How do I identify all dbSNP frequency data coming from the HapMap CEU population?
The HapMap Handle is “CSHL-HAPMAP” and the HapMap CEU population ID is “HapMap-CEU”. Using the dbSNP “Population Detail” search, enter HapMap-CEU in the test box in the grey query section, and then select “submitter population ID” and “exact”. Click on the “HapMap-CEU” link you get in your response to get the details for the HapMap-CEU population. One way to get the allele frequency information for this population is to parse the genotype and allele frequency (genoExchange format) xml files found in the human genotype directory of the dbSNP FTP site. You can find documentation for the genoExchange format online. All of the “ByPop” elements that have the attribute pop_id=”1409″ are from the HapMap CEU population. If you are interested in finding allele frequency information for specific variations, or variations located in specific genes, SNPs, or particular regions, you may want to use the dbSNP’s genotype query. Users can specify genotype query output as XML, HTML or text.
