Although the efficient choice of tag SNPs is one use of the Phase II HapMap, for most disease studies the tag SNPs genotyped will be primarily determined by the choice of a commercial platform for the experiment17,18. Using Phase II data, we estimated the coverage of several available products on which genome-wide association studies are already underway (Table 4). Similar to earlier estimates17,18, these products typically perform well in CEU and CHB+JPT, and some also perform well in YRI. For example, arrays of approximately 500,000 SNPs capture 68–88% (depending on selection method) of all HapMap Phase II variation with r2≥0.8 in CEU. SNPs that are not included in the Phase II HapMap will be covered more poorly because most genotyping products were designed using HapMap data.
