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Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75108 Uppsala, Sweden.;Galderma, Dept Preclin Dev, Uppsala, Sweden..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Karolinska Inst, Ctr Biosci, Dept Biosci & Nutr, Huddinge, Sweden..
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2016 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 107, no 6, 248-254 p.Article in journal (Refereed) Published
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Abstract [en]

Genome-wide association studies (GWAS) point to regions with associated genetic variants but rarely to a specific gene and therefore detailed knowledge regarding the genes contributing to complex traits and diseases remains elusive. The functional role of GWAS-SNPs is also affected by linkage disequilibrium with many variants on the same haplotype and sometimes in the same regulatory element almost equally likely to mediate the effect. Using ChIP-seq data on many transcription factors, we pinpointed genetic variants in HepG2 and HeLa-S3 cell lines which show a genome-wide significant difference in binding between alleles. We identified a collection of 3713 candidate functional regulatory variants many of which are likely drivers of GWAS signals or genetic difference in expression. A recent study investigated many variants before finding the functional ones at the GALNT2 locus, which we found in our genome-wide screen in HepG2. This illustrates the efficiency of our approach.

Place, publisher, year, edition, pages
2016. Vol. 107, no 6, 248-254 p.
Keyword [en]
Allele-specific regulation, Association to GWAS/eQTLs, Functional variants
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-299903DOI: 10.1016/j.ygeno.2016.04.006ISI: 000378623700004PubMedID: 27126307OAI: oai:DiVA.org:uu-299903DiVA: diva2:950365
Funder
Swedish Research Council, 2010-3505Swedish Diabetes Association, 2015-064
Available from: 2016-07-29 Created: 2016-07-29 Last updated: 2017-11-28Bibliographically approved

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Cavalli, MarcoPan, GangWallerman, OlaWadelius, Claes

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