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Nature Research, Nature Genetics, 1(49), p. 131-138

DOI: 10.1038/ng.3721

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Disease variants alter transcription factor levels and methylation of their binding sites

Journal article published in 2015 by Peter van t. Hof ORCID, Marc Jan Bonder ORCID, René Luijk ORCID, Daria V. Zhernakova ORCID, Matthijs Moed ORCID, Patrick Deelen ORCID, Martijn Vermaat ORCID, Maarten van Iterson ORCID, Freerk van Dijk ORCID, Michiel van Galen ORCID, Jan Bot ORCID, Roderick C. Slieker ORCID, P. Mila Jhamai ORCID, P. Mila Jhamai, Michael Verbiest ORCID and other authors.
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Data provided by SHERPA/RoMEO

Abstract

Most disease-associated genetic variants are noncoding, making it challenging to design experiments to understand their functional consequences. Identification of expression quantitative trait loci (eQTLs) has been a powerful approach to infer the downstream effects of disease-associated variants, but most of these variants remain unexplained. The analysis of DNA methylation, a key component of the epigenome, offers highly complementary data on the regulatory potential of genomic regions. Here we show that disease-associated variants have widespread effects on DNA methylation in trans that likely reflect differential occupancy of trans binding sites by cis-regulated transcription factors. Using multiple omics data sets from 3,841 Dutch individuals, we identified 1,907 established trait-associated SNPs that affect the methylation levels of 10,141 different CpG sites in trans (false discovery rate (FDR)