inherited allele also showed nominally significant association, but the effect of allele T was protective (OR = 0.87, P = 0.020). Tested directly, the difference between the effects of the paternally and maternally inherited alleles was also genome-wide significant (P = 7.0 × 10−9). This SNP falls within 350 Kb of a large cluster of imprinted genes, making the results even more compelling. Still, the observation that allele T is protective when maternally inherited called for replication. For this, we used an additional set of 783 chip-typed T2D cases. All tests involving parental origin were significantly replicated. For the combined analysis of the two sample sets (Supplementary Information and Supplementary Figure 3), the paternally inherited allele had an OR of 1.35 (P = 4.7 × 10−10) and the maternally inherited allele has an OR of 0.86 (P = 0.0020). The 2-df test and the paternal versus maternal tests gave P of 5.7 × 10−11 and 4.1 × 10−11 respectively.
