The strongest signal for association in the combined analysis of males and females was detected in chromosome 7p22.2, in the vicinity the SDK1 gene, for rs6462756 (odds ratio (OR)=1.84 (1.45–2.33), P=5.5 × 10−7). As no other variant within 500 kb (250 kb down/upstream, including 135 SNPs) of it gave any signal, it was considered spurious, and was not selected for replication in this study. The next strongest associations were observed for rs9268528 (OR=0.58 (0.46–0.72), P=9.9 × 10−7) and rs9268542 (OR=0.58 (0.46–0.72), P=1.1 × 10−6), located on chromosome 6p21.32, intragenic of the BNTL2 and HLA-DRA genes. These two variants were selected for replication, together with an additional nearby intragenic variant, rs2395163 (OR=0.59 (0.46–0.77), P=6.2 × 10−5), and an intronic variant of HLA-DRA gene, rs2239804 (OR=0.61 (0.49–0.77), P=1.2 × 10−5). All the association signals of these variants in the vicinity of the HLA-DRA gene originated from the major allele. Supplementary Figure 2a shows the regional Manhattan plot of chromosome 6 for the analysis of the whole sample.
