I'm trying to retrieve population specific (EUR) allele frequencies for a few hundred SNPs I got from the GWAS Catalog. Somehow, I can't find any of those SNPs in the 1000 genomes vcf file ( ftp://ftp.ensembl.org/pub/release-91/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz), but searching for them via the Ensembl webpage works well (and gives data that they have also been called in the 1000 genomes phase 3).
According to the FAQ the data in the GWAS Catalog is currently mapped to genome assembly GRCh38.p12 and dbSNP Build 150, hence should match the 1000GENOMES-phase_3.vcf (stated above). I also tried using BioMart, but could only retrieve the Global AF :(
So, is there any way to get the EUR AF through BioMart or any other way/source than the 1000 genomes?
I'll paste just a few SNPs here that I want the EUR_AF for (e.g. in case somebody wants to try out a code): rs61839660, rs1265564, rs2304256, rs941576, rs539514, rs478222, rs924043 etc.
Thanks to all responders :)