Currently, the Phase II HapMap provides the most complete available resource for selecting tag SNPs genome-wide. Using a simple pairwise tagging approach, we find that 1.09 million SNPs are required to capture all common Phase II SNPs with r2≥0.8 in YRI, with slightly more than 500,000 required in CEU and CHB+JPT (Table 3). These numbers are approximately twice those required to capture SNPs in the Phase I HapMap (which has one-third as many SNPs). The number of SNPs required to achieve perfect tagging (r2=1.0) in each analysis panel is almost double that required to achieve the r2≥0.8 threshold. It becomes increasingly expensive to improve the coverage afforded by tags from the Phase I and, now, the Phase II HapMap, because additional tag SNPs are unlikely to capture large groups of additional SNPs.
