GTEX - how to upload more than one rsIDs to get gene expression or eQTL information
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2.5 years ago
SGMS ▴ 70

Hi everyone,

I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically.

I looked on GTEx but I only found the option of using one SNP at a time or put a list of SNPs but that is with additional info I don't have.

Does anyone know how to upload multiple rsIDs on GTEx?

Thanks a lot

GTEx snps rsids • 923 views
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Did you figure it out?

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6 months ago

Did you figure it out?

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Hello,

I downloaded the latest GTEx version which included SNPs and found common SNPs of GTEx with my dataset. I then compared the effect sizes (direction of betas) of my dataset to the ones in GTEx.

Hope that helps!

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I want to Know how to get the GTEx data? Thanks for your help

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Hi, sure!

You can download anything you need from https://www.gtexportal.org/home/datasets.

I wanted version 7 (v7) which has to do with the assembly hg19 but there's a newer version for hg18 as well. I specifically downloaded the GTEx_Analysis_v7.metasoft.txt.gz from: "Multi-tissue eQTL data" and GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLI.

Hope this helps!

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