For the subset of LD (linkage disequilibrium)-independent SNPs with P < 1×10−6 in the meta-analysis, we next obtained results from deCODE genetics (1,513 cases and 66,236 controls of European ancestry). We define LD-independent SNPs as those with low LD (r2 < 0.1) to a more significantly associated SNP within a 500 kb window. Given high LD in the extended MHC region spans ~8 Mb, we conservatively include only a single MHC SNP to represent this locus. The deCODE data were then combined with those from the primary GWAS to give a dataset of 36,989 cases and 113,075 controls. In this final analysis, 128 LD-independent SNPs surpassed genome-wide significance (P ≤ 5×10−8) (Supplementary Table 2).
