include {generate_m_healthy_cudf} from './main_synthea.nf'
include {generate_f_healthy_cudf} from './main_synthea.nf'
//BORZOI
include {FILTER_VCF} from './main_borzoi.nf'
include {PREDICT_EXPRESSION} from './main_borzoi.nf'
include {CREATE_PROTEIN_CLUSTER} from './main_borzoi.nf'
//VCF2PROT
include {VCF2PROT} from './main_vcf2prot.nf'
//RNA2PROTEINEXPRESSION
include {RNA2PROTEXPRESSION} from './main_rna2proteinexpression'
//CORTO
include {CORTO} from './main_corto.nf'
//CIBERSORT
include {CONVERT_TO_TXT} from './main_cibersortx.nf'
include {CIBERSORTx_FRACTIONS} from './main_cibersortx.nf'
include {CIBERSORTx_HIRES} from './main_cibersortx.nf'
include {ADD_TISSUE_NAMES_TO_CIBERSORTX} from './main_cibersortx.nf'
//FILTERING PROCESSES
include {FILTER_VARIANTS} from './main_filter_outputs.nf'
include {FILTER_TRANSCRIPTOME} from './main_filter_outputs.nf'
include {FILTER_PROTEOME} from './main_filter_outputs.nf'
include {FILTER_IMMUNE_CELLS} from './main_filter_outputs.nf'
include {FILTER_METABOLOME} from './main_filter_outputs.nf'
include {FILTER_MUTATED_PROTEINS} from './main_filter_outputs.nf'
include {CREATE_SUMMARY_REPORT} from './main_filter_outputs.nf'
workflow {
pheno_store_ch = file(params.pheno_store)
imputed_store_ch = file(params.imputed_store)
synthea_support_ch = file(params.synthea_support_dir)
regulon_ch = file(params.regulon)
signature_matrix_ch = file(params.signature_matrix)
mane_ch = file(params.mane)
health_dir_ch = file(params.healthy_dir)
//SYNTHEA
switch (params.disease) {
case 'healthy':
//healthy
generate_m_healthy_cudf(health_dir_ch)
generate_f_healthy_cudf(health_dir_ch)
m_healthy = generate_m_healthy_cudf.out
f_healthy = generate_f_healthy_cudf.out
txt_ch = f_healthy.mix(m_healthy).flatten()
break
default:
//disease
get_disease_stats_no_patients(pheno_store_ch, imputed_store_ch)
generate_m_variants_cudf(get_disease_stats_no_patients.out)
generate_f_variants_cudf(get_disease_stats_no_patients.out)
f_var = generate_f_variants_cudf.out
m_var = generate_m_variants_cudf.out
txt_ch = f_var.mix(m_var).flatten()
}
make_vcfs(txt_ch, synthea_support_ch)
// TODO: ADD STEP TO CREATE AVERAGED COHORT (HEALTHY)
// TODO: ADD STEP TO CREATE AVERAGED DISEASED
// TODO: ADD STEP TO CALCULATE STATISTICS LOG2FC and ADJ PVAL
//BORZOI
// Prepare the VCF file(s)
//vcf_ch = Channel.fromPath(make_vcfs.out)
// THIS IS USES TO CREATE PROTEIN CLUSTER ON A SAME BORZOI INPUT AND SPLIT ONES TOO BIG FOR BORZOI (LEN = 524288)
// THIS STEP NEEDS TO BE RUN TO CREATE DATA FOR NEXT STEP ONLY IF NEW REFERENCE/RNAS ARE GOING TO BE USED
//CREATE_PROTEIN_CLUSTER(params.mane)
FILTER_VCF(mane_ch, make_vcfs.out)
PREDICT_EXPRESSION(FILTER_VCF.out, mane_ch)
//VCF2PROT
VCF2PROT(make_vcfs.out, FILTER_VCF.out)
//RNA2PROTEINEXPRESSION
// Updated RNA to protein expression step to run only a single process at a time, avoids CUDA out-of-memory errors.
