I took a brief look at the paper scanning for multiple hypothesis testing corrections. "Neandertal variants have been hypothesized to influence many phenotypes

I took a brief look at the paper scanning for multiple hypothesis testing corrections. "Neandertal variants have been hypothesized to influence many phenotypes in AMHs, including lipid metabolism, immunity, depression, digestion, hair, and skin, on the basis of the enrichment of Neandertal variants in regions of the genome relevant to these traits. Accordingly, we first tested these hypotheses using genome-wide complex trait analysis (GCTA) to estimate the phenotypic risk explained by 1495 genotyped common (minor allele frequency > 1%) Neandertal SNPs for a set of 46 highprevalence phenotypes from the hypothesized categories, using age, sex, and eMERGE site as covariates." When testing these 46 traits they controlled the FDR < 0.05 (false discovery rate). Then they replicated the associations in an independent sample. The effect sizes are pretty small (1-2%), so having the explanatory variants won't have much bearing whether or not you'll get these complex traits.