Exonic and promoter SNPs were directly assigned to their target genes based on their genomic location using a gene model Gencode v26 https://www.gencodegenes.org/human/release_26lift37.html), and promoter definition as 2kb upstream of transcription start sites (TSS) of each gene isoform. Intronic and intergenic SNPs were assigned to their cognate genes based on chromatin interactions with promoters and exons as previously described3,4. Briefly, we generated a background Hi-C interaction profile by pooling 9 million imputed SNPs from schizophrenia GWAS summary statistics58. Using this background Hi-C interaction profile, we fit the distribution of Hi-C contacts at each distance from each chromosome using the fitdistrplus package (https://cran.r-project.org/web/packages/fitdistrplus/index.html). Significance for a given Hi-C contact was calculated as the probability of observing a stronger contact under the fitted Weibull distribution matched by chromosome and distance. Hi-C contacts with FDR<0.01 were selected as significant interactions. Significant Hi-C interacting regions were overlapped with Gencode v26 exon and promoter coordinates to identify exon- and promoter-based interactions. We used exon- and promoter-based interactions, because our previous study comparing Hi-C data with eQTLs have demonstrated the gene regulatory potential of exon-level interactions3.
