We were interested in whether one or more causal SNPs might explain the observed association in regions showing genome-wide significant association with UC. To explore this question we fit a conditional logistic model, with pairs of SNPs in the model, conditional on ancestry and gender. P values for the SNPs are interpretable as the residual variation explained by the SNP, conditional on the inclusion of the other SNP. Significant residual association signal was defined as P < 0.05 in the conditional analysis. We also computed pairwise r2 values in our GWAS control data for the same pairs of SNPs.
