Science Advances

The PDF file includes:

• Supplementary Materials and Methods
• Fig. S1. CNON Hi-C datasets.
• Fig. S2. Chromatin interactions with different q value cutoffs.
• Fig. S3. H3K27ac ChIP-seq clustering results.
• Fig. S4. NOMe-seq depth and number of NDRs.
• Legends for tables S1 to S11
• References (55–67)

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). Information about the CNON ChIP-seq, NOMe-seq, and Hi-C datasets.
• Table S2 (Microsoft Excel format). CNON TADs identified by Hi-C.
• Table S3 (Microsoft Excel format). CNON ChIP-seq peaks classified as promoters, enhancers, insulators, repressed, or heterochromatin regions.
• Table S4 (Microsoft Excel format). CNON chromatin interactions identified by Hi-C.
• Table S5 (Microsoft Excel format). Epigenomic classification of CNON Hi-C chromatin interactions.
• Table S6 (Microsoft Excel format). Predicted target genes of enhancers using CNON Hi-C.
• Table S7 (Microsoft Excel format). Coordinates of promoter H3K4me3, non-promoter H3K27ac, and CTCF peaks found in many individuals of CNON datasets.
• Table S8 (Microsoft Excel format). Identification and classification of NDRs identified by CNON NOMe-seq.
• Table S9 (Microsoft Excel format). Enhancers linked to genotype, gender, smoking status, and schizophrenia diagnosis.
• Table S10 (Microsoft Excel format). Classification and characterization of SCZ risk-associated variants.
• Table S11 (Microsoft Excel format). Predicted target genes of enhancers linked to individual variations.