FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3

Bioinformation. 2008;3(3):139-41. doi: 10.6026/97320630003139. Epub 2008 Nov 9.


The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a genomewide test on allele frequency variation among 11 HapMap3 samples. Common SNPs with minor allele frequency greater than 5 cent from each of 11 HapMap3 samples were included in the present analysis. The population differentiation is measured in terms of fixation index (Fst), and the SNPs with Fst values over 0.5 were defined as highly differentiated SNPs. Our tests were carried out between all pairs of the 11 HapMap3 samples or among subgroups with the same continental ancestries. Altogether we carried out 64 genomewide Fst tests and identified 28,215 highly differentiated SNPs for 49 different combinations of HapMap3 samples in the current database.

Availability: http://FstSNP-hapmap3.googlecode.com/

Keywords: Fst; HapMap3; SNP; database; human genome; population differentiation.