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A second generation human haplotype map of over 3.1 million SNPs

A second generation human haplotype
map of over 3.1 million SNPs
The International HapMap Consortium*
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs)
genotyped in 270 individuals from four geographically diverse populations and includes 2535% of common SNP variation in
the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2
between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide
genotyping products captures common Phase II SNPs with an average maximum r2
of up to 0.8 in African and up to 0.95 in
non-African populations, and that potential gains in power in association studies can be obtained through imputation. These
data also reveal novel aspects of the structure of linkage disequilibrium. We show that 1030% of pairs of individuals within
a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all
common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination
rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased
differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or
efficacy of natural selection between populations.
Advances made possible by the Phase I haplotype map
The International HapMap Project was launched in 2002 with the


Source: Abecasis, Goncalo - Department of Biostatistics, University of Michigan


Collections: Biology and Medicine; Mathematics