In the CEU sample, of the 198 SNP assays in our Illumina panel, 18 did not yield readable genotypes and an additional 8 assays had a call rate <0.95. In total, we were able to design assays (or obtain data from HapMap) for a high proportion (~71%) of the likely genuine SNPs (supplemental table 8). Of 172 SNPs we obtained new data for, only 22 (13%) with MAF ≥0.01 were not previously tagged at r2=1 and only 16 (9%) at r2=0.9. This low yield of untagged SNPs suggests further sequencing endeavours (or efforts to genotype the SNPs for which we could not design Illumina assays) are unlikely to extract much additional genetic information from the region. Information about the 172 confirmed SNPs is provided in supplemental table 9.
