Despite the SNP density of the Phase II HapMap, there are high-frequency SNPs for which no tag can be identified. Among high-frequency SNPs (MAF≥0.2), we marked as untaggable SNPs to which no other SNP within 100 kb has an r2 value of at least 0.2. In Phase II, approximately 0.5–1.0% of all high-frequency SNPs are untaggable and the proportion in YRI is approximately twice as high as in the other panels. Similar proportions are observed across the ten HapMap ENCODE regions.
