After distance (300 kb) and LD pruning (r2>0.1), three regions had multiple SNPs with p-values less than 1.0×10−6 in the meta-analysis results. We tested SNPs in each of these regions for independence in the replication dataset using Wald and likelihood ratio tests. We conducted this analysis in the replication dataset to avoid SNP selection bias from the original findings. By conditioning on each SNP within the models at each locus we find two SNPs in each of the TMEM161B-MEF2C and NEGR1 regions are likely independent (rs10514299 and rs454214, rs11209948 and rs2422321, respectively), with the variance in the region being explained best by both SNPs, while most of the variance in the MLF1 region is explained by rs1656369 alone (with no additional significance provided by inclusion of rs4645169) (Supplementary Table 5).
