Cell Specific eQTL Analysis without Sorting Cells

PLoS Genet. 2015 May 8;11(5):e1005223. doi: 10.1371/journal.pgen.1005223. eCollection 2015 May.


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.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

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


  • NOD2 protein, human
  • Nod2 Signaling Adaptor Protein

Associated data

  • GEO/GSE20142
  • GEO/GSE33828
  • GEO/GSE36382
  • GEO/GSE48152
  • GEO/GSE48348