In Phase II of the HapMap Project, a further 2.1 million SNPs were successfully genotyped on the same individuals. The resulting HapMap has an SNP density of approximately one per kilobase and is estimated to contain approximately 25–35% of all the 9–10 million common SNPs (minor allele frequency (MAF)≥0.05) in the assembled human genome (that is, excluding gaps in the reference sequence alignment; see Supplementary Text 1), although this number shows extensive local variation. This paper describes the Phase II resource, its implications for genome-wide association studies and additional insights into the fine-scale structure of linkage disequilibrium, recombination and natural selection.
