How can I download SNPs from HapMap European populations?
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6 weeks ago
rheab1230 ▴ 110

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 • 188 views
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6 weeks ago
Vincent Laufer ★ 2.4k

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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