The extended major histocompatibility complex (MHC) region contains high amounts of long-range LD, making it challenging to accurately map association signals in this region. For this reason, and following the work of others (Zheng et al. 2016; B. Bulik-Sullivan et al. 2015), we excluded this region from our analyses (chromosome 6, base positions 25×106 to 35×106). Additional SNP quality control (QC) routines followed those implemented by the GWAS authors and the defaults employed with the LDSC munge_sumstats.py function; this function checks alleles to ensure that the supplied alleles match those in the HapMap3 reference panel. For each dataset, we estimated the phenotype’s heritability. The results of this analysis, along with features of each GWAS dataset (sample size, number of QC-positive SNPs, genomic inflation factor, etc.), are shown for all phenotypes in Supplementary Table 1. All phenotypes with sample size ≥ 5000 and estimated SNP heritability z-score ≥ 3 were retained for correlation analysis (indicated in Supplementary Table 1 in green highlight). Pair-wise genetic correlations were assessed between retained phenotypes based on the intersection of QC-positive SNPs, and heatmaps were constructed to depict these relationships. For correlation coefficients returned within the bounds of the LDSC software, p-values were corrected using the