PREDICT_EXPRESSION.out
.collect()
.flatten()
.set { rna_input }
RNA2PROTEXPRESSION(rna_input)
//CORTO
CORTO(PREDICT_EXPRESSION.out, regulon_ch)
//CIBERSORT
signature_file = Channel.fromPath(signature_matrix_ch, checkIfExists: true)
CONVERT_TO_TXT(PREDICT_EXPRESSION.out)
CIBERSORTx_FRACTIONS(CONVERT_TO_TXT.out, signature_file)
CIBERSORTx_HIRES(CONVERT_TO_TXT.out, CIBERSORTx_FRACTIONS.out, signature_file)
ADD_TISSUE_NAMES_TO_CIBERSORTX(CONVERT_TO_TXT.out, CIBERSORTx_HIRES.out)
// ==================== FILTERING STAGE ====================
if (params.enable_filtering) {
// Filter variants
FILTER_VARIANTS(make_vcfs.out)
// Filter transcriptome
FILTER_TRANSCRIPTOME(PREDICT_EXPRESSION.out)
// Filter proteome
FILTER_PROTEOME(RNA2PROTEXPRESSION.out)
// Filter immune cells
FILTER_IMMUNE_CELLS(ADD_TISSUE_NAMES_TO_CIBERSORTX.out)
// Filter metabolome
FILTER_METABOLOME(CORTO.out)
// Filter mutated proteins
FILTER_MUTATED_PROTEINS(VCF2PROT.out, FILTER_VARIANTS.out.filtered_vcf)
// Create summary report
CREATE_SUMMARY_REPORT(
FILTER_TRANSCRIPTOME.out,
FILTER_PROTEOME.out,
FILTER_IMMUNE_CELLS.out,
FILTER_METABOLOME.out,
FILTER_VARIANTS.out.filtered_vcf
)
}
}

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nextflow.enable.dsl=2
//SYNTHEA
params.n_pat = 2//10 //number of patients to generate, must be => 2 (one male one female)
params.percent_male = 0.5 // between 0-1, percant of mail patients
//params.age = '18-80' //age range of the population, expressed as age-age
//params.state = '"District of Columbia"' //'Hawaii' //'Texas' //'Georgia'
//params.city = '' //'Washington' //'' //'Honolulu' //'Houston' //'Atlanta'
params.imputed_store = '/mnt/Avatar/imputed/ukbb/imputed' //'/rosalind/ukbb/imputed'
params.pheno_store = '/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv'
params.disease = 'healthy' //'schizophrenia' //'healthy' //'leukaemia' //'leukaemia' //'Purpura and other haemorrhagic conditions' //['tongue cancer', 'dementia', 'arthritis'] //'tongue cancer' //'dementia'
params.healthy_dir = '/Workspace/next/registry/pipelines/digital_patient' //'/mnt/Avatar/digital_patient' // data copy is here
//params.n_var = 100
params.outdir = '/mnt/OmicNAS/dd/digital_patient'
//BORZOI
params.container_borzoi = 'borzoi:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.project_name = 'test'
params.mane = '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
//VCF2PROT
params.container_vcf2prot = "vcf2prot:latest"
//RNA2PROTEINEXPRESSION
params.container_rna2protexpression = 'rna2protexpression:latest'
params.containerOptions_rna2protexpression = '--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs'
//CORTO
params.container_corto = 'corto:latest'
params.regulon = '/Workspace/next/registry/pipelines/digital_patient/regulon.rda'
//CIBERSORT
params.cibersortx_username = "gabriel.richman.2009@anderson.ucla.edu"
params.cibersortx_token = "b5b39e563fb947df4cfd4843d40fdb99"
params.container_ecotyper = 'ecotyper:latest'
params.signature_matrix = "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
params.ecotyper_outdir = "/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
//SYNTHEA
include {get_disease_stats_no_patients} from './main_synthea.nf'
include {generate_m_variants_cudf} from './main_synthea.nf'
include {generate_f_variants_cudf} from './main_synthea.nf'
include {make_vcfs} from './main_synthea.nf'
include {generate_m_healthy_cudf} from './main_synthea.nf'
include {generate_f_healthy_cudf} from './main_synthea.nf'
//BORZOI
include {FILTER_VCF} from './main_borzoi.nf'
include {PREDICT_EXPRESSION} from './main_borzoi.nf'
include {CREATE_PROTEIN_CLUSTER} from './main_borzoi.nf'
//VCF2PROT
include {VCF2PROT} from './main_vcf2prot.nf'
