r 2≥0.8 with a SNP from the array; that is, the number of SNPs not tagged by the array. For example, we found that 57% of the common SNPs in these genes were not tagged by the Affymetrix 5.0 SNP microarray in the African population. In other words, due to the haplotype/LD structure in the African population, 43% of the common genetic variation in these regions fails to be captured by this microarray. Table S1 gives a broader view of how microarray coverage depends on biology, and shows that the Illumina coverage tends to improve with the prioritization score, while the Affymetrix coverage is uniform.
