Next, we identified shared loci for each psychotic-cannabis phenotype pair using the conjFDR approach. For SCZ and LCU, SCZ and CUD, BIP and LCU, and BIP and CUD, we identified 27, 21, 14, and 3 shared loci, respectively (Figure 3, Supplementary Table 4). Five loci were identified as shared by more than one phenotype pair (Supplementary Table 5). For example, three loci shared between LCU and SCZ were overlapped with loci shared between LCU and BIP. When investigating the direction of effects, the majority of shared lead SNPs for each pair exhibited concordant effects (ranging from 67% to 93%, Supplementary Table 4). Additionally, the SNP sign test replicated sign concordance in independent samples for SCZ and BIP at 67.5% and 73.3% of shared lead SNPs, respectively (Supplementary Tables 6–7).
