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Allele-specific tra...
Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals
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- Cavalli, Marco (författare)
- Uppsala universitet,Medicinsk genetik och genomik
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- Pan, Gang (författare)
- Uppsala universitet,Medicinsk genetik och genomik
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- Nord, Helena (författare)
- Uppsala universitet,Medicinsk genetik och genomik,Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75108 Uppsala, Sweden.;Galderma, Dept Preclin Dev, Uppsala, Sweden.
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- Arzt, Emelie Wallén (författare)
- Uppsala universitet,Medicinsk genetik och genomik,Karolinska Inst, Ctr Biosci, Dept Biosci & Nutr, Huddinge, Sweden.
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- Wallerman, Ola (författare)
- Uppsala universitet,Medicinsk genetik och genomik
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- Wadelius, Claes (författare)
- Uppsala universitet,Medicinsk genetik och genomik
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(creator_code:org_t)
- Elsevier BV, 2016
- 2016
- Engelska.
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Ingår i: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646. ; 107:6, s. 248-254
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- Allele-specific regulation
- Association to GWAS/eQTLs
- Functional variants
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Genomics
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