Download all eQTL data for all the 9 tissues from GTEx Portal
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7.5 years ago
komal.rathi ★ 3.9k

Hi,

We are working on eQTL analyis of Human Heart samples and would like to use the eQTL data (for all the 9 tissues like Adipose Subcutaneous, Artery Tibial, Blood, Heart Left Ventricle, Lung, Muscle Skeletal, Nerve Tibial, Skin Sun Exposed, Thyroid) from GTEx for the sake of comparison. However, I find that I can only download/copy data for 1000 most significant SNPs for any gene per tissue (Go to http://www.gtexportal.org/home/ -> Search -> Search eQTLs -> Browse Significant eQTLs -> Select Tissue). You have to click on the + sign on the left side of a Gene-SNP (most significant) pair entry to expand it and find all other SNPs related to that gene. But I would like to download all the eQTL data i.e. all SNPs per gene in each of the 9 tissues. Has anyone been able to do that? Any help would be much appreciated.

Thanks to @rbagnall, the data is available here: https://www.gtexportal.org/home/datasets

GTEx-Portal eQTL • 7.5k views
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7.5 years ago
Ana ▴ 30

One of the investigators involved in the GTEx (Tuuli Lappalainen) replayed on twitter: "I think that GTEx eQTL bulk downloads aren't available before pilot paper publication. Will confirm.".

Often these consortia give prepublication access to all their data upon request. I suggest you email them about it.

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Thanks Ana

I did email them and they said the full eQTL data should be released in a few weeks.

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7.1 years ago
sekharsj • 0

Hi Komal,

Did you manage to download that data, now ? even i wanted it and couldn't figure out the way to get it .

 

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sekharsj No, I couldn't. Like I said, you can download data only for 1000 most significant SNPs for any gene per tissue. They haven't released the complete data just yet.

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Thank you Komal. I am sure that you are working on Genomics too. can you drop an email on sekharsj@gmail.com ?

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5.7 years ago

Is all the data from GETx available now?. In addition to significant associations I'm also interested in the P-values for non-significant associations. Are these available now?

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2.5 years ago
kunal368 • 0

I am looking to download the same data. Is it possible to download now? Nobody has been able to download?

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Yes, from here: https://www.gtexportal.org/home/datasets

Scroll down to single tissue eQTL data or multi tissue eQTL data. Read the descriptions, some files are very large.

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Can you move this to an answer so I can accept it? Thanks!

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