Our tagSNP analysis showed that only 19% (179/935, Table 2 and Figure 1) of variants seen in the re-sequencing set are also represented in HapMap. This discrepancy is based on the facts that HapMap mainly supports common variants (MAF ≥5%) and that those variants were chosen to distribute relatively uniformly across genomic regions. In our re-sequencing data, 28% (264/935) of all variants are singletons, emphasizing the abundance of private variants within individuals. Contributions of these rare variants to individual disease risk cannot be evaluated solely using HapMap tagSNPs.
