In Phase 2 a total of 31,039 SNPs (93.9%) were successfully genotyped, of which 30,568 provided reliable genotypes according to our quality control metrics (Figure 1b). Of the 2,484 cases and 3,036 controls attempted, 2,465 cases and 3,014 controls were successfully genotyped and of these 2,465 cases and 3,005 controls were suitable for analysis (Figure 1b). In the combined analysis of Phase 1 and 2 (Supplementary Table 1), the strongest associations identified were found at polymorphic sites defined by SNPs mapping to 15q25.1 (rs12914385; P = 3.19 × 10−16), 5p15.33 (rs4975616; P = 6.66 ×10−7), and 6p21.33 (rs3117582; P = 9.13 × 10−7), which have been the subject of previous fast-tracking analyses.
