Since our primary goal is to identify neurobiological mechanisms underlying brain disorders, we leveraged two Hi-C datasets obtained from human brain tissue, one from the developing cortex4 and the other from the adult dorsolateral prefrontal cortex3 (DLPFC), to generate gene-SNP pairs that serve as an input file for MAGMA (Fig. 1a, Methods). Exonic and promoter SNPs were directly assigned to their target genes based on their genomic location, while intronic and intergenic SNPs were assigned to their cognate genes based on chromatin interactions (Fig. 1a). We also generated a cMAGMA input file that utilizes the same set of genes and SNPs as H-MAGMA whereby all intronic and intergenic SNPs were annotated by positional mapping with a generous gene definition that includes 35kb upstream and 10kb downstream of each gene.
