For those associations we could confirm, we then did a conditional analysis within the associated region to identify any signal in the region that was independent of the lead SNP in every case. For every association, we selected regions used in the conditional analysis on the basis of adjacent recombination hotspots, meaning we analysed different numbers of SNPs for every locus (appendix). We used logistic regression in every centre, using imputed genotype dosages to model the effect of the lead SNP on risk as a covariate. We then did a meta-analysis of the results using a fixed-effects, inverse-variance weighted model. We used our suggestive significance threshold (p<5×10−6) to identify SNPs that were statistically independent of the lead SNP for every locus.
