We carried forward to Stage 2 all independent loci with association with any of the four traits at P<2×10−5, except for SNPs in the known T2D genes TCF7L2 and SLC30A8 for which no further validation was sought (Table 1, Supplementary Table 2). We also included the nominally associated top SNP from a strong biological candidate (IRS1, P=10−4 for HOMA-IR) and a locus with P values that approached genome-wide significance in several Stage 1 discovery cohorts (PLXDC2/NEBL), even though their overall Stage 1 P-values were >2×10−5 (Table 1, Supplementary Table 2). In total, 25 loci were chosen for replication.
