We performed Hi-C and H3K27ac HiChIP assays in MNT1 cells. Hi-C is a high-throughput method for detecting chromatin interactions at whole genome scale and is often used to identify topologically associating domains (TADs) in the nucleus. H3K27ac HiChIP can identify chromatin interactions enriched for H3K27ac, a histone modification associated with active promoters and enhancers. We performed bridge linker mediated Hi-C and H3K27ac HiChIP using double (Hae3+Alu1) as well as single (Hae3) enzyme digestion in MNT-1 cells. For Hi-C_Hae3+Alu1, Hi-C_Hae3, HiChIP_Hae3+Alu1, and HiChIP_Hae3 assays, respectively, we sequenced 399 million (M), 430 M, 257 M, and 181 M paired reads and obtained 299 M, 305 M, 151 M, and 94 M valid interactions (cis-pairs >= 1 kb and trans-pairs) using pairtools. Using the Hi-C data, we identified 80,333 TADs in MNT-1 cells using onTAD software 60 and the genes located in the same TAD with MFVs. Using four different tools, cooltools-dots, cLoops, mustache and FitHiChIP , we detected 201,862 loops based on Hi-C and H3K27ac HiChIP data and identified 8,569 loops for 597 tested MPRA SNPs. Using the Hi-C and HiChIP data, we constructed a high-resolution chromatin interaction map of MNT-1 cells. This map serves as an invaluable resource for investigating the interactions between the regulatory elements and their target genes in melanoma cells, thereby facilitating the elucidation of regulatory networks underlying human skin phenotype and diseases.

This is a dataset related a project on skin pigmentation: Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans

{"references": ["Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans"]}