For the remainder of the regions, we performed linkage disequilibrium pruning using the PLINK1.9 –clump procedure with an r2 of 0.5, additionally examining these SNPs for the number of cohorts with passing quality control at each variant and including SNPs in strong LD (i.e., part of the same clump) with a lower degree of missingness. To identify independent results, we used GCTA-COJO58,59 on the Stage 1 meta-analysis for variants with P < 5×10−6 using the default distance of 10Mb. We used the COPDGene non-Hispanic whites (as the largest representative population) as the reference population for these analyses. An overall meta-analysis across the Stage 1 and Stage 2 (UK BiLEVE) cohorts was performed and variants with P < 5×10−8 were considered genome-wide significant (Figure 1).
