Patterns of cis regulatory variation in diverse human populations.
paper
Cited
Public
- Authors
- Stranger, Barbara E; Montgomery, Stephen B; Dimas, Antigone S; Parts, Leopold; Stegle, Oliver; Ingle, Catherine E; Sekowska, Magda; Smith, George Davey; Evans, David; Gutierrez-Arcelus, Maria; Price, Alkes; Raj, Towfique; Nisbett, James; Nica, Alexandra C; Beazley, Claude; Durbin, Richard; Deloukas, Panos; Dermitzakis, Emmanouil T
- Year
- 2012
- Journal
- PLoS genetics
- PMID
- 22532805
- DOI
- 10.1371/journal.pgen.1002639
- PMCID
- PMC3330104
The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.
Spearman's rho for each significant SNP-probe cis- association shared by at least two populations.Shown are plots of rho for significant associations (permutation threshold 0.01) for each pairwise combination of populations. Within a panel, dots shown in upper left and lower right quadrants indicate significant SNP-probe associations where the allelic direction of the association is in opposite directions in the two populations being compared.
Expression level fold-change for significant SNP-probe cis- associations shared by pairs of populations.Shown are plots of the absolute value of expression level fold-change between median expression levels of homozygote classes for significant associations (permutation threshold 0.01) for each pairwise combination of populations. Within a panel, deviating from the 1 to 1 line (lower left to upper right) indicates differences in expression level fold-change (effect size) on log2 scale in the two populations being compared.
Distribution of cis- associations in each population relative to the transcription start site (TSS).βlog10 of the p-value is plotted against distance measured in base pairs from the associated SNP to the TSS. Each dot represents the most significant SNP for a significant gene (permutation threshold 0.01) in a population. Each panel represents a different population.
Distribution of cis- associations relative to the transcription start site (TSS) and in relation to population sharing.βlog10 of the p-value is plotted against distance measured in base pairs from the associated SNP to the TSS. Each dot represents the most significant SNP for a significant gene (permutation threshold 0.01) in a population. Panels separate associations that were significant in one population, two populations, etc. All populations are lumped together.
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| GWAS identifies two susceptibility loci for lamotrigine-induced skin rash in patients with epilepsy. | Jang HW et al. | β | 2015 | β |
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| Meta-analysis of two Chinese populations identifies an autoimmune disease risk allele in 22q11.21 as associated with systemic lupus erythematosus. | Zhang Y et al. | β | 2015 | β |
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| RAB2A Polymorphism impacts prefrontal morphology, functional connectivity, and working memory. | Li J et al. | β | 2015 | β |
| Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer. | Timofeeva MN et al. | β | 2015 | β |
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| Aberrant methylation of the MSH3 promoter and distal enhancer in esophageal cancer patients exposed to first-hand tobacco smoke. | Vogelsang M et al. | β | 2014 | β |
| A cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death. | Salinas RE et al. | β | 2014 | β |
| ADAM19 and HTR4 variants and pulmonary function: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. | London SJ et al. | β | 2014 | β |
| A genome-wide association study identifies a functional ERAP2 haplotype associated with birdshot chorioretinopathy. | Kuiper JJ et al. | β | 2014 | β |
| A genome-wide association study of serum levels of prostate-specific antigen in the Japanese population. | Terao C et al. | β | 2014 | β |
| A genome-wide survey of CD4(+) lymphocyte regulatory genetic variants identifies novel asthma genes. | Sharma S et al. | β | 2014 | β |
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| A meta-analysis of gene expression quantitative trait loci in brain. | Kim Y et al. | β | 2014 | β |
| Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. | Yang HC et al. | β | 2014 | β |
| Approaches for establishing the function of regulatory genetic variants involved in disease. | Knight JC | β | 2014 | β |
| Associating disease-related genetic variants in intergenic regions to the genes they impact. | Macintyre G et al. | β | 2014 | β |
| A three-stage genome-wide association study identifies a susceptibility locus for late radiotherapy toxicity at 2q24.1. | Fachal L et al. | β | 2014 | β |
| A two-stage association study suggests BRAP as a susceptibility gene for schizophrenia. | Zhang F et al. | β | 2014 | β |
| A type I interferon transcriptional signature precedes autoimmunity in children genetically at risk for type 1 diabetes. | Ferreira RC et al. | β | 2014 | β |
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| Chromosome 16q22 variants in a region associated with cardiovascular phenotypes correlate with ZFHX3 expression in a transcript-specific manner. | Martin RI et al. | β | 2014 | β |
| Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. | Tsaprouni LG et al. | β | 2014 | β |
| Coeliac disease-associated polymorphisms influence thymic gene expression. | Amundsen SS et al. | β | 2014 | β |
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| Intersection of population variation and autoimmunity genetics in human T cell activation. | Ye CJ et al. | β | 2014 | β |
| Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians. | Pierce BL et al. | β | 2014 | β |
| Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type. | Smith AK et al. | β | 2014 | β |
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| Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation. | Du X et al. | β | 2014 | β |
| Predicting DNA methylation level across human tissues. | Ma B et al. | β | 2014 | β |
| Protein quantitative trait loci identify novel candidates modulating cellular response to chemotherapy. | Stark AL et al. | β | 2014 | β |
| Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. | Ding Z et al. | β | 2014 | β |
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| Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. | Gibbons JG et al. | β | 2014 | β |
| RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses. | Ma B et al. | β | 2014 | β |
| SCN1A variations and response to multiple antiepileptic drugs. | Yip TS et al. | β | 2014 | β |
| The KMO allele encoding Arg452 is associated with psychotic features in bipolar disorder type 1, and with increased CSF KYNA level and reduced KMO expression. | Lavebratt C et al. | β | 2014 | β |
| The marriage of quantitative genetics and cell biology: a novel screening approach reveals people have genetically encoded variation in microtubule stability. | Ko DC et al. | β | 2014 | β |
| Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. | Martin AR et al. | β | 2014 | β |
| Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. | Walsh KM et al. | β | 2014 | β |
| Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. | Mostafavi S et al. | β | 2014 | β |
| VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes. | Burren OS et al. | β | 2014 | β |
| Whole exome sequencing of a dominant retinitis pigmentosa family identifies a novel deletion in PRPF31. | Villanueva A et al. | β | 2014 | β |
| Wnt signaling pathway pharmacogenetics in non-small cell lung cancer. | Stewart DJ et al. | β | 2014 | β |
| A common functional promoter variant links CNR1 gene expression to HDL cholesterol level. | Feng Q et al. | β | 2013 | β |
| A genome-wide association study in Han Chinese identifies a susceptibility locus for primary SjΓΆgren's syndrome at 7q11.23. | Li Y et al. | β | 2013 | β |
| A genome-wide association study of chronic otitis media with effusion and recurrent otitis media identifies a novel susceptibility locus on chromosome 2. | Allen EK et al. | β | 2013 | β |
| Anorectal atresia and variants at predicted regulatory sites in candidate genes. | Carter TC et al. | β | 2013 | β |
| Association of Parkinson disease with structural and regulatory variants in the HLA region. | Wissemann WT et al. | β | 2013 | β |
| Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. | Gokcumen O et al. | β | 2013 | β |
| Beyond GWASs: illuminating the dark road from association to function. | Edwards SL et al. | β | 2013 | β |
| Chromosome 2q31.1 associates with ESRD in women with type 1 diabetes. | Sandholm N et al. | β | 2013 | β |
| Common genetic variants in ARNTL and NPAS2 and at chromosome 12p13 are associated with objectively measured sleep traits in the elderly. | Evans DS et al. | β | 2013 | β |
| Common risk alleles for inflammatory diseases are targets of recent positive selection. | Raj T 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 |
| 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 |
| Detecting regulatory gene-environment interactions with unmeasured environmental factors. | Fusi N et al. | β | 2013 | β |
| 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 |
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| FCGR2B and FCRLB gene polymorphisms associated with IgA nephropathy. | Zhou XJ et al. | β | 2013 | β |
| Gene expression drives local adaptation in humans. | Fraser HB | β | 2013 | β |
| Genetic and nongenetic variation revealed for the principal components of human gene expression. | Goldinger A et al. | β | 2013 | β |
| Genetic predictors of risk and resilience in psychiatric disorders: a cross-disorder genome-wide association study of functional impairment in major depressive disorder, bipolar disorder, and schizophrenia. | McGrath LM et al. | β | 2013 | β |
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| Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. | Wheeler E et al. | β | 2013 | β |
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| How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility. | Su WH et al. | β | 2013 | β |
| Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts. | Nguyen TT et al. | β | 2013 | β |
| Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. | Brown CD et al. | β | 2013 | β |
| Large-scale genotyping identifies 41 new loci associated with breast cancer risk. | Michailidou K et al. | β | 2013 | β |
| Meta-analysis supports association of a functional SNP (rs1801133) in the MTHFR gene with Parkinson's disease. | Zhu ZG et al. | β | 2013 | β |
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| Possible associations of NTRK2 polymorphisms with antidepressant treatment outcome: findings from an extended tag SNP approach. | Hennings JM et al. | β | 2013 | β |
| Preferential binding to Elk-1 by SLE-associated IL10 risk allele upregulates IL10 expression. | Sakurai D et al. | β | 2013 | β |
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| Robust prediction of expression differences among human individuals using only genotype information. | Manor O et al. | β | 2013 | β |
| rs2072135, a low-penetrance variant for chronic lymphocytic leukaemia? | Sava GP et al. | β | 2013 | β |
| The CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma. | Weinhold N et al. | β | 2013 | β |
| 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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| Variants in the 17q21 asthma susceptibility locus are associated with allergic rhinitis in the Japanese population. | Tomita K et al. | β | 2013 | β |
| Variation and genetic control of protein abundance in humans. | Wu L 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 |
| Bayesian refinement of association signals for 14 loci in 3 common diseases. | Wellcome Trust Case Control Consortium et al. | β | 2012 | β |
| Calling sample mix-ups in cancer population studies. | Lynch AG 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 |
| Exploiting gene expression variation to capture gene-environment interactions for disease. | Idaghdour Y 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 |
| Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. | Gamazon ER 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 |
| Sex-biased genetic effects on gene regulation in humans. | Dimas AS et al. | β | 2012 | β |
| Rare and common regulatory variation in population-scale sequenced human genomes. | Montgomery SB et al. | β | 2011 | β |
| Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. | Price AL et al. | β | 2011 | β |