In joint analysis of locus 1 and locus 3, locus 1 (rs16969968) yields a p-value of 3.52×10−36, OR = 1.47 (1.38–1.56); locus 3 (rs588765) gives p = 6.03×10−9, OR = 1.17 (1.11–1.23). Thus locus 3 attains genome-wide significance (p<5×10−8) after adjusting for the effect of locus 1. Note that adjusting for locus 1 changes the direction of effect for locus 3 (OR>1) compared to the single-SNP results. In the 33 datasets that have both loci genotyped, we obtain p = 5.39×10−29, OR = 1.32 for locus 1 alone, and p = 0.00027, OR = 0.93 (0.89–0.97) for locus 3 alone. The evidence for association in the joint model is stronger than when each SNP is analyzed alone. In fact, when locus 1 is not taken into account, the effect of locus 3 is potentially masked, and the effect of the minor allele is in an opposite direction (protective versus risk).
