To identify loci with differential effects on BP and SCZ, we compared 9,252 BP cases against 7,129 SCZ cases. No SNPs reached genome-wide significance with the smallest p-value at rs7219021 at chr17:44195540 (p=1.31 × 10−7) (Figure 1b). A lack of genome-wide significant findings does not preclude the existence of many small effect loci that in aggregate can significantly discriminate BP from SCZ. We applied a previously used risk profiling approach (12, 44) to our BP vs SCZ data. For each of the nine samples defined by ancestry and array technology (Supplementary Table 2), we computed a risk score using the association data from eight samples as our discovery set and then assessed the ability of those risk scores to predict BP vs SCZ status in the remaining sample. This allowed us to maximize our sample size and ensure no particular sample was disproportionately contributing to the result. Risk scores were calculated for p-value thresholds from 0.001 to 1 as defined in (12). All samples had at least one threshold reaching nominal significance with all but one sample explaining at least
