Question: Annotation of GWAS results with GTEx
gravatar for LNA
3.5 years ago by
LNA30 wrote:

Dear all,

I have a list of SNPs as a GWAS result and I would like add the information whether a SNP is a known eQTL according to GTEx (and the respective tissue) to each of the entries of this list. This seems to me like a common problem, but somehow I cannot find a "direct way" to do this. If I check a single SNP rsID on the GTEx site, they provide a table with the respective gene, p value, effect size and tissue, which is exactly what I was looking for, but there seems to be no way to get the information for a whole list of SNPs.

On the NCBI Phenotype-genotype integrator website it is written, that the GTEx information is part of the output, but when I upload a list of SNPs, I obtain eQTL data only for very few SNPs and when I checked single SNPs for which data is available on the GTEx portal, their eQTL data is not included in the Phenotype-genotype integrator output.

How can I obtain this information? Is there any portal/program which makes the data easily accessible just by giving a list of SNP ids or SNP positions as input? Do I have to apply for data access at dbGaP? If I need access via dbGaP, what would be the recommended way to process the data?

Thank you for your help!

gtex eqtl snp gwas • 2.2k views
ADD COMMENTlink modified 3.5 years ago by alioniya0 • written 3.5 years ago by LNA30

Have you tried the 'Downloads' section in the GTEx portal, under 'Datasets'? You need to register first though.

ADD REPLYlink written 3.5 years ago by Denise CS5.1k

My mistake... You're right, all the information is in the download section. Thank you very much for the hint. I somehow misinterpreted the description and thought all the data has to be obtained from dbGaP. Of course it would be easier if there was a the possibility to get the data for a predefined SNP list (like I expected it to work with the Phenotype-Genotype integrator), but one can get everything from the files on the GTEx page.

ADD REPLYlink written 3.5 years ago by LNA30
gravatar for alioniya
3.5 years ago by
alioniya0 wrote:

I have the same problem. Could you pls specify which exactly dataset you used? I tried to download Single Tissue cis-eQTL Data: GTEx_Analysis_v6p_eQTL.tar and Single Tissue trans-eQTL Data:GTEx_Analysis_v6p_trans_eQTLs.xlsx and there is no rsids and files for each tissue are downloaded separately.

ADD COMMENTlink written 3.5 years ago by alioniya0

I used the GTEx_Analysis_V6_eQTLs.tar.gz from Single Tissue eQTL Data in "GTEx Analysis V6 (dbGaP Accession phs000424.v6.p1)". It was not clear to me why the V6 data provides only one file and the V6p data provides two files for cis and for trans. Finally, I used the V6 data, I don't know how much difference this makes (?). The archive includes separate files for each tissue. So there is no table that includes all the information. There are two columns in each file that contain rsids: snp_id_1kg_project_phaseI_v3 and rs_id_dbSNP142_GRCh37p13, but I don't know what they refer to, because I didn't use the rsid but the chromosome and position information (columns snp_chrom and snp_position).

ADD REPLYlink written 3.5 years ago by LNA30
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