In the joint analysis of locus 1 and locus 2, there is suggestive evidence of distinct effects, but the association at locus 2 is no longer genome-wide significant in the presence of locus 1. Both SNPs become less significant compared to their single locus models: in the joint model, locus 1 gives p = 2.15×10−22, OR = 1.27 (1.21–1.33) and locus 2 gives p = 4.50×10−7, OR = 0.87 (0.83–0.92). When each SNP is placed individually in the model and meta-analyzed across the 32 datasets that provided data for both loci, locus 1 gives p = 1.41×10−32, OR = 1.34 while locus 2 gives p = 1.38×10−25, OR = 0.76. The risk-increasing alleles at locus 1 (C) and locus 2 (R) are positively correlated, even though the minor alleles are negatively correlated.
