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Data Download

All Phase 1 NIEHS SNPs Variation Data

Bulk Download of All Variation Data Files

WARNING: This is a very large file and will take several minutes to download. The file is a compressed and "tarred" unix file containing the entire directory of text data files. These are the same text data files which appear in the data pages for each candidate gene in our Finished Genes Table. Please see our Usage Policy if this work is to be used in a publication.

Download of Variation Data (Single File)

Global Prettybase File

This is a tab delimited text file in our "prettybase" format that describes all SNP sites discovered by NIEHS SNPs. The format of this file is:

Line format:
<chromosome position-chromosome-HUGO_NAME > <EGP Sample ID> <Allele1> <Allele2>

Example: 99504884-REV1L-2 DY07 G G

The 'chromosome position' is generated from mapping to the most recent genome assembly available from the UCSC Genome Assembly.

Download of EGP Variation Data by Chromosome

These are tab delimited text files in our "prettybase" format that describe all SNP sites discovered by NIEHS SNPs but separated into files based on chromosome. The format of this file is:

Line format:
<chromosome position-chromosome-HUGO_NAME > <EGP Sample ID> <Allele1> <Allele2>

Example: 99504884-REV1L-2 DY07 G G

The 'chromosome position' is generated from mapping the most recent genome assembly available from the UCSC Genome Assembly.

Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
Chromosome 6
Chromosome 7
Chromosome 8
Chromosome 9
Chromosome 10
Chromosome 11
Chromosome 12
Chromosome 13
Chromosome 14
Chromosome 15
Chromosome 16
Chromosome 17
Chromosome 18
Chromosome 19
Chromosome 20
Chromosome 21
Chromosome 22
X Chromosome
Y Chromosome

NIEHS SNPs SIFT/PolyPhen Data

Putative functional changes in a candidate gene's protein function were assessed by taking the nonsynonymous coding SNPs (cSNPs) for each gene and using both SIFT and PolyPhen. Generally, each nonsynonymous amino acid change is analyzed in the context of other evolutionarily similar proteins to determine the likelihood of the polymorphic nonsynonymous change and then statistically classified. These programs classify each coding SNP as tolerant or intolerant (SIFT), or as benign, possibly damaging, or probably damaging (PolyPhen).

Combined SIFT/PolyPhen Data for NIEHS SNPs Nonsynonymous SNPs

Combined SIFT/PolyPhen Data for NIEHS SNPs Nonsynonymous SNPs (Intolerant or Potentially Damaging)

SIFT Data for NIEHS SNPs Nonsynonymous SNPs (Potentially Intolerant)

PolyPhen Data for NIEHS SNPs Nonsynonymous Genes (Potentially Damaging)

Download of dbSNP rs IDs for All Variations (Single File)

rsEGP.txt.gz

This is a tab-delimited text file that lists the NCBI dbSNP rs IDs (Build 126). In addition, the chromosome positions for UCSC Browser builds hg17 and hg18 are given.

Following several header lines, the columns are:

<gene name><EGP local ID><chromosome number><hg17 position><hg18 position><rs ID>

Example:

sftpb    SFTPB-002233    chr2    85805543    85747396    rs3024799


 
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