I want to download flat files that list all SNPs for which allele frequencies exist across the major human populations (European, East Asian, and African). Where can I find such data?
We currently do not have a flat file report of allele frequencies across major populations for all human SNPs. If you can work with XML files, you can find FTP files of genotype data (including genotype and allele frequency data) in the dbSNP FTP site. They are organized by chromosomes: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype/ ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/genotype_by_gene/ If you are working with a set of SNPs, you could use eutils to fetch the allele frequency information. In the meantime, we will look at making a new FTP file format for reporting SNP frequencies.
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