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.
Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA
Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network
Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression
Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles
DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts
Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs
Loss of estrogen-mediated immunoprotection underlies female gender bias in experimental Crohn's-like ileitis
Biological function integrated prediction of severe radiographic progression in rheumatoid arthritis: a nested case control study
Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk
TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis
Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases.
Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants.
Hypertension Susceptibility Loci are Associated with Anthracycline-related Cardiotoxicity in Long-term Childhood Cancer Survivors
Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity
Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin
Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells
A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn's Disease in Japanese Individuals
Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.
Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm.
Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution.
Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease.
B cells: Gene Expression
B lymphocytes are white blood cells that play a role in the adaptive immune system by secreting antibodies. Here is the latest research on gene expression in B cells.