Joshua S Martin1, Zheng Xu2,3, Alex P Reiner4,5, Karen L Mohlke1, Patrick Sullivan1,6, Bing Ren7, Ming Hu8, Yun Li1,9,10. 1. Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA. 2. Department of Statistics. 3. Quantitative Life Sciences Initiative, University of Nebraska, Lincoln, NE 68583, USA. 4. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. 5. Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA. 6. Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden. 7. Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, UCSD Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA. 8. Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA. 9. Department of Biostatistics. 10. Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA.
Abstract
MOTIVATION: High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability. RESULTS: We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTL results and functional genomics data. AVAILABILITY AND IMPLEMENTATION: HUGIn is available at http://yunliweb.its.unc.edu/HUGIn. CONTACT: yunli@med.unc.edu or hum@ccf.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability. RESULTS: We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTL results and functional genomics data. AVAILABILITY AND IMPLEMENTATION: HUGIn is available at http://yunliweb.its.unc.edu/HUGIn. CONTACT: yunli@med.unc.edu or hum@ccf.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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