Cell Specific eQTL Analysis without Sorting Cells.
Westra H-J., Arends D., Esko T., Peters MJ., Schurmann C., Schramm K., Kettunen J., Yaghootkar H., Fairfax BP., Andiappan AK., Li Y., Fu J., Karjalainen J., Platteel M., Visschedijk M., Weersma RK., Kasela S., Milani L., Tserel L., Peterson P., Reinmaa E., Hofman A., Uitterlinden AG., Rivadeneira F., Homuth G., Petersmann A., Lorbeer R., Prokisch H., Meitinger T., Herder C., Roden M., Grallert H., Ripatti S., Perola M., Wood AR., Melzer D., Ferrucci L., Singleton AB., Hernandez DG., Knight JC., Melchiotti R., Lee B., Poidinger M., Zolezzi F., Larbi A., Wang DY., van den Berg LH., Veldink JH., Rotzschke O., Makino S., Salomaa V., Strauch K., Völker U., van Meurs JBJ., Metspalu A., Wijmenga C., Jansen RC., Franke L.
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.