High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation
Open accessAbstract
Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA levels in cis. Strikingly, we found a strong enrichment of eQTLs in the 250 bp just upstream of the transcription end site (TES), in addition to an enrichment around the transcription start site (TSS). Most eQTLs lie either within genes or close to genes; for example, we estimate that only 5% of eQTLs lie more than 20 kb upstream of the TSS. After controlling for position effects, SNPs in exons are approximately 2-fold more likely than SNPs in introns to be eQTLs. Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Cis-eSNPs were enriched in genic elements and non-coding RNAs, especially within 100 kb of transcription start and end sites, and were depleted in intergenic regions.
“Cis-eSNPs were enriched within genic elements and non-coding RNAs, particularly within 100 kb of the transcription start and end sites12, and depleted in intergenic regions (Fig. 1A, B).”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [12]
Cis-eSNPs are enriched within genic elements and non-coding RNAs, particularly within 100 kb of transcription start and end sites, and depleted in intergenic regions.
“Cis-eSNPs were enriched within genic elements and non-coding RNAs, particularly within 100 kb of the transcription start and end sites12, and depleted in intergenic regions (Fig. 1A, B).”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [12]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858 · see citing works
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441 · see citing works
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438 · see citing works
Algorithms for Minimization Without Derivatives
G., D., & Brent, R. P. (1974) · Mathematics of Computation · doi:10.2307/2005713 · Cited by 2,917 · see citing works
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C., Beazley, C., Thorne, N., Redon, R., Bird, C., Grassi, A., Lee, C., et al. (2007) · Science · doi:10.1126/science.1136678 · Cited by 1,709 · see citing works
Self-citationGenetics of gene expression surveyed in maize, mouse and man
Schadt, E., Monks, S. A., Drake, T., Lusis, A., Che, N., Colinayo, V. V., Ruff, T., Milligan, S. B., Lamb, J., Cavet, G., et al. (2003) · Nature · doi:10.1038/nature01434 · Cited by 1,594 · see citing works
The evolutionary significance of cis-regulatory mutations
Wray, G. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2063 · Cited by 1,521 · see citing works
Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works
Genetic Dissection of Transcriptional Regulation in Budding Yeast
Brem, R. B., Yvert, G., Clinton, R., & Kruglyak, L. (2002) · Science · doi:10.1126/science.1069516 · Cited by 1,392 · see citing works
Genetics of gene expression and its effect on disease
Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A. S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G. B., Gunnarsdottir, S., et al. (2008) · Nature · doi:10.1038/nature06758 · Cited by 1,296 · see citing works
Assessing computational tools for the discovery of transcription factor binding sites
Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1053 · Cited by 1,268 · see citing works
Genetic analysis of genome-wide variation in human gene expression
Morley, M. P., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004) · Nature · doi:10.1038/nature02797 · Cited by 1,207 · see citing works
The Evolution of Transcriptional Regulation in Eukaryotes
Wray, G. A. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg140 · Cited by 1,204 · see citing works
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works
Population genomics of human gene expression
Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A. S., Bird, C., Beazley, C., Ingle, C., Dunning, M., Flicek, P., Koller, D., et al. (2007) · Nature Genetics · doi:10.1038/ng2142 · Cited by 1,132 · see citing works
Self-citationAnalysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works
A genome-wide association study of global gene expression
Dixon, A. L., Liang, L., Moffatt, M. F., Chen, W., Heath, S. C., Wong, K., Taylor, J. C., Burnett, E. C., Gut, I. G., Farrall, M., et al. (2007) · Nature Genetics · doi:10.1038/ng2109 · Cited by 946 · see citing works
Transcriptional Regulatory Elements in the Human Genome
Maston, G. A., Evans, S. K., & Green, M. R. (2006) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.7.080505.115623 · Cited by 937 · cited 2× · see citing works
“However, for most genes, transcription initiation is usually thought to be the principal determinant of the overall mRNA gene expression profile [34,35].”
BackgroundLong-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease
Kleinjan, D. A., & van Heyningen, V. (2004) · The American Journal of Human Genetics · doi:10.1086/426833 · Cited by 868 · see citing works
Orchestrated response: a symphony of transcription factors for gene controlPreprint
Lemon, B. D., & Tjian, R. (2000) · Genes & Development · doi:10.1101/gad.831000 · Cited by 762 · see citing works
Precision and functional specificity in mRNA decay
Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D., & Brown, P. O. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092538799 · Cited by 708 · see citing works
Mapping determinants of human gene expression by regional and genome-wide association
Cheung, V. G., Spielman, R. S., Ewens, K. G., Weber, T. M., Morley, M. P., & Burdick, J. T. (2005) · Nature · doi:10.1038/nature04244 · Cited by 588 · see citing works
Natural variation in human gene expression assessed in lymphoblastoid cells
Cheung, V. G., Conlin, L. K., Weber, T. M., Arcaro, M., Jen, K., Morley, M. P., & Spielman, R. S. (2003) · Nature Genetics · doi:10.1038/ng1094 · Cited by 550 · see citing works
Revealing the architecture of gene regulation: the promise of eQTL studies
Gilad, Y., Rifkin, S. A., & Pritchard, J. K. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.06.001 · Cited by 531 · see citing works
Self-citationImputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits
Servin, B., & Stephens, M. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030114 · Cited by 520 · see citing works
Self-citationCommon genetic variants account for differences in gene expression among ethnic groups
Spielman, R. S., Bastone, L. A., Burdick, J. T., Morley, M. P., Ewens, W. J., & Cheung, V. G. (2007) · Nature Genetics · doi:10.1038/ng1955 · Cited by 516 · see citing works
Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes
Göring, H. H. H., Curran, J. E., Johnson, M. P., Dyer, T. D., Charlesworth, J., Cole, S. A., Jowett, J. B. M., Abraham, L. J., Rainwater, D. L., Comuzzie, A. G., et al. (2007) · Nature Genetics · doi:10.1038/ng2119 · Cited by 503 · see citing works
Carthew, R. W. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.02.012 · Cited by 472 · see citing works
Messenger RNA Turnover in Eukaryotes: Pathways and Enzymes
Meyer, S., Temme, C., & Wahle, E. (2004) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230490513991 · Cited by 342 · see citing works
Post‐transcriptional regulation of gene expression by degradation of messenger RNAs
Bevilacqua, A., Ceriani, M. C., Capaccioli, S., & Nicolin, A. (2003) · Journal of Cellular Physiology · doi:10.1002/jcp.10272 · Cited by 316 · see citing works
Gene-Expression Variation Within and Among Human Populations
Storey, J. D., Madeoy, J. J., Strout, J. L., Wurfel, M. M., Ronald, J., & Akey, J. M. (2007) · The American Journal of Human Genetics · doi:10.1086/512017 · Cited by 310 · see citing works
Xie, X., Mikkelsen, T. S., Gnirke, A., Lindblad-Toh, K., Kellis, M., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701811104 · Cited by 305 · see citing works
Genome-wide analysis of transcript isoform variation in humans
Kwan, T., Benovoy, D., Dias, C., Gurd, S., Provencher, C., Beaulieu, P., Hudson, T. J., SLADEK, R. M., & Majewski, J. (2008) · Nature Genetics · doi:10.1038/ng.2007.57 · Cited by 305 · see citing works
Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region
Eberle, A. B., Stalder, L., Mathys, H., Orozco, R. Z., & Mühlemann, O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060092 · Cited by 300 · see citing works
Blanchette, M., Bataille, A. R., Chen, X., Poitras, C., Laganière, J., Lefèbvre, C., Deblois, G., Giguère, V., Ferretti, V., Bergeron, D., et al. (2006) · Genome Research · doi:10.1101/gr.4866006 · Cited by 258 · see citing works
Regulatory polymorphisms underlying complex disease traits.
Knight, J. C. (2005) · Journal of Molecular Medicine · doi:10.1007/s00109-004-0603-7 · Cited by 246 · see citing works
DBTSS: database of transcription start sites, progress report 2008
Wakaguri, H., Yamashita, R., Suzuki, Y., Sugano, S., & Nakai, K. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm901 · Cited by 221 · see citing works
Local Regulatory Variation in Saccharomyces cerevisiae
Ronald, J., Brem, R. B., Whittle, J., & Kruglyak, L. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010025 · Cited by 157 · see citing works
Sequence Polymorphisms Cause Many False cis eQTLs
Alberts, R., Terpstra, P., Li, Y., Breitling, R., Nap, J., & Jansen, R. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000622 · Cited by 142 · see citing works
Idaghdour, Y., Storey, J. D., Jadallah, S. J., & Gibson, G. C. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000052 · Cited by 109 · see citing works
GuhaThakurta, D., Xie, T., Anand, M., Edwards, S. W., Li, G., Wang, S. S., & Schadt, E. E. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-235 · Cited by 44 · see citing works
Using Reporter Gene Assays to IdentifycisRegulatory Differences Between Humans and Chimpanzees
Chabot, A. E., Shrit, R. A., Blekhman, R., & Gilad, Y. (2007) · Genetics · doi:10.1534/genetics.107.073429 · Cited by 19 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
The GTEx Consortium, Ardlie, K. G., Deluca, D. S., Segrè, A. V., Sullivan, T. J., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Maller, J. B., Tukiainen, T., et al. (2015) · Science · doi:10.1126/science.1262110 · Cited by 5,062 · see citing works
Self-citationMapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works
Transcriptome and genome sequencing uncovers functional variation in humans
The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature · doi:10.1038/nature12531 · Cited by 1,888 · see citing works
Self-citationUnderstanding mechanisms underlying human gene expression variation with RNA sequencing
Pickrell, J. K., Marioni, J. C., Pai, A. A., Degner, J. F., Engelhardt, B. E., Nkadori, E., Veyrieras, J.-B., Stephens, M., Gilad, Y., & Pritchard, J. K. (2010) · Nature · doi:10.1038/nature08872 · Cited by 1,256 · see citing works
Self-citationGene expression elucidates functional impact of polygenic risk for schizophrenia
Fromer, M., Roussos, P., Sieberts, S. K., Johnson, J. S., Kavanagh, D. H., Perumal, T. M., Ruderfer, D. M., Oh, E. C., Topol, A., Shah, H. R., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4399 · Cited by 1,091 · see citing works
A simple new approach to variable selection in regression, with application to genetic fine mapping
Wang, G., Sarkar, A., Carbonetto, P., & Stephens, M. (2020) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/rssb.12388 · Cited by 1,121 · see citing works
Self-citationDNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
Bell, J. T., Pai, A. A., Pickrell, J. K., Gaffney, D. J., Pique-Regi, R., Degner, J. F., Gilad, Y., & Pritchard, J. K. (2011) · Genome Biology · doi:10.1186/gb-2011-12-1-r10 · Cited by 838 · see citing works
Self-citationMapping complex disease traits with global gene expression
Cookson, W., Liang, L., Abecasis, G., Moffatt, M., & Lathrop, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2537 · Cited by 849 · see citing works
Transcriptome genetics using second generation sequencing in a Caucasian population
Montgomery, S. B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R. P., Ingle, C., Nisbett, J., Guigo, R., & Dermitzakis, E. T. (2010) · Nature · doi:10.1038/nature08903 · Cited by 797 · see citing works
Self-citationAbundant quantitative trait loci exist for DNA methylation and gene expression in human brain
Gibbs, J. R., van der Brug, M. P., Hernandez, D. G., Traynor, B. J., Nalls, M. A., Lai, S.-L., Arepalli, S., Dillman, A., Rafferty, I. P., Troncoso, J., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000952 · Cited by 769 · see citing works
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp579 · Cited by 502 · see citing works
Self-citationSegrè, A. V., DIAGRAM Consortium, MAGIC investigators, Groop, L., Mootha, V. K., Daly, M. J., & Altshuler, D. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001058 · Cited by 463 · see citing works
Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.027 · Cited by 480 · see citing works
Wagner, J. R., Busche, S., Ge, B., Kwan, T., Pastinen, T., & Blanchette, M. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r37 · Cited by 446 · see citing works
Sun, Y. V., & Hu, Y.-J. (2016) · Advances in Genetics · doi:10.1016/bs.adgen.2015.11.004 · Cited by 459 · see citing works
Rossin, E. J., Lage, K., Raychaudhuri, S., Xavier, R. J., Tatar, D., Benita, Y., Constortium, I. I. B. D. G., Cotsapas, C., & Daly, M. J. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001273 · Cited by 438 · see citing works
The Genetics of Transcription Factor DNA Binding Variation
Deplancke, B., Alpern, D., & Gardeux, V. (2016) · Cell · doi:10.1016/j.cell.2016.07.012 · Cited by 390 · see citing works
Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder
Holmans, P., Green, E. K., Pahwa, J. S., Ferreira, M. A. R., Purcell, S. M., Sklar, P., Owen, M. J., O'Donovan, M. C., & Craddock, N. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.05.011 · Cited by 378 · see citing works
Systematic differences in discovery of genetic effects on gene expression and complex traits
Mostafavi, H., Spence, J. P., Naqvi, S., & Pritchard, J. K. (2023) · Nature Genetics · doi:10.1038/s41588-023-01529-1 · Cited by 336 · see citing works
Self-citationPopulation-specificity of human DNA methylation
Fraser, H. B., Lam, L. L., Neumann, S. M., & Kobor, M. S. (2012) · Genome Biology · doi:10.1186/gb-2012-13-2-r8 · Cited by 313 · see citing works
Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells
Rouhani, F., Kumasaka, N., de Brito, M. C., Bradley, A., Vallier, L., & Gaffney, D. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004432 · Cited by 294 · see citing works
A Map of Transcriptional Heterogeneity and Regulatory Variation in Human Microglia
Young, A. M. H., Kumasaka, N., Calvert, F., Hammond, T. R., Knights, A., Panousis, N., Park, J. S., Schwartzentruber, J., Liu, J., Kundu, K., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00875-2 · Cited by 213 · see citing works
The study of eQTL variations by RNA-seq: from SNPs to phenotypes
Majewski, J., & Pastinen, T. (2011) · Trends in Genetics · doi:10.1016/j.tig.2010.10.006 · Cited by 232 · see citing works
Poelmans, G., Pauls, D. L., Buitelaar, J. K., & Franke, B. (2011) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2010.10070948 · Cited by 223 · see citing works
Rogers, P. J., Hohoff, C., Heatherley, S. V., Mullings, E. L., Maxfield, P. J., Evershed, R. P., Deckert, J., & Nutt, D. J. (2010) · Neuropsychopharmacology · doi:10.1038/npp.2010.71 · Cited by 212 · see citing works
Gene set analysis of genome-wide association studies: Methodological issues and perspectives
Wang, L., Jia, P., Wolfinger, R. D., Chen, X., & Zhao, Z. (2011) · Genomics · doi:10.1016/j.ygeno.2011.04.006 · Cited by 207 · see citing works
Association of Parkinson Disease with Structural and Regulatory Variants in the HLA Region
Wissemann, W. T., Hill-Burns, E. M., Zabetian, C. P., Factor, S. A., Patsopoulos, N., Hoglund, B., Holcomb, C., Donahue, R. J., Thomson, G., Erlich, H., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.009 · Cited by 189 · see citing works
Ding, J., Gudjonsson, J. E., Liang, L., Stuart, P. E., Li, Y., Chen, W., Weichenthal, M., Ellinghaus, E., Franke, A., Cookson, W., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.024 · Cited by 180 · see citing works
Inferring relevant cell types for complex traits by using single-cell gene expression
Calderon, D., Bhaskar, A., Knowles, D. A., Golan, D., Raj, T., Fu, A. Q., & Pritchard, J. K. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.09.009 · Cited by 127 · see citing works
RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
Lalonde, E., Ha, K. C. H., Wang, Z., Bemmo, A., Kleinman, C. L., Kwan, T., Pastinen, T., & Majewski, J. (2011) · Genome Research · doi:10.1101/gr.111211.110 · Cited by 111 · see citing works
Kendler, K. S., Kalsi, G., Holmans, P. A., Sanders, A. R., Aggen, S. H., Dick, D. M., Aliev, F., Shi, J., Levinson, D. F., & Gejman, P. V. (2011) · Alcoholism: Clinical and Experimental Research · doi:10.1111/j.1530-0277.2010.01427.x · Cited by 121 · see citing works
Akula, N., Barb, J., Jiang, X., Wendland, J. R., Choi, K. H., Sen, S. K., Hou, L., Chen, D. T. W., Laje, G., Johnson, K., et al. (2014) · Molecular Psychiatry · doi:10.1038/mp.2013.170 · Cited by 116 · see citing works
Systems genetics analysis of gene-by-environment interactions in human cells
Romanoski, C. E., Lee, S., Kim, M. J., Ingram-Drake, L., Plaisier, C. L., Yordanova, R., Tilford, C., Guan, B., He, A., Gargalovic, P. S., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.02.002 · Cited by 111 · see citing works
Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms
del Rosario, R. C.-H., Poschmann, J., Rouam, S. L., Png, E., Khor, C. C., Hibberd, M. L., & Prabhakar, S. (2015) · Nature Methods · doi:10.1038/nmeth.3326 · Cited by 58 · see citing works
Hause, R. J., Stark, A. L., Antao, N. N., Gorsic, L. K., Chung, S. H., Brown, C. D., Wong, S. S., Gill, D. F., Myers, J. L., To, L. A., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.07.005 · Cited by 43 · see citing works
Adaptive variation regulates the expression of the human SGK1 gene in response to stress
Luca, F., Kashyap, S., Southard, C., Zou, M., Witonsky, D., Di Rienzo, A., & Conzen, S. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000489 · Cited by 45 · see citing works
Wojcik, G. L., Kao, W. L., & Duggal, P. (2015) · BMC Genetics · doi:10.1186/s12863-015-0191-2 · Cited by 33 · see citing works
Engelken, J., Espadas, G., Mancuso, F. M., Bonet, N., Scherr, A.-L., Jímenez-Álvarez, V., Codina-Solà, M., Medina-Stacey, D., Spataro, N., Stoneking, M., et al. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msv267 · Cited by 31 · see citing works
<scp>PSEA</scp>: Phenotype Set Enrichment Analysis—A New Method for Analysis of Multiple Phenotypes
Ried, J. S., Döring, A., Oexle, K., Meisinger, C., Winkelmann, J., Klopp, N., Meitinger, T., Peters, A., Suhre, K., Wichmann, H. ‐., et al. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21617 · Cited by 21 · see citing works
Kang, T., Moore, E. C., Kopania, E. E. K., King, C. D., Schilling, B., Campisi, J., Good, J. M., & Brem, R. B. (2023) · G3: Genes, Genomes, Genetics · doi:10.1093/g3journal/jkad091 · Cited by 10 · see citing works
Interpreting noncoding genetic variation in complex traits and human disease
Ward, L. D., & Kellis, M. (2012) · Nature Biotechnology · doi:10.1038/nbt.2422 · Cited by 6 · see citing works
- Authors
- Veyrieras, J.-B., Kudaravalli, S., Kim, S. Y., Dermitzakis, E. T., Gilad, Y., Stephens, M., & Pritchard, J. K.
- Affiliations
- University of Chicago (US)
- Wellcome Sanger Institute (GB)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Veyrieras, Jean-Baptiste
- Gilad, Yoav
- Stephens, Matthew
- Pritchard, Jonathan K.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-10-10
- Volume
- 4
- Issue
- 10
- Pages
- e1000214
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2556086
- OpenAlex
- W2136091734
- Cited by
- 536
- References
- 46
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 8 · 2023: 9 · 2022: 12 · 2021: 11 · 2020: 15 · 2019: 17 · 2018: 35 · 2017: 29 · 2016: 49 · 2015: 50 · 2014: 53 · 2013: 53 · 2012: 63
- FWCI
- 23.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- Knowledge@UChicago (University of Chicago) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- University of Chicago (cc-by)
- Funders
- Howard Hughes Medical Institute
- Institut National de la Recherche Agronomique
- National Institutes of Health (HG02585)
- National Human Genome Research Institute (R56HG002585, R01HG002772, HG02585-01, HG002772, R01HG002585)
- National Institute of General Medical Sciences (GM077959, R01GM077959)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- expression quantitative trait loci, eQTL mapping, gene expression regulation, cis-regulatory effects, transcription start sites, mRNA stability, steady-state mRNA levels, position effect, Bayesian hierarchical model
- MeSH terms
- Bayes Theorem, Chromosome Mapping, Gene Expression Regulation, Genetic Complementation Test, Humans, Introns, Models, Genetic, RNA, Messenger, Terminator Regions, Genetic, Genome, Human, Polymorphism, Single Nucleotide, RNA Stability, Transcription Initiation Site, Databases, Genetic, Quantitative Trait Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
