reported in LD-Hub (http://ldsc.broadinstitute.org/), using what appears to be the same datasets, although referencing a related article (Liu et al., 2015; = 27,432). The analyses portrayed in our main text utilized a larger BD dataset (Hou et al., N = 40,225), the same dataset for UC (Liu et al., 2015; N = 27,432), and uniform criteria for SNP retention based on inclusion in the HapMap3 panel and MAF ≥ 5 % within the 1000 Genomes Project Phase 3 European samples. In order to resolve apparent discrepancies, we obtained additional versions of the available data for BD, SZ, CD, and UC and pre-filtered under both inclusive (imputation INFO score ≥ 0.9 or all SNPs, when INFO score unavailable) or exclusive criteria (MAF > 5 % within the 1000 Genomes Project Phase 3 European samples). We found that correlations between SZ and each of CD, PBC, and UC tended to be more positive and more significant (i.e., reaching a BH-corrected threshold) when using the SZ data filtered at MAF > 5% (Supplementary Figure 3). A similar pattern held true for inclusive vs. exclusive pre-filtering for the BD dataset generated by Sklar et al., but this was not the case for the larger
