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.

dx.doi.org/10.1371/journal.pgen.1005223, hdl.handle.net/1765/88532
PL o S Genetics (Online)
This work was funded by the European Commission 7th Framework Programme; grant id fp7/261433 - Biobank Standardisation and Harmonisation for Research Excellence in the European Union (BIOSHARE-EU), This work was funded by the European Commission 7th Framework Programme; grant id fp7/201413 - European Network for Genetic and Genomic Epidemiology (ENGAGE)
Department of Internal Medicine

Westra, H.J, Arends, D, Esko, T, Peters, M.J, Schurmann, C, Schramm, K, … Franke, L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PL o S Genetics (Online), 11(5). doi:10.1371/journal.pgen.1005223