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I have a list of SNPs associated with a trait and I'd like to create a list of up- and down-regulated genes associated with these SNPs (using eQTL data I guess). What's the fastest way I could go about doing this?

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  • $\begingroup$ Each SNP presumably affects a single gene (with few exceptions such as overlapping genes). Do you mean you want to find cases where this specific gene has been seen in an individual and the associated gene was deregulated in certain tissues? What species are you working with? Have you looked at gtexportal.org/home? $\endgroup$
    – terdon
    Oct 15 at 9:03
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When working with human data, the eQTL data from the GTEx portal is a fantastic resource. For your list of variant IDs, you can actually retrieve the eQTL beta correlations and their p-values from the GTEx project using the Ensembl REST API with the following endpoint:

http://rest.ensembl.org/documentation/info/species_variant

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