//RNA2PROTEINEXPRESSION
include {RNA2PROTEXPRESSION} from './main_rna2proteinexpression'
//CORTO
include {CORTO} from './main_corto.nf'
//CIBERSORT
include {CONVERT_TO_TXT} from './main_cibersortx.nf'
include {CIBERSORTx_FRACTIONS} from './main_cibersortx.nf'
include {CIBERSORTx_HIRES} from './main_cibersortx.nf'
include {ADD_TISSUE_NAMES_TO_CIBERSORTX} from './main_cibersortx.nf'
workflow {
//SYNTHEA
switch (params.disease) {
case 'healthy':
//healthy
generate_m_healthy_cudf(params.healthy_dir)
generate_f_healthy_cudf(params.healthy_dir)
m_healthy = generate_m_healthy_cudf.out
f_healthy = generate_f_healthy_cudf.out
txt_ch = f_healthy.mix(m_healthy).flatten()
break
default:
//disease
get_disease_stats_no_patients()
generate_m_variants_cudf(get_disease_stats_no_patients.out)
generate_f_variants_cudf(get_disease_stats_no_patients.out)
f_var = generate_f_variants_cudf.out
m_var = generate_m_variants_cudf.out
txt_ch = f_var.mix(m_var).flatten()
}
make_vcfs(txt_ch)
//BORZOI
// Prepare the VCF file(s)
//vcf_ch = Channel.fromPath(make_vcfs.out)
// THIS IS USES TO CREATE PROTEIN CLUSTER ON A SAME BORZOI INPUT AND SPLI ONES TO BIG FOR BORZOI (LEN = 524288)
// THIS STEP NEEDS TO BR RUN TO CREATE DATA FOR NEXT STEP ONLY IF NEW REFERENCE/RNAS ARE GOING TO BE USE
//CREATE_PROTEIN_CLUSTER(params.mane)
FILTER_VCF(params.mane, make_vcfs.out)
PREDICT_EXPRESSION(FILTER_VCF.out, params.mane)
//VCF2PROT
VCF2PROT(make_vcfs.out, FILTER_VCF.out)
//RNA2PROTEINEXPRESSION
//collect is here onyl to stop RNA2PROTEXPRESSION run at the same time as BORZOI (not enough CUDA space)
RNA2PROTEXPRESSION(PREDICT_EXPRESSION.out.collect())
//CORTO
CORTO(PREDICT_EXPRESSION.out, params.regulon)
//CIBERSORT
signature_file = Channel.fromPath(params.signature_matrix, checkIfExists: true)
CONVERT_TO_TXT(PREDICT_EXPRESSION.out)
CIBERSORTx_FRACTIONS(CONVERT_TO_TXT.out, signature_file)
CIBERSORTx_HIRES(CONVERT_TO_TXT.out, CIBERSORTx_FRACTIONS.out, signature_file)
ADD_TISSUE_NAMES_TO_CIBERSORTX(CONVERT_TO_TXT.out, CIBERSORTx_HIRES.out)
}

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nextflow.enable.dsl=2
//SYNTHEA
params.n_pat = 2 //10 //number of patients to generate, must be => 2 (one male one female)
params.percent_male = 0.5 // between 0-1, percent of male patients
params.age = '18-80' //age range of the population, expressed as age-age
// params.state = '"District of Columbia"' //'Hawaii' //'Texas' //'Georgia'
// params.city = '' //'Washington' //'' //'Honolulu' //'Houston' //'Atlanta'
params.imputed_store = '/mnt/Avatar/imputed/ukbb/imputed' //'/rosalind/ukbb/imputed'
params.pheno_store = '/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv'
// Keep both versions of disease params
params.disease = 'schizophrenia' //'schizophrenia' //'healthy' //'leukaemia' //'leukaemia' //'Purpura and other haemorrhagic conditions' //['tongue cancer', 'dementia', 'arthritis'] //'tongue cancer' //'dementia'
params.healthy_dir = '/Workspace/next/registry/pipelines/digital_patient' //'/mnt/Avatar/digital_patient' // data copy is here
//params.n_var = 100
params.outdir = '/mnt/OmicNAS/dd/digital_patient'
//BORZOI
params.container_borzoi = 'borzoi:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.project_name = 'test'
params.mane = '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
//VCF2PROT
params.container_vcf2prot = "vcf2prot:latest"
//RNA2PROTEINEXPRESSION
params.container_rna2protexpression = 'rna2protexpression:latest'
params.containerOptions_rna2protexpression = '--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs'
//CORTO
params.container_corto = 'corto:latest'
params.regulon = '/Workspace/next/registry/pipelines/digital_patient/regulon.rda'
//CIBERSORT
params.cibersortx_username = "gabriel.richman.2009@anderson.ucla.edu"
params.cibersortx_token = "b5b39e563fb947df4cfd4843d40fdb99"
params.container_ecotyper = 'ecotyper:latest'
params.signature_matrix = "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
params.ecotyper_outdir = "/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
//SYNTHEA
include {generate_patients} from './main_synthea.nf'
// include {get_disease_stats_no_patients} from './main_synthea.nf'
// include {generate_m_variants_cudf} from './main_synthea.nf'
// include {generate_f_variants_cudf} from './main_synthea.nf'
// include {make_vcfs} from './main_synthea.nf'
// include {generate_m_healthy_cudf} from './main_synthea.nf'
// include {generate_f_healthy_cudf} from './main_synthea.nf'
// //BORZOI
// include {FILTER_VCF} from './main_borzoi.nf'
// include {PREDICT_EXPRESSION} from './main_borzoi.nf'
// include {CREATE_PROTEIN_CLUSTER} from './main_borzoi.nf'
// //VCF2PROT
// include {VCF2PROT} from './main_vcf2prot.nf'
// //RNA2PROTEINEXPRESSION
// include {RNA2PROTEXPRESSION} from './main_rna2proteinexpression'
// //CORTO
// include {CORTO} from './main_corto.nf'
// //CIBERSORT
// include {CONVERT_TO_TXT} from './main_cibersortx.nf'
// include {CIBERSORTx_FRACTIONS} from './main_cibersortx.nf'
// include {CIBERSORTx_HIRES} from './main_cibersortx.nf'
// include {ADD_TISSUE_NAMES_TO_CIBERSORTX} from './main_cibersortx.nf'
workflow {
generate_patients()
// //SYNTHEA
// switch (params.disease) {
// case 'healthy':
// //healthy
// generate_m_healthy_cudf(params.healthy_dir)
// generate_f_healthy_cudf(params.healthy_dir)
// m_healthy = generate_m_healthy_cudf.out
// f_healthy = generate_f_healthy_cudf.out
// txt_ch = f_healthy.mix(m_healthy).flatten()
// break
// default:
// //disease
// get_disease_stats_no_patients()
// generate_m_variants_cudf(get_disease_stats_no_patients.out)
// generate_f_variants_cudf(get_disease_stats_no_patients.out)
// f_var = generate_f_variants_cudf.out
// m_var = generate_m_variants_cudf.out
// txt_ch = f_var.mix(m_var).flatten()
// }
// make_vcfs(txt_ch)
// //BORZOI
// // Prepare the VCF file(s)
// //vcf_ch = Channel.fromPath(make_vcfs.out)
// // THIS IS USES TO CREATE PROTEIN CLUSTER ON A SAME BORZOI INPUT AND SPLIT ONES TOO BIG FOR BORZOI (LEN = 524288)
// // THIS STEP NEEDS TO BE RUN TO CREATE DATA FOR NEXT STEP ONLY IF NEW REFERENCE/RNAS ARE GOING TO BE USED
// //CREATE_PROTEIN_CLUSTER(params.mane)
// FILTER_VCF(params.mane, make_vcfs.out)
// PREDICT_EXPRESSION(FILTER_VCF.out, params.mane)
// //VCF2PROT
// VCF2PROT(make_vcfs.out, FILTER_VCF.out)
// //RNA2PROTEINEXPRESSION
// // Updated RNA to protein expression step to run only a single process at a time, avoids CUDA out-of-memory errors.
// PREDICT_EXPRESSION.out
// .collect()
// .flatten()
// .set { rna_input }
// RNA2PROTEXPRESSION(rna_input)
// //CORTO
// CORTO(PREDICT_EXPRESSION.out, params.regulon)
// //CIBERSORT
// signature_file = Channel.fromPath(params.signature_matrix, checkIfExists: true)
// CONVERT_TO_TXT(PREDICT_EXPRESSION.out)
// CIBERSORTx_FRACTIONS(CONVERT_TO_TXT.out, signature_file)
// CIBERSORTx_HIRES(CONVERT_TO_TXT.out, CIBERSORTx_FRACTIONS.out, signature_file)
// ADD_TISSUE_NAMES_TO_CIBERSORTX(CONVERT_TO_TXT.out, CIBERSORTx_HIRES.out)
}

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nextflow.enable.dsl=2
params.container_borzoi = 'borzoi:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/borzoi/outputs'
params.project_name = 'test'
params.mane = '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
include {PREDICT_EXPRESSION_NO_MUTATIONS} from './main_no_mutations.nf'
workflow {
PREDICT_EXPRESSION_NO_MUTATIONS(params.mane)
}

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