Common regulatory variation impacts gene expression in a cell type-dependent manner.
paper
Cited
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- Authors
- Dimas, Antigone S; Deutsch, Samuel; Stranger, Barbara E; Montgomery, Stephen B; Borel, Christelle; Attar-Cohen, Homa; Ingle, Catherine; Beazley, Claude; Gutierrez Arcelus, Maria; Sekowska, Magdalena; Gagnebin, Marilyne; Nisbett, James; Deloukas, Panos; Dermitzakis, Emmanouil T; Antonarakis, Stylianos E
- Year
- 2009
- Journal
- Science (New York, N.Y.)
- PMID
- 19644074
- DOI
- 10.1126/science.1174148
- PMCID
- PMC2867218
Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 individuals. We detected cell type-specific genetic effects, with 69 to 80% of regulatory variants operating in a cell type-specific manner, and identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type-specific eQTLs were found at larger distances from genes and at lower effect size, similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity.
Genome-wide map of cis-eQTLs in three cell types; cis-eQTLs at 0.001 permutation threshold are shown as color-coded lines on their corresponding chromosomal location. Internal black lines represent genes with eQTLs in all cell types.
SNP-probe pair nominal (uncorrected) p-value distributions for the two secondary cell-types conditional on the reference cell type eQTL, significant at 0.001 permutation threshold are shown. The panels on the horizontal axis correspond (from left to right) to (i) the full p-value distribution of the secondary cell type, (ii) the p-value distribution after excluding significant eQTLs at 0.001 permutation threshold in secondary cell type, and (iii) similar to (ii) at 0.01 permutation threshold.
Localization of cis-eQTLs A) Distance to transcription start site (TSS) of all independent cis-eQTLs in each cell type (0.001 permutation threshold). A) shared in all three cell types (0.001 permutation threshold). C) cell type-specific cis-eQTLs (0.001 permutation threshold).
Fine-scale overlap of regulatory signals in three cell types A) Cell type-shared and cell type-specific independent cis-eQTLs (regulatory intervals) for all genes with a significant association at the 0.001 permutation threshold. B) genes significant in at least two cell types C) genes significant in all three cell types.
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| Novel genetic approach to investigate the role of plasma secretory phospholipase A2 (sPLA2)-V isoenzyme in coronary heart disease: modified Mendelian randomization analysis using PLA2G5 expression levels. | Holmes MV et al. | β | 2014 | β |
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| Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. | Nica AC et al. | β | 2013 | β |
| Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease. | van Meurs JB et al. | β | 2013 | β |
| Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer. | Henrion M et al. | β | 2013 | β |
| Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk. | Chubb D et al. | β | 2013 | β |
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| Decoding asthma: translating genetic variation in IL33 and IL1RL1 into disease pathophysiology. | Grotenboer NS et al. | β | 2013 | β |
| Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. | Hinks A et al. | β | 2013 | β |
| Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data. | Quinn EM et al. | β | 2013 | β |
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| Effect of catechol-o-methyltransferase-gene (COMT) variants on experimental and acute postoperative pain in 1,000 women undergoing surgery for breast cancer. | Kambur O et al. | β | 2013 | β |
| Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human intestine. | Kabakchiev B et al. | β | 2013 | β |
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| Expression variation of the porcine ADRB2 has a complex genetic background. | Murani E et al. | β | 2013 | β |
| Functional relevance for associations between genetic variants and systemic lupus erythematosus. | Deng FY et al. | β | 2013 | β |
| Genetic and epigenetic variants contributing to clofarabine cytotoxicity. | Eadon MT et al. | β | 2013 | β |
| Genetics of human gene expression. | Stranger BE et al. | β | 2013 | β |
| Genome scan study of prostate cancer in Arabs: identification of three genomic regions with multiple prostate cancer susceptibility loci in Tunisians. | Shan J et al. | β | 2013 | β |
| Genome-wide-associated variants in migraine susceptibility: a replication study from North India. | Ghosh J et al. | β | 2013 | β |
| Genome-wide association study for biomarker identification of Rapamycin and Everolimus using a lymphoblastoid cell line system. | Jiang J et al. | β | 2013 | β |
| Genome-wide association study identifies a novel susceptibility locus at 12q23.1 for lung squamous cell carcinoma in han chinese. | Dong J et al. | β | 2013 | β |
| Genome-wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4. | Ma RC et al. | β | 2013 | β |
| Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia. | Khor SS et al. | β | 2013 | β |
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| Genome-wide search for exonic variants affecting translational efficiency. | Li Q et al. | β | 2013 | β |
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| Refining susceptibility loci of chronic obstructive pulmonary disease with lung eqtls. | Lamontagne M et al. | β | 2013 | β |
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| The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome. | Sailani MR et al. | β | 2013 | β |
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| Transcription factor and chromatin features predict genes associated with eQTLs. | Wang D et al. | β | 2013 | β |
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| Variants in exons and in transcription factors affect gene expression in trans. | Kreimer A et al. | β | 2013 | β |
| Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype. | Migliorini G et al. | β | 2013 | β |
| Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma. | Frampton M et al. | β | 2013 | β |
| A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11. | Siddiq A et al. | β | 2012 | β |
| A meta-analysis of genome-wide association studies of follicular lymphoma. | Skibola CF et al. | β | 2012 | β |
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| A non-human primate system for large-scale genetic studies of complex traits. | Jasinska AJ et al. | β | 2012 | β |
| Association analyses identify multiple new lung cancer susceptibility loci and their interactions with smoking in the Chinese population. | Dong J et al. | β | 2012 | β |
| Association study of nicotinic acetylcholine receptor genes identifies a novel lung cancer susceptibility locus near CHRNA1 in African-Americans. | Walsh KM et al. | β | 2012 | β |
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| Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. | Zou F et al. | β | 2012 | β |
| Cd14 SNPs regulate the innate immune response. | Liu HH et al. | β | 2012 | β |
| Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies. | Xu W et al. | β | 2012 | β |
| Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. | Dunlop MG et al. | β | 2012 | β |
| Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. | Schroder K et al. | β | 2012 | β |
| Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity. | Stranger BE et al. | β | 2012 | β |
| Current genetic methodologies in the identification of disaster victims and in forensic analysis. | ZiΔtkiewicz E et al. | β | 2012 | β |
| Differential allelic expression of IL13 and CSF2 genes associated with asthma. | Burkhardt J et al. | β | 2012 | β |
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| Distinct and replicable genetic risk factors for acute respiratory distress syndrome of pulmonary or extrapulmonary origin. | Tejera P et al. | β | 2012 | β |
| Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. | Maia AT et al. | β | 2012 | β |
| Evaluating the prognostic significance of FBXW7 expression level in human breast cancer by a meta-analysis of transcriptional profiles. | Wei G et al. | β | 2012 | β |
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| Extensive natural variation for cellular hydrogen peroxide release is genetically controlled. | Attar H et al. | β | 2012 | β |
| From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. | Baxter AG et al. | β | 2012 | β |
| Functional evaluation of genetic variation in complex human traits. | Peters DT et al. | β | 2012 | β |
| Functional investigation of a schizophrenia GWAS signal at the CDC42 gene. | Gilks WP et al. | β | 2012 | β |
| Functional variants in NFKBIE and RTKN2 involved in activation of the NF-ΞΊB pathway are associated with rheumatoid arthritis in Japanese. | Myouzen K et al. | β | 2012 | β |
| Gene expression as a quantitative trait: what about translation? | Polychronakos C | β | 2012 | β |
| Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level. | Basu M et al. | β | 2012 | β |
| Genetic and environmental factors influencing the Placental Growth Factor (PGF) variation in two populations. | Sorice R et al. | β | 2012 | β |
| Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis. | Grisanzio C et al. | β | 2012 | β |
| Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. | Powell JE et al. | β | 2012 | β |
| Genetics. Gene losses in the human genome. | Quintana-Murci L | β | 2012 | β |
| Genetics of coronary artery disease: genome-wide association studies and beyond. | Prins BP et al. | β | 2012 | β |
| Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. | Fairfax BP et al. | β | 2012 | β |
| Genome-wide association analysis identifies susceptibility loci for migraine without aura. | Freilinger T et al. | β | 2012 | β |
| Genome-wide association and functional follow-up reveals new loci for kidney function. | Pattaro C et al. | β | 2012 | β |
| Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. | Fox CS et al. | β | 2012 | β |
| Genome-wide association of pericardial fat identifies a unique locus for ectopic fat. | Fox CS et al. | β | 2012 | β |
| Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4. | Xu J et al. | β | 2012 | β |
| Genome-wide association study of multiple sclerosis confirms a novel locus at 5p13.1. | Matesanz F et al. | β | 2012 | β |
| Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy. | Hu L et al. | β | 2012 | β |
| Identification of cis-regulatory variation influencing protein abundance levels in human plasma. | Lourdusamy A et al. | β | 2012 | β |
| Identification of IGF1, SLC4A4, WWOX, and SFMBT1 as hypertension susceptibility genes in Han Chinese with a genome-wide gene-based association study. | Yang HC et al. | β | 2012 | β |
| Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG. | Abo R et al. | β | 2012 | β |
| Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. | Auer PL et al. | β | 2012 | β |
| Imputing gene expression from selectively reduced probe sets. | Donner Y et al. | β | 2012 | β |
| Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. | Chasman DI et al. | β | 2012 | β |
| Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies. | IL6R Genetics Consortium Emerging Risk Factors Collaboration et al. | β | 2012 | β |
| Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. | Cubillos FA et al. | β | 2012 | β |
| Mapping cis- and trans-regulatory effects across multiple tissues in twins. | Grundberg E et al. | β | 2012 | β |
| Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. | Stolk L et al. | β | 2012 | β |
| Meta-analysis and brain imaging data support the involvement of VRK2 (rs2312147) in schizophrenia susceptibility. | Li M et al. | β | 2012 | β |
| Multiple sclerosis risk variant HLA-DRB1*1501 associates with high expression of DRB1 gene in different human populations. | Alcina A et al. | β | 2012 | β |
| Novel genetic association of the VTCN1 region with rheumatoid arthritis. | Daha NA et al. | β | 2012 | β |
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| Resolving the variable genome and epigenome in human disease. | Knight JC | β | 2012 | β |
| seeQTL: a searchable database for human eQTLs. | Xia K et al. | β | 2012 | β |
| Sex-biased genetic effects on gene regulation in humans. | Dimas AS et al. | β | 2012 | β |
| Statistical colocalization of monocyte gene expression and genetic risk variants for type 1 diabetes. | Wallace C et al. | β | 2012 | β |
| Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. | Perry JR et al. | β | 2012 | β |
| Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB. | Borel C et al. | β | 2012 | β |
| The autoimmunity-associated BLK haplotype exhibits cis-regulatory effects on mRNA and protein expression that are prominently observed in B cells early in development. | Simpfendorfer KR et al. | β | 2012 | β |
| The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics. | Powell JE et al. | β | 2012 | β |
| The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. | Cusanovich DA et al. | β | 2012 | β |
| The genetics of sudden cardiac death. | Arking DE et al. | β | 2012 | β |
| The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. | Pham MH et al. | β | 2012 | β |
| The use of the twin model to investigate the genetics and epigenetics of skin diseases with genomic, transcriptomic and methylation data. | Bataille V et al. | β | 2012 | β |
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| Transcriptional enhancers in development and disease. | Sakabe NJ et al. | β | 2012 | β |
| Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. | Fu J et al. | β | 2012 | β |
| Use of functional genomics to identify candidate genes underlying human genetic association studies of vascular diseases. | Yang X | β | 2012 | β |
| Variation in the ICAM1-ICAM4-ICAM5 locus is associated with systemic lupus erythematosus susceptibility in multiple ancestries. | Kim K et al. | β | 2012 | β |
| A genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia. | Hu Z et al. | β | 2011 | β |
| A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. | Nicholson G et al. | β | 2011 | β |
| A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS. | Richardson K et al. | β | 2011 | β |
| Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. | Wood AR et al. | β | 2011 | β |
| An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. | Swafford AD et al. | β | 2011 | β |
| An evolutionary analysis of RAC2 identifies haplotypes associated with human autoimmune diseases. | Sironi M et al. | β | 2011 | β |
| An interaction between Nrf2 polymorphisms and smoking status affects annual decline in FEV1: a longitudinal retrospective cohort study. | Masuko H et al. | β | 2011 | β |
| A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. | Greenawalt DM et al. | β | 2011 | β |
| Chromatin and heritability: how epigenetic studies can complement genetic approaches. | Birney E | β | 2011 | β |
| Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers. | Cox DG et al. | β | 2011 | β |
| Current status of genome-wide association studies in cancer. | Chung CC et al. | β | 2011 | β |
| Dissecting cis regulation of gene expression in human metabolic tissues. | Dobrin R et al. | β | 2011 | β |
| DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. | Bell JT et al. | β | 2011 | β |
| Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. | Teng L et al. | β | 2011 | β |
| Epistatic selection between coding and regulatory variation in human evolution and disease. | Lappalainen T et al. | β | 2011 | β |
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| Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder. | Williams HJ et al. | β | 2011 | β |
| From expression QTLs to personalized transcriptomics. | Montgomery SB et al. | β | 2011 | β |
| Gene expression differences among primates are associated with changes in a histone epigenetic modification. | Cain CE et al. | β | 2011 | β |
| Genetic neuropathology of schizophrenia: new approaches to an old question and new uses for postmortem human brains. | Kleinman JE et al. | β | 2011 | β |
| Genetics of sputum gene expression in chronic obstructive pulmonary disease. | Qiu W et al. | β | 2011 | β |
| Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. | Kooner JS et al. | β | 2011 | β |
| Global analysis of the impact of environmental perturbation on cis-regulation of gene expression. | Grundberg E et al. | β | 2011 | β |
| Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. | Borel C et al. | β | 2011 | β |
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| Integrative genomics strategies to elucidate the complexity of drug response. | Kasarskis A et al. | β | 2011 | β |
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| Mapping rare and common causal alleles for complex human diseases. | Raychaudhuri S | β | 2011 | β |
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| Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. | Glubb DM et al. | β | 2011 | β |
| Mouse models for Down syndrome-associated developmental cognitive disabilities. | Liu C et al. | β | 2011 | β |
| Progress and promise of genome-wide association studies for human complex trait genetics. | Stranger BE et al. | β | 2011 | β |
| Quantitative trait analysis suggests polymorphisms of estrogen-related genes regulate human sperm concentrations and motility. | Lee IW et al. | β | 2011 | β |
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| Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. | Schlattl A et al. | β | 2011 | β |
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| The effect of ACACB cis-variants on gene expression and metabolic traits. | Ma L et al. | β | 2011 | β |
| The effects of EBV transformation on gene expression levels and methylation profiles. | Caliskan M et al. | β | 2011 | β |
| The impact of cis-acting polymorphisms on the human phenotype. | Jones BL et al. | β | 2011 | β |
| The study of eQTL variations by RNA-seq: from SNPs to phenotypes. | Majewski J et al. | β | 2011 | β |
| The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. | Min JL et al. | β | 2011 | β |
| Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. | Fehrmann RS et al. | β | 2011 | β |
| Understanding type 1 diabetes through genetics: advances and prospects. | Polychronakos C et al. | β | 2011 | β |
| 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. | Ahmadiyeh N et al. | β | 2010 | β |
| Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. | Gibbs JR et al. | β | 2010 | β |
| A genome-wide association scan on estrogen receptor-negative breast cancer. | Li J et al. | β | 2010 | β |
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| Allelic skewing of DNA methylation is widespread across the genome. | Schalkwyk LC et al. | β | 2010 | β |
| Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis. | Pomerantz MM et al. | β | 2010 | β |
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| An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. | Hsu YH et al. | β | 2010 | β |
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| Genes and pathways contributing to obesity: a systems biology view. | Drake TA | β | 2010 | β |
| Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. | Cooper DN et al. | β | 2010 | β |
| Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. | Zeller T et al. | β | 2010 | β |
| Genetic sensitivity to the environment: the case of the serotonin transporter gene and its implications for studying complex diseases and traits. | Caspi A et al. | β | 2010 | β |
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