the final list of putative signals to be taken for follow-up in stage 2. Where novel signals for different traits were in linkage disequilibrium (r2 > 0.2), the variant for the trait with the most significant association was followed up. Due to the extended LD structure in the MHC region, conditional analyses and GCTA were run over a 9Mb region (chr6:24,126,750-33,126,689). Two pairs of signals previously reported as being independent (rs16909859:G>A11 and rs16909898:A>G14 in PTCH1, and rs34712979:G>A16 and rs6856422:T>G15, in NPNT) were found to be correlated in our data.
