To further examine the interrelationship between Hi-C and eQTLs, we compared H-MAGMA-derived outputs with two eQTL-based gene mapping tools, coloc and TWAS. Consistent with the previous finding3,11, we detected a substantial overlap. While eQTL-based gene mapping is in no doubt a powerful approach, H-MAGMA can provide a complementary platform to understand the mechanism of GWAS for the following reasons. First, Hi-C can provide comprehensive genome-wide maps for tissues or cell-types with limited access. One example is Hi-C datasets from iPSC-derived neurons and astrocytes that allow GWAS annotation in a cell-type specific manner37, which is currently not available with eQTL. Second, it has been recently shown that the variants associated with chromatin accessibility capture stimulus-sensitive signals and explain a significant proportion of heritability, even more so than eQTLs47,48. Supporting this claim, we found that H-MAGMA derived genes explain a significant proportion of heritability in addition to eQTL derived genes. These results collectively suggest that chromatin architecture such as Hi-C and chromatin accessibility may provide complementary regulatory phenotypes that can be missed by eQTLs. It is of note that H-MAGMA also has
