How can I download SNPs from HapMap European populations?
Entering edit mode
13 months ago
rheab1230 ▴ 140

Hello, Does anyone knows how to download or get only snp from hapmap EUR population for gtex v8 models? I tried to get the snp annotation file from gtex portal and downloaded the lookup table in order to get the snp_annotation file. Thank you.

snp annotation gtex • 396 views
Entering edit mode
13 months ago
LauferVA 3.7k

Hi Rheab,

Yes, certainly! First, for JUST hapmap, go to hapmap's FTP site.

One thing, though. Nowadays, there are more comprehensive options out there. Two that I recommend, for various reasons, are:

  1. Check out Ensembl VEP. Steps: click link, paste in an rsID > run job > once job is finished, you will see a table in your browser. You can download this, including columns broken out by global MAF, then MAF for each ancestry specifically. Example result for a variant I just ran.

  2. If you want to take a deeper dive into a confined genomic locus (max 50,000bp in length) then Kaviar is a good option. This database contains more variants than dbSNP, even, and includes allele fractions down to very low percentages.


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