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      HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants

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          Abstract

          Background

          Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and therefore it is challenging to hypothesize the functions of these non-coding GWAS variants. Recent large efforts such as the ENCODE and Roadmap Epigenomics projects have predicted a large number of regulatory elements. However, the target genes of these regulatory elements remain largely unknown. Chromatin conformation capture based technologies such as Hi-C can directly measure the chromatin interactions and have generated an increasingly comprehensive catalog of the interactome between the distal regulatory elements and their potential target genes. Leveraging such information revealed by Hi-C holds the promise of elucidating the functions of genetic variants in human diseases.

          Results

          In this work, we present HiView, the first integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. HiView is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation.

          Conclusions

          We believe that as the first GWAS variants-centered Hi-C genome browser, HiView is a useful tool guiding post-GWAS functional genomics studies. HiView is freely accessible at: http://www.unc.edu/~yunmli/HiView.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s13104-016-1947-0) contains supplementary material, which is available to authorized users.

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          Most cited references6

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          Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24.

          Prostate cancer is the most prevalent noncutaneous cancer in males in developed regions, with African American men having among the highest worldwide incidence and mortality rates. Here we report a second genetic variant in the 8q24 region that, in conjunction with another variant we recently discovered, accounts for about 11%-13% of prostate cancer cases in individuals of European descent and 31% of cases in African Americans. We made the current discovery through a genome-wide association scan of 1,453 affected Icelandic individuals and 3,064 controls using the Illumina HumanHap300 BeadChip followed by four replication studies. A key step in the discovery was the construction of a 14-SNP haplotype that efficiently tags a relatively uncommon (2%-4%) susceptibility variant in individuals of European descent that happens to be very common (approximately 42%) in African Americans. The newly identified variant shows a stronger association with affected individuals who have an earlier age at diagnosis.
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            • Article: not found

            Gene regulation in the third dimension.

            Job Dekker (2008)
            Analysis of the spatial organization of chromosomes reveals complex three-dimensional networks of chromosomal interactions. These interactions affect gene expression at multiple levels, including long-range control by distant enhancers and repressors, coordinated expression of genes, and modification of epigenetic states. Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations.
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              • Record: found
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              • Article: not found

              Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.

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                Author and article information

                Contributors
                xuzheng@email.unc.edu
                gszhang@email.unc.edu
                qduan@email.unc.edu
                shengjie@email.unc.edu
                zhangbaqun@ruc.edu.cn
                wucong0451@outlook.com
                fulai.jin@case.edu
                fyue@hmc.psu.edu
                yunli@med.unc.edu
                ming.hu@nyumc.org
                Journal
                BMC Res Notes
                BMC Res Notes
                BMC Research Notes
                BioMed Central (London )
                1756-0500
                11 March 2016
                11 March 2016
                2016
                : 9
                : 159
                Affiliations
                [ ]Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599 USA
                [ ]Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
                [ ]Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599 USA
                [ ]Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599 USA
                [ ]School of Statistics, Renmin University of China, Beijing, 100872 China
                [ ]College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
                [ ]Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106 USA
                [ ]Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
                [ ]Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
                Article
                1947
                10.1186/s13104-016-1947-0
                4788823
                26969411
                6f6e907e-d781-4040-b479-202a7651a5c1
                © Xu et al. 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 2 November 2015
                : 22 February 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01-HG006292
                Award ID: R01-HG006703
                Award ID: 1U54KD107977
                Award Recipient :
                Categories
                Technical Note
                Custom metadata
                © The Author(s) 2016

                Medicine
                integrative genome browser,hi-c data,gwas variants
                Medicine
                integrative genome browser, hi-c data, gwas variants

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