In contrast to our novel finding in CGASP of genome-wide significance for locus 3 when analyzed jointly with locus 1, none of the other consortia report strong evidence for locus 3 when paired with locus 1. In the Oxford-GSK study [13], imputation using 1000 Genomes data detected the most significant single-SNP association for CPD at the locus 1 SNP rs55853698 (r2>0.96 with rs16969968). After conditioning on rs55853698, the strongest residual signal was detected at a locus 2 SNP, rs6495308 (p = 3.96×10−5; r2 = 0.825 with rs578776 in HapMap CEU); they do not report the association result for rs588765 in the conditioned analysis, although it must have been less significant than 3.96×10−5. In their single-SNP analysis, rs6495308 (locus 2) gave a p-value of 2.2×10−10. Their results for locus 2 are therefore consistent with our observation that in joint analysis of locus 1 and locus 2, the significance at locus 2 is reduced compared to the single-SNP analysis. They do not report on whether the evidence for locus 1 and locus 3 strengthens in the joint analysis compared to single-SNP analysis,
