The QQ plots (Supplementary Figure 5 A-B) of Z-score p-values indicated no significant SDEs (top ten SDEs, Table 2), and that the difference in effect size for SDEs was not driven by minor allele frequency (MAF) differences between sexes (Supplementary Figure 6). The MAF distributions for SDEs and all tested SNPs were identical, and sexually-differentiated loci were distributed across the genome proportional to chromosome length (Supplementary Figure 6D). P-values from a genotype-sex interaction test (Supplementary Figure 5 C-D) were highly correlated with Z-score p-values from the sex-stratified analysis (autosomal SNPs Pearson’s r=0.65, p<2.2e-16, X chromosome SNPs Pearson’s r=0.71, p<2.2e-16). Furthermore, GWAS results in the combined sample with or without sex as a covariate were highly correlated (LDSC rg=0.999, se=0.001).
