We retrieved the HapMap release 23a CEU (n = 60 founders) and YRI (n = 60 founders) phase II genotype data for chromosome 22 from http://www.hapmap.org. Quality control filters for inclusion were a minor allele frequency of ≥1%, a genotyping success rate ≥80%, a Hardy-Weinberg equilibrium test p-value ≥1.0×10-3, ≤1 Mendelian inheritance error, and ≤1 duplicate discrepancy. These quality control filters were applied to the two panels separately. After data cleaning, the phase II CEU reference panel consisted of 30,245 SNPs, the phase II YRI panel consisted of 33,499 SNPs, and the combined phase II CEU+YRI reference panel consisted of 40,281 SNPs (Fig. 1).
