In Table 2 and Supplementary Table 4, we denote regions of association by the most significant marker. Associated SNPs with r2 ≥ 0.2 in HapMap3 (CEU+TSI populations) were not considered independent. However, we noticed instances where multiple SNPs within 250 kb of each other yielded evidence for association (P < 10−5) despite weak LD (r2 < 0.2) between them. For regions with P < 10−6, we performed a conditional analysis using as covariates the dosages of the strongest associated SNP, principal components 1–4 and 6 and study indicator. We observed multiple statistically independent signals at the MHC. Although a number of SNPs within the MHC were potentially independent per HapMap r2 values, only rs9272105 withstood formal conditional analysis, showing P = 1.8 × 10−6 conditional on association to the best SNP, rs2021722 (stage 1 P = 4.3 × 10−11, inter-SNP distance = 2.4 Mb, r2 = 0.01 in HapMap). Excluding the MHC region, we identified six regions with at least one SNP associated at P < 10−5 and a second SNP with a conditionally independent P < 10−3 (Supplementary Table
