We identified the independent variant (p < 5 × 10−8) in each locus (1 Mb genomic window) based on the smallest p value and r2 < 0.1 with other independent variants and assigned these variants to the independent variant’s clump. Any two independent variants less than 1 Mb apart whose clumped regions overlapped were merged into one locus. Given the known long-range LD for the ADH gene cluster on chromosome 4, we defined chr4q23–q24 (~97.2 Mb – 102.6 Mb) as one locus. When multiple independent variants were present in a locus, we ran conditional analyses using GCTA-COJO [52] to define conditionally independent variants. For each variant other than the most significant one (index), we tested the marginal associations conditioning on the index variant using Europeans (n = 503) from the 1000 Genomes as the LD reference sample. Variants with significant marginal associations (p < 5 × 10−8) were defined as conditionally independent variants (i.e., independent when conditioned on other variants in the region) and subject to another round of conditional analyses for each significant association.
