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 Hou et al., dataset. A side-by-side comparison of the effects of different pre-filtering decisions for the BD, SZ, CD, and UC datasets in relation to the other phenotypes is provided in Supplementary Figure 4. These observations indicate that decisions pertaining to SNP inclusion can have a considerable effect on the result of the LDSC analysis; this idea is further supported by the observation that stratified genetic correlation analyses based on MAF thresholds can produce different levels of statistical significance and opposite patterns of correlation directionality (Lu et al. 2017). Thus, our study suggests that genetic correlations between psychiatric and immune-related disorders may be more significant when analyses are restricted to common variation. Reassuringly, the developers of the HESS method use the same datasets examined presently, and also report positive genetic correlations between SZ and the inflammatory bowel disorders (Shi et al. 2017). The results of the HESS analysis of putative causal directionality indicate that the local genetic correlations are higher
