{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T06:58:04Z","timestamp":1773817084722,"version":"3.50.1"},"reference-count":159,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,6,9]],"date-time":"2018-06-09T00:00:00Z","timestamp":1528502400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004895","name":"European Social Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004895","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin\u2013chromatin and chromatin\u2013protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution.<\/jats:p>\n               <jats:p>We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.<\/jats:p>","DOI":"10.1093\/bib\/bby039","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T11:08:23Z","timestamp":1525864103000},"page":"1639-1654","source":"Crossref","is-referenced-by-count":92,"title":["Regulatory variants: from detection to predicting impact"],"prefix":"10.1093","volume":"20","author":[{"given":"Elena","family":"Rojano","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro","family":"Seoane","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan A G","family":"Ranea","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James R","family":"Perkins","sequence":"additional","affiliation":[{"name":"Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,6,8]]},"reference":[{"issue":"5","key":"2020080807563110900_bby039-B1","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.ajhg.2013.10.012","article-title":"Beyond GWASs: illuminating the dark road from association to function","volume":"93","author":"Edwards","year":"2013","journal-title":"Am J Hum Genet"},{"issue":"7146","key":"2020080807563110900_bby039-B2","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"Birney","year":"2007","journal-title":"Nature"},{"key":"2020080807563110900_bby039-B3","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkr1012","article-title":"ENCODE whole-genome data in the UCSC Genome Browser: update 2012","volume":"40","author":"Rosenbloom","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2020080807563110900_bby039-B4","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1093\/bfgp\/elp014","article-title":"Identifying regulatory elements in eukaryotic genomes","volume":"8","author":"Narlikar","year":"2009","journal-title":"Brief Funct Genomics Proteomics"},{"key":"2020080807563110900_bby039-B5","first-page":"980","article-title":"In the loop: promoter\u2013enhancer interactions and bioinformatics","volume":"17","author":"Mora","year":"2016","journal-title":"Brief Bioinform"},{"issue":"1","key":"2020080807563110900_bby039-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bib\/bbs075","article-title":"Identifying miRNAs, targets and functions","volume":"15","author":"Liu","year":"2014","journal-title":"Brief Bioinform"},{"issue":"1","key":"2020080807563110900_bby039-B7","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/bfgp\/elv022","article-title":"Advances in long noncoding RNAs: identification, structure prediction and function annotation","volume":"15","author":"Guo","year":"2016","journal-title":"Brief Funct Genomics"},{"key":"2020080807563110900_bby039-B8","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.cell.2017.06.049","article-title":"A genetic variant associated with five vascular diseases is a distal regulator of endothelin-1 gene expression","volume":"170","author":"Gupta","year":"2017","journal-title":"Cell"},{"issue":"1","key":"2020080807563110900_bby039-B9","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.cell.2013.08.034","article-title":"Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway","volume":"155","author":"Lee","year":"2013","journal-title":"Cell"},{"issue":"4","key":"2020080807563110900_bby039-B10","first-page":"1003","article-title":"A GWAS SNP for schizophrenia is linked to the internal mir137 promoter and supports differential allele-specific expression. 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