Local genetic correlations in 2,495 loci analyzed using LAVA48 (Supplementary Figure S9-2 and Table S6B) generally supported the results of the MiXeR analyses. The proportion of loci with positive genetic correlations was significantly correlated with the proportion of MiXeR-estimated influencing variants with concordant effects (Pearson’s correlation r=0.76, P=0.0069, supplementary figure S9-3). Although LAVA estimates generally appear to be more extreme than MiXeR, these findings support the validity of MiXeR estimates of mixed effect directions (Supplementary Figure S9-1 and Supplementary Table S6A).
