How to identify the nearest gene associated with a specific SNPs?
Hi,
I have a (what I think is) a very naive question but I am not an geneticist. I need to compile a list of gene to screen later in my in vitro model. I decided to define this list by using GWAS studies. Most papers have on their supplementary material the SNPs as well as the gene associated to that specific locus. However some papers don't.
How do I identify the nearest gene associated with that SNPs if I have only the Reference SNP cluster ID (RSID)?
Also is there a tool that can speed up this search?
Thank you very much
Camilla
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This is a common question on bioinformatics forums. Have you tried Googling it? https://www.google.com/search?q=snp+nearest+gene
You can search for RSIDs one at a time on gnomAD:
gnomAD
Under the Variant Effect Predictor section, it will tell you what gene your SNP is located in. There's probably a way to automate this that others on this forum will know about.