We previously predicted that the vast majority of common SNPs would be correlated to Phase II HapMap SNPs by extrapolation from the ten HapMap ENCODE regions3. Using the actual Phase II marker spacing and frequency distributions (Table 2), we repeated the simulations and estimate that Phase II HapMap marker sets capture the overwhelming majority of all common variants at high r2. For common variants (MAF≥0.05) the mean maximum r2 of any SNP to a typed one is 0.90 in YRI, 0.96 in CEU and 0.95 in CHB+JPT. The impact of the increased density of the Phase II HapMap is most notable in YRI (in the Phase I HapMap the mean maximum r2 was 0.67). Similar results are found if a threshold of r2≥0.8 is used to determine whether an SNP is captured (Table 2). As expected, very common SNPs with MAF>0.25 are captured extremely well (mean maximum r2 of 0.93 in YRI to 0.97 in CEU), whereas rarer SNPs with MAF<0.05 are less well covered (mean maximum r2 of 0.74 in CHB+JPT to 0.76 in YRI). The latter figure is
