The Phase II HapMap differs from the Phase I HapMap not only in SNP spacing, but also in minor allele frequency distribution and patterns of linkage disequilibrium (Supplementary Fig. 4). Because the criteria for choosing additional SNPs did not include consideration of SNP spacing or preferential selection for high MAF, the SNPs added in Phase II are, on average, more clustered and have lower MAF than the Phase I SNPs. Because MAF predictably influences the distribution of linkage disequilibrium statistics, the average r2 at a given physical distance is typically lower in Phase II than in Phase I; conversely, the |D′| statistic is typically higher (data not shown). One notable consequence is that the Phase II HapMap includes a better representation of rare variation than the Phase I HapMap.
