Partitioning heritability enrichment analyses using LDSC [13, 14] showed the most significantly enriched cell type group to be central nervous system (CNS, p = 3.53 × 10−9), followed by adrenal and pancreas (p = 1.89 × 10−3), and immune and hematopoietic (p = 3.82 × 10−3, Supplementary Figure 2). Significant enrichments were also observed in six baseline annotations, including conserved regions, conserved regions with 500bp extended (ext), fetal DHS (DNase I hypersensitive sites) ext, weak enhancers ext, histone mark H3K4me1 ext, and TSS (transcription start site) ext (Supplementary Figure 3). We also investigated heritability enrichments using Roadmap data, which contains six annotations (DHS, H3K27ac, H3K4me3, H3K4me1, H3K9ac, and H3K36me3) in a subset of 88 primary cell types and tissues [14, 15]. Significant enrichments were observed for H3K4me1 and DHS in fetal brain, and H3K4me3 in fetal brain and in brain germinal matrix (Supplementary Table 6). Although no heritability enrichment was observed in tissues using gene expression data from GTEx [16], the top nominally enriched tissues were all in brain (Supplementary Figure 4).
