Five SNPs were selected for replication genotyping on the basis of their strong association with T2D in the DGI GWA study (2 SNPs), association with T2D and with insulinogenic index in the DGI study (1 SNP), and overlap with FUSION or WTCCC (p<0.05 in DGI and one or both studies; 2 SNPs). For known T2D loci (TCF7L2, CDKAL1, IGF2BP2, KCNJ11, HHEX/IDE, SLC30A8, CDKN2A/2B region, WFS1, TCF2, and FTO) we excluded from follow-up all SNPs that resided within the surrounding region, with region boundaries defined by the furthest neighboring SNPs with p values remaining ~0.01 (n=1,981). For the PPARG region, we identified a SNP, rs17036101, with a p value two orders of magnitude lower than the established Pro12Ala susceptibility variant, rs1801282, and took this signal forward to replication. A total of 69 SNPs were taken forward to stage 2 genotyping.
