A large excess of associated SNPs in stages 2 and 3 was observed. In stage 2, out of 65 independent signals, 10 achieved a p-value<0.05 for association with T2D, whereas only 1.6 were expected to achieve this by chance. In stage 3, out of 10 independent signals, 7 reached a p-value<0.05 with T2D, as opposed to an expected 0.25 under the null. It is noteworthy that the associated SNPs all had small observed effect sizes, with the largest allelic odds ratio being only 1.15. This underlines the need for very large-scale meta-analysis replication efforts.
