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Using a global background model, we propose SnapHiC-G, a computational method, to identify long-range enhancer\u2013promoter interactions from scHi-C data. We applied SnapHiC-G to scHi-C datasets generated from mouse embryonic stem cells and human brain cortical cells. SnapHiC-G achieved high sensitivity in identifying long-range enhancer\u2013promoter interactions. Moreover, SnapHiC-G can identify putative target genes for noncoding genome-wide association study (GWAS) variants, and the genetic heritability of neuropsychiatric diseases is enriched for single-nucleotide polymorphisms (SNPs) within SnapHiC-G-identified interactions in a cell-type-specific manner. In sum, SnapHiC-G is a powerful tool for characterizing cell-type-specific enhancer\u2013promoter interactions from complex tissues and can facilitate the discovery of chromatin interactions important for gene regulation in biologically relevant cell types.<\/jats:p>","DOI":"10.1093\/bib\/bbae426","type":"journal-article","created":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T18:07:56Z","timestamp":1723572476000},"source":"Crossref","is-referenced-by-count":4,"title":["SnapHiC-G: identifying long-range enhancer\u2013promoter interactions from single-cell Hi-C data via a global background model"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2278-8946","authenticated-orcid":false,"given":"Weifang","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biostatistics, University of North Carolina at Chapel Hill , 135 Dauer Drive, Chapel Hill, NC 27599, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wujuan","family":"Zhong","sequence":"additional","affiliation":[{"name":"Biostatistics and Research Decision Sciences, Merck & Co., Inc. , 126 East Lincoln Ave, Rahway, New Jersey 07065, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Giusti-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, University of Florida , 1149 Newel Dr., Gainesville, FL 32611, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyun","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill , 120 Mason Farm Road, Chapel Hill, NC 27599, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoffery W","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina at Chapel Hill , 135 Dauer Drive, Chapel Hill, NC 27599, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huaigu","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill , 120 Mason Farm Road, Chapel Hill, NC 27599, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0987-2916","authenticated-orcid":false,"given":"Ming","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences , Lerner Research Institute, , 9500 Euclid Avenue, Cleveland, OH 44196, United States"},{"name":"Cleveland Clinic Foundation , Lerner Research Institute, , 9500 Euclid Avenue, Cleveland, OH 44196, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9275-4189","authenticated-orcid":false,"given":"Yun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina at Chapel Hill , 135 Dauer Drive, Chapel Hill, NC 27599, United States"},{"name":"Department of Genetics, University of North Carolina at Chapel Hill , 120 Mason Farm Road, Chapel Hill, NC 27599, United States"},{"name":"Department of Computer Science, University of North Carolina at Chapel Hill , 201 S. 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