Using the stage 1 results, a 95% ‘credible set’ of variants (i.e. the set of variants that were 95% likely to contain the underlying causal variant, based on Bayesian refinement) was defined for all (novel and previously reported) association signals for which this was feasible (67 signals, Online Methods Supplementary Figures 3, 4 and 5 and Supplementary Table 5); 13 of these signals were fine-mapped to <=10 plausible causal variants and for 63 of the 67 signals fine-mapped, the sentinel (lowest P value) variant was also the top ranked variant by posterior probability. In addition, by refining six chromosome 6 MHC region association signals using imputation of classical alleles and amino acid changes (Online methods), we identified the MHC class II HLA-DQB1 gene product, HLA-DQβ1, amino acid change at position 57 (alanine compared to non-alanine) as the main driver of signals in the MHC region for both FEV1 (β (s.e.) = 0.048 (0.007), P=5.71×10-13, Supplementary Figure 6a) and FEV1/FVC (β (s.e.) = 0.062 (0.007), P=1.17×10-20, Supplementary Figure 6c) with secondary non-HLA gene signals in the MHC region remaining after conditioning
