The three boldfaced links at https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 provide one solution. With that dataset downloaded, plink2 can report allele frequencies for any predefined population, as well as any population you define yourself. (You can also export VCF files from it, and subsetting is frequently >10x faster than bcftools.)

I would suggest downloading the sites VCF from here, http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ and using bcftools to subset it to SNPs of interest using the -R or -T flag.

Link to the sites file: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi

Hello bioinforesearchquestions ,

if you are able to code use ensembl's REST-API, especially the variation endpoint. There also an endpoint for query multiple IDs at once.

fin swimmer