Within these 136 loci, multi-SNP-based conditional analysis (Yang et al., 2012) identified 10 additional SNPs with independent associations, resulting in a total of 146 independent lead SNPs (Table S3.1). To provide a quantitative estimate of the best fit configuration of cross-disorder genotype-phenotype relationships, we estimated the posterior probability of association (referred to as the m-value) with each disorder using a Bayesian statistical framework (Han and Eskin, 2012) (Online Methods; Table S3.2) As recommended (Han and Eskin, 2012), an m-value threshold of 0.9 was used to predict with high confidence that a particular SNP was associated with a given disorder. Also, m-values of < 0.1 were taken as strong evidence against association. Plots of the SNP p-value vs. m-value for all 146 lead SNPs are shown in Data S2. Nearly 75% (109/146) of the genome-wide significant SNPs were pleiotropic (i.e., associated with more than one disorder). As expected, configurations of disease association reflected the differences in the statistical power and genetic correlations between the samples (Fig. S1). Of the 109 pleiotropic loci, 83% and 72% involved SCZ and BIP, respectively. MD,
