Cell Specific eQTL Analysis without Sorting Cells.

PLoS Genetics. 2015;11(5):e1005223 DOI 10.1371/journal.pgen.1005223


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Journal Title: PLoS Genetics

ISSN: 1553-7390 (Print); 1553-7404 (Online)

Publisher: Public Library of Science (PLoS)

LCC Subject Category: Science: Biology (General): Genetics

Country of publisher: United States

Language of fulltext: English

Full-text formats available: PDF, HTML, XML



Harm-Jan Westra
Danny Arends
Tõnu Esko
Marjolein J Peters
Claudia Schurmann
Katharina Schramm
Johannes Kettunen
Hanieh Yaghootkar
Benjamin P Fairfax
Anand Kumar Andiappan
Yang Li
Jingyuan Fu
Juha Karjalainen
Mathieu Platteel
Marijn Visschedijk
Rinse K Weersma
Silva Kasela
Lili Milani
Liina Tserel
Pärt Peterson
Eva Reinmaa
Albert Hofman
André G Uitterlinden
Fernando Rivadeneira
Georg Homuth
Astrid Petersmann
Roberto Lorbeer
Holger Prokisch
Thomas Meitinger
Christian Herder
Michael Roden
Harald Grallert
Samuli Ripatti
Markus Perola
Andrew R Wood
David Melzer
Luigi Ferrucci
Andrew B Singleton
Dena G Hernandez
Julian C Knight
Rossella Melchiotti
Bernett Lee
Michael Poidinger
Francesca Zolezzi
Anis Larbi
De Yun Wang
Leonard H van den Berg
Jan H Veldink
Olaf Rotzschke
Seiko Makino
Veikko Salomaa
Konstantin Strauch
Uwe Völker
Joyce B J van Meurs
Andres Metspalu
Cisca Wijmenga
Ritsert C Jansen
Lude Franke


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Time From Submission to Publication: 26 weeks


Abstract | Full Text

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.