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.
Hi Rheab,

Yes, certainly! First, for JUST hapmap, go to [hapmap's FTP site][1]. 

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

1. Check out [Ensembl VEP][2].  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][3]. 

2. If you want to take a deeper dive into a confined genomic locus (max 50,000bp in length) then [Kaviar][4] is a good option. This database contains more variants than dbSNP, even, and includes allele fractions down to very low percentages.


  [1]: https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html
  [2]: https://www.ensembl.org/Tools/VEP
  [3]: https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=TykABz8JFAblrPFQ-8512135
  [4]: https://db.systemsbiology.net/kaviar/