Conditional eQTL analysis reveals allelic heterogeneity of gene expression
Open accessAbstract
In recent years, multiple eQTL (expression quantitative trait loci) catalogs have become available that can help understand the functionality of complex trait-related single nucleotide polymorphisms (SNPs). In eQTL catalogs, gene expression is often strongly associated with multiple SNPs, which may reflect either one or multiple independent associations. Conditional eQTL analysis allows a distinction between dependent and independent eQTLs. We performed conditional eQTL analysis in 4,896 peripheral blood microarray gene expression samples. Our analysis showed that 35% of genes with a cis eQTL have at least two independent cis eQTLs; for several genes up to 13 independent cis eQTLs were identified. Also, 12% (671) of the independent cis eQTLs identified in conditional analyses were not significant in unconditional analyses. The number of GWAS catalog SNPs identified as eQTL in the conditional analyses increases with 24% as compared to unconditional analyses. We provide an online conditional cis eQTL mapping catalog for whole blood (https://eqtl.onderzoek.io/), which can be used to lookup eQTLs more accurately than in standard unconditional whole blood eQTL databases.
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?
The Alzheimer's disease-associated INPP5D SNP rs35349669 increases INPP5D gene expression in whole blood.
“The AD-associated INPP5D SNP (rs35349669) increases INPP5D gene expression in whole blood (Jansen et al., 2017).”
From Microglia in Alzheimer’s disease (2018) · cites this paper as Jansen et al., 2017
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
Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works
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
Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004383 · Cited by 4,261 · see citing works
Willer (2013) · doi:10.1038/ng.2797 · Cited by 2,983 · see citing works
Integrative approaches for large-scale transcriptome-wide association studies
Gusev, A., Ko, A., Shi, H., Bhatia, G., Chung, W., Penninx, B. W. J. H., Jansen, R., de Geus, E. J. C., Boomsma, D. I., Wright, F. A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3506 · Cited by 2,479 · 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
A gene-based association method for mapping traits using reference transcriptome data
Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., Eyler, A. E., Denny, J. C., Nicolae, D. L., Cox, N. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3367 · Cited by 1,762 · see citing works
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
Shabalin, A. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts163 · Cited by 1,694 · see citing works
Systematic identification of trans eQTLs as putative drivers of known disease associations
Westra, H.-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K., Powell, J. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2756 · Cited by 1,658 · see citing works
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus
Musunuru, K., Strong, A., Frank-Kamenetsky, M., Lee, N. E., Ahfeldt, T., Sachs, K. V., Li, X., Li, H., Kuperwasser, N., Ruda, V. M., et al. (2010) · Nature · doi:10.1038/nature09266 · Cited by 1,140 · see citing works
The role of regulatory variation in complex traits and disease
Albert, F. W., & Kruglyak, L. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3891 · Cited by 1,047 · see citing works
The Netherlands Study of Depression and Anxiety (NESDA): rationale, objectives and methods
Penninx, B. W. J. H., Beekman, A. T. F., Smit, J. H., Zitman, F. G., Nolen, W. A., Spinhoven, P., Cuijpers, P. J., de Jong, P. J., van Marwijk, H., Assendelft, W. J., et al. (2008) · International Journal of Methods in Psychiatric Research · doi:10.1002/mpr.256 · Cited by 918 · see citing works
Effects of an Anti-TSLP Antibody on Allergen-Induced Asthmatic Responses
Gauvreau, G. M., O’Byrne, P. M., Boulet, L., Wang, Y., Cockcroft, D. W., Bigler, J., FitzGerald, J. M., Boedigheimer, M. J., Davis, B. E., Dias, C. S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1402895 · Cited by 790 · see citing works
Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S. H., Czajkowski, J., Esko, T., Fall, T., Kilpeläinen, T. O., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005378 · Cited by 664 · see citing works
Genetic variability in the regulation of gene expression in ten regions of the human brain
UK Brain Expression Consortium, Ramasamy, A., North American Brain Expression Consortium, Trabzuni, D., Guelfi, S., Varghese, V., Smith, C., Walker, R., De, T., Coin, L., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3801 · Cited by 644 · see citing works
Netherlands Twin Register: From Twins to Twin Families
Boomsma, D., de Geus, E. D., Vink, J., Stubbe, J., Distel, M., Hottenga, J., Posthuma, D., van Beijsterveldt, T. V., Hudziak, J., Bartels, M., et al. (2006) · Twin Research and Human Genetics · doi:10.1375/twin.9.6.849 · Cited by 551 · see citing works
Self-citationBattle, A., Mostafavi, S., Zhu, X., Potash, J. B., Weissman, M. M., McCormick, C., Haudenschild, C. D., Beckman, K. B., Shi, J., Mei, R., et al. (2014) · Genome Research · doi:10.1101/gr.155192.113 · Cited by 547 · see citing works
Impact of regulatory variation from RNA to protein
Battle, A., Khan, Z., Wang, S. H., Mitrano, A., Ford, M. J., Pritchard, J. K., & Gilad, Y. (2015) · Science · doi:10.1126/science.1260793 · Cited by 471 · see citing works
Matrix eQTL: Ultra fast eQTL analysis via large matrix operationsPreprint
Shabalin, A. A. (2011) · arXiv (Cornell University) · doi:10.17615/g28n-r219 · Cited by 452 · see citing works
Identification of context-dependent expression quantitative trait loci in whole blood
Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van 't Hof, P., Mei, H., van Dijk, F., Westra, H.-J., et al. (2017) · Nature Genetics · doi:10.1038/ng.3737 · Cited by 441 · see citing works
Nica, A. C., Montgomery, S. B., Dimas, A. S., Stranger, B. E., Beazley, C., Barroso, I., & Dermitzakis, E. T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000895 · Cited by 423 · see citing works
Netherlands Twin Register: From Twins to Twin Families
Boomsma, D. I., de Geus, E. J. C., Vink, J. M., Stubbe, J. H., Distel, M. A., Hottenga, J., Danielle Posthuma, B., van Beijsterveldt, T. C. E. M., Hudziak, J. J., Bartels, M., et al. (2006) · Twin Research and Human Genetics · doi:10.1375/183242706779462426 · Cited by 401 · see citing works
Heritability and genomics of gene expression in peripheral blood
Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362 · see citing works
Self-citationPaşaniuc, B., & Zaitlen, N. (2013) · eScholarship (California Digital Library) · Cited by 362 · see citing works
Fehrmann, R. S. N., Jansen, R. C., Veldink, J. H., Westra, H.-J., Arends, D., Bonder, M. J., Fu, J., Deelen, P., Groen, H. J. M., Smolonska, A., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002197 · Cited by 330 · see citing works
den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J. J. M., Peal, D. S., Evans, D. M., Nolte, I. M., Segrè, A. V., Hólm, H., Handsaker, R. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2610 · Cited by 296 · see citing works
Genome-Wide Complex Trait Analysis (GCTA): Methods, Data Analyses, and Interpretations
Yang, J., Lee, S., Goddard, M. E., & Visscher, P. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-447-0_9 · Cited by 236 · see citing works
Fu, J., Wolfs, M. G. M., Deelen, P., Westra, H.-J., Fehrmann, R. S. N., Meerman, G. J. T., Buurman, W. A., Rensen, S. S., Groen, H. J. M., Weersma, R. K., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002431 · Cited by 216 · see citing works
Draisma, H. H. M., Pool, R., Kobl, M., Jansen, R., Petersen, A.-K., Vaarhorst, A. A. M., Yet, İ., Haller, T., Demirkan, A., Esko, T., et al. (2015) · Nature Communications · doi:10.1038/ncomms8208 · Cited by 196 · see citing works
Sex differences in the human peripheral blood transcriptome
Jansen, R., Batista, S., Brooks, A. I., Tischfield, J. A., Willemsen, G. A. H. M., van Grootheest, G., Hottenga, J., Milaneschi, Y., Mbarek, H., Madar, V., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-33 · Cited by 166 · see citing works
Statistics requantitates the central dogma
Li, J. J., & Biggin, M. D. (2015) · Science · doi:10.1126/science.aaa8332 · Cited by 164 · see citing works
Boomsma, D. I., Willemsen, G. A. H. M., Sullivan, P. F., Heutink, P., Meijer, P., Sondervan, D., Kluft, C., Smit, G., Nolen, W. A., Zitman, F. G., et al. (2008) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201979 · Cited by 154 · see citing works
Population structure, migration, and diversifying selection in the Netherlands
Abdellaoui, A., Hottenga, J., de Knijff, P., Nivard, M. G., Xiao, X., Scheet, P. A., Brooks, A. I., Ehli, E. A., Hu, Y., Davies, G. E., et al. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.48 · Cited by 149 · see citing works
Statistical Testing of Shared Genetic Control for Potentially Related Traits
Wallace, C. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21765 · Cited by 115 · see citing works
Cousminer, D. L., Stergiakouli, E., Berry, D. J., Ang, W., Groen‐Blokhuis, M. M., Körner, A., Siitonen, N., Ντάλλα, Ι., Marinelli, M., Perry, J. R. B., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu150 · Cited by 92 · see citing works
A meta-analysis of gene expression quantitative trait loci in brain
Kim, Y., Xia, K., Tao, R., Giusti-Rodriguez, P., Vladimirov, V, van den Oord, E., & Sullivan, P. F. (2014) · Translational Psychiatry · doi:10.1038/tp.2014.96 · Cited by 73 · see citing works
Further confirmation of the association between anxiety and CTNND2 : replication in humans
Nivard, M. G., Mbarek, H., Hottenga, J., Smit, J. H., Jansen, R., Penninx, B. W. J. H., Middeldorp, C. M., & Boomsma, D. I. (2013) · Genes Brain & Behavior · doi:10.1111/gbb.12095 · Cited by 45 · see citing works
Vaez, A., Jansen, R., Prins, B. P., Hottenga, J., de Geus, E. J. C., Boomsma, D. I., Penninx, B. W. J. H., Nolte, I. M., Snieder, H., & Alizadeh, B. Z. (2015) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.114.000714 · Cited by 27 · see citing works
RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses
Ma, B., Huang, J. J., & Liang, L. (2014) · Database · doi:10.1093/database/bau066 · Cited by 8 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The GTEx Consortium atlas of genetic regulatory effects across human tissues
The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science · doi:10.1126/science.aaz1776 · Cited by 5,547 · see citing works
eQTLGen, Wray, N. R., 23andMe, the Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Ripke, S., Mattheisen, M., Trzaskowski, M., Byrne, E. M., Abdellaoui, A., Adams, M. J., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0090-3 · Cited by 3,005 · see citing works
Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Yazar, S., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00913-z · Cited by 2,607 · see citing works
Microglia in Alzheimer’s disease
Hansen, D. V., Hanson, J. E., & Sheng, M. (2018) · Journal of Cell Biology · doi:10.1083/jcb.201709069 · Cited by 1,935 · see citing works
“TREM2-deficient microglia fail to congregate or proliferate around plaques, lack the typical morphological changes of microglial activation, and show increased apoptosis (Jay et al., 2015; Wang et al., 2015, 2016; Mazaheri et al., 2017).”
Backgroundvan der Harst, P., & Verweij, N. (2018) · Circulation Research · doi:10.1161/circresaha.117.312086 · Cited by 1,141 · see citing works
Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Kasela, S., et al. (2018) · doi:10.1101/447367 · Cited by 2,607 · see citing works
Self-citationShrine, N. R. G., Guyatt, A. L., Erzurumluoglu, A. M., Jackson, V. E., Hobbs, B. D., Melbourne, C., Batini, C., Fawcett, K. A., Song, K. S., Sakornsakolpat, P., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0321-7 · Cited by 539 · see citing works
The GTEx Consortium atlas of genetic regulatory effects across human tissuesPreprint
Aguet, F., Barbeira, A., Bonazzola, R., Brown, A. A., Castel, S. E., Jo, B., Kasela, S., Kim-Hellmuth, S., Liang, Y., Oliva, M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/787903 · Cited by 379 · see citing works
HIPSCI Consortium, Alasoo, K., Rodrigues, J., Mukhopadhyay, S., Knights, A. J., Mann, A. L., Kundu, K., Hale, C., Dougan, G., & Gaffney, D. J. (2018) · Nature Genetics · doi:10.1038/s41588-018-0046-7 · Cited by 338 · see citing works
Genome-wide association study of susceptibility to idiopathic pulmonary fibrosis
Allen, R. J., Guillen-Guio, B., Oldham, J. M., Ma, S.-F., Dressen, A., Paynton, M. L., Kraven, L. M., Obeidat, M., Li, X., Ng, M., et al. (2020) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201905-1017oc · Cited by 329 · see citing works
Multivariate genome-wide analyses of the well-being spectrum
BIOS consortium, Baselmans, B. M. L., Social Science Genetic Association Consortium, Jansen, R., Ip, H. F., van Dongen, J., Abdellaoui, A., van de Weijer, M. P., Bao, Y., Smart, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0320-8 · Cited by 320 · see citing works
Self-citationA genome-wide association study of serum proteins reveals shared loci with common diseases
Guðjónsson, A., Guðmundsdóttir, V., Axelsson, G. T., Gudmundsson, E. F., Jonsson, B. G., Launer, L. J., Lamb, J. R., Jennings, L. L., Aspelund, T., Emilsson, V., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27850-z · Cited by 276 · see citing works
The genetics of asthma and the promise of genomics-guided drug target discovery
Elhusseini, Z. W., Gosens, R., Dekker, F. J., & Koppelman, G. H. (2020) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(20)30363-5 · Cited by 162 · see citing works
Microglial inflammation and phagocytosis in Alzheimer's disease: Potential therapeutic targets
Nizami, S., Hall‐Roberts, H., Warrier, S., Cowley, S. A., & Di Daniel, E. (2019) · British Journal of Pharmacology · doi:10.1111/bph.14618 · Cited by 147 · see citing works
Dobbyn, A. L., Huckins, L. M., Boocock, J., Sloofman, L. G., Glicksberg, B. S., Giambartolomei, C., Hoffman, G. E., Perumal, T. M., Girdhar, K., Jiang, Y., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.04.011 · Cited by 142 · see citing works
Power, false discovery rate and Winner’s Curse in eQTL studies
Huang, Q. Q., Ritchie, S. C., Brożyńska, M., & Inouye, M. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky780 · Cited by 137 · see citing works
An integrative study of five biological clocks in somatic and mental health
Jansen, R., Han, L. K., Verhoeven, J. E., Aberg, K. A., van den Oord, E. C., Milaneschi, Y., & Penninx, B. W. (2021) · eLife · doi:10.7554/elife.59479 · Cited by 127 · see citing works
Overlap of Genetic Risk between Interstitial Lung Abnormalities and Idiopathic Pulmonary Fibrosis
Hobbs, B. D., Putman, R. K., Araki, T., Nishino, M., Guðmundsson, G., Gudnason, V. G., Eiríksdóttir, G., Zilhäo, N. R., Dupuis, J., Xu, H., et al. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201903-0511oc · Cited by 115 · see citing works
Deciphering the Emerging Complexities of Molecular Mechanisms at GWAS Loci
Cannon, M. E., & Mohlke, K. L. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.10.001 · Cited by 109 · see citing works
Neavin, D. R., Nguyen, Q. H., Daniszewski, M., Liang, H. H., Chiu, H. S., Wee, Y. K., Senabouth, A., Lukowski, S. W., Crombie, D. E., Lidgerwood, G. E., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02293-3 · Cited by 104 · see citing works
study, T. A. I. B. A. L., Nabais, M. F., Initiative, T. A. D. N., Laws, S. M., Lin, T., Vallerga, C. L., Armstrong, N. J., Blair, I. P., Kwok, J. B., Mather, K. A., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02275-5 · Cited by 99 · see citing works
Zeng, B., Bendl, J. M., Kosoy, R., Fullard, J. F., Hoffman, G. E., & Roussos, P. (2022) · Nature Genetics · doi:10.1038/s41588-021-00987-9 · Cited by 89 · see citing works
Widespread Allelic Heterogeneity in Complex Traits
Hormozdiari, F., Zhu, A., Kichaev, G., Ju, C. J. ‐., Segrè, A. V., Joo, J. W. J., Won, H., Sankararaman, S., Paşaniuc, B., Shifman, S., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.04.005 · Cited by 87 · see citing works
Verweij, N., van de Vegte, Y. J., & van der Harst, P. (2018) · Nature Communications · doi:10.1038/s41467-018-03395-6 · Cited by 84 · see citing works
Shang, L., Smith, J. A., Zhao, W., Kho, M., Turner, S. T., Mosley, T. H., Kardia, S. L. R., & Zhou, X. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.03.002 · Cited by 76 · see citing works
Raulerson, C. K., Ko, A., Kidd, J., Currin, K. W., Brotman, S. M., Cannon, M. E., Wu, Y., Spracklen, C. N., Jackson, A., Stringham, H. M., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.09.001 · Cited by 74 · see citing works
Sources of gene expression variation in a globally diverse human cohort
Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Yan, S. M., Wojcik, G. L., Battle, A. J., & McCoy, R. C. (2024) · Nature · doi:10.1038/s41586-024-07708-2 · Cited by 79 · see citing works
Genetic influences on susceptibility to rheumatoid arthritis in African-Americans
Laufer, V. A., Tiwari, H. K., Reynolds, R. J., Danila, M. I., Wang, J., Edberg, J. C., Kimberly, R. P., Kottyan, L. C., Harley, J. B., Mikuls, T. R., et al. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy395 · Cited by 78 · see citing works
Ortiz‐Fernández, L., Saruhan‐Direskeneli, G., Alıbaz-Öner, F., Kaymaz‐Tahra, S., Coit, P., Kong, X., Kiprianos, A. P., Maughan, R. T., Aydın, S. Z., Aksu, K., et al. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.11.014 · Cited by 75 · see citing works
Shared genetic risk factors and causal association between psoriasis and coronary artery disease
Patrick, M. T., Li, Q., Wasikowski, R., Mehta, N. N., Gudjonsson, J. E., Elder, J. T., Zhou, X., & Tsoi, L. C. (2022) · Nature Communications · doi:10.1038/s41467-022-34323-4 · Cited by 75 · see citing works
Genetic heterogeneity: Challenges, impacts, and methods through an associative lens
Woodward, A., Urbanowicz, R. J., Naj, A. C., & Moore, J. H. (2022) · Genetic Epidemiology · doi:10.1002/gepi.22497 · Cited by 69 · see citing works
Mitra, S., Malik, R., Wong, W., Rahman, A., Hartemink, A. J., Pritykin, