@article{Zhernakova2016, abstract = {Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers. Of the 23,060 significant cis-regulated genes (false discovery rate (FDR) ≤ 0.05), 2,743 (12%) showed context-dependent eQTL effects. The majority of these effects were influenced by cell type composition. A set of 145 cis-eQTLs depended on type I interferon signaling. Others were modulated by specific transcription factors binding to the eQTL SNPs.}, author = {Zhernakova, Daria V. and Deelen, Patrick and Vermaat, Martijn and van Iterson, Maarten and van Galen, Michiel and Arindrarto, Wibowo and van 't Hof, Peter and Mei, Hailiang and van Dijk, Freerk and Westra, Harm-Jan and Bonder, Marc Jan and van Rooij, Jeroen and Verkerk, Marijn and Jhamai, P. Mila and Mila Jhamai, P. and Moed, Matthijs and Kielbasa, Szymon M. and Bot, Jan and Nooren, Irene and Pool, René and van Dongen, Jenny and Hottenga, Jouke J. and Stehouwer, Coen D. A. and van der Kallen, Carla J. H. and Schalkwijk, Casper G. and Zhernakova, Alexandra and Li, Yang and Tigchelaar, Ettje F. and de Klein, Niek and Beekman, Marian and Deelen, Joris and van Heemst, Diana and van den Berg, Leonard H. and Hofman, Albert and Uitterlinden, André G. and van Greevenbroek, Marleen M. J. and Veldink, Jan H. and Boomsma, Dorret I. and van Duijn, Cornelia M. and Wijmenga, Cisca and Eline Slagboom, P. and Slagboom, P. Eline and Swertz, Morris A. and Isaacs, Aaron and van Meurs, Joyce B. J. and Jansen, Rick and Heijmans, Bastiaan T. and 't Hoen, Peter A. C. and C. 't Hoen, Peter A. and Franke, Lude}, doi = {10.1038/ng.3737}, journal = {Nature Genetics}, month = {dec}, pages = {139-145}, title = {Identification of context-dependent expression quantitative trait loci in whole blood}, url = {https://oadoi.org/10.1038/ng.3737}, volume = {49}, year = {2016} }