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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.

Original publication

DOI

10.1371/journal.pgen.1005223

Type

Journal article

Journal

Plos genet

Publication Date

05/2015

Volume

11

Keywords

Cell Line, Crohn Disease, Gene Expression Regulation, Genome-Wide Association Study, Humans, Lymphocytes, Neutrophils, Nod2 Signaling Adaptor Protein, Phenotype, Polymorphism, Single Nucleotide, Principal Component Analysis, Quantitative Trait Loci, Reproducibility of Results