Bivariate gaussian mixture models were applied to the GWAS summary statistics for BD and other complex traits using the MiXeR tool49,50 to estimate the number of variants influencing each trait that explain 90% of hSNP2 and their overlap between traits. MiXeR estimated that approximately 8.6 k (s.e. = 0.2 k) variants influence BD, which is similar to the estimate for schizophrenia (9.7 k, s.e. = 0.2 k) and somewhat lower than that for major depression (12.3 k, s.e. = 0.6 k) (Supplementary Table 17 and Supplementary Fig. 9). When considering the number of shared loci as a proportion of the total polygenicity of each trait, the vast majority of loci influencing BD were also estimated to influence major depression (97%) and schizophrenia (96%) (Supplementary Table 17 and Supplementary Fig. 9). Interestingly, within these shared components, the variants that influenced both BD and schizophrenia had high concordance in direction of effect (80%, s.e. = 2%), while the portion of concordant variants between BD and MDD was only 69% (s.e. = 1%) (Supplementary Table 17).
