Properly evaluating the statistical significance of the susceptibility variants described above requires adjusting for relatedness of the participants using the method of genomic control14. This required performing genome scans for these diseases (Supplementary Table 4 gives parental-origin test results for established susceptibility variants located outside the selected regions). The T2D scan performed with the initial sample set (Supplementary Information and Supplementary Figure 2) gave a striking result (Table 1). Allele T of rs2334499, at 11p15 (Figure 2), showed such a weak association (OR = 1.11, P = 0.017) in the standard case-control test that it does not stand out in a genome-wide scan. However, taking into account parental origin, both the paternally inherited allele (OR = 1.41, P = 4.3 × 10−9) and the 2-df of freedom test (P = 3.5 × 10−9) were genome-wide significant. Most intriguing, the maternally 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
