GWA studies attempt to identify these common disease-causing variants by using high-throughput genotyping technologies to assay hundreds of thousands of common single nu-cleotide polymorphisms (SNPs) and relate them to clinical conditions and measurable traits. Because of the strong associations among SNPs in most chromosomal regions, only a few carefully chosen SNPs need to be typed in each region to predict the likely alleles at the rest of the SNPs in that region. Selecting the best tag SNPs requires precise mapping of the patterns of linkage disequilibrium (LD) among SNPs, which differ somewhat across ancestral groups. The need for precise LD maps to facilitate genetic association studies was the stimulus for developing the human haplotype map (2, 4).
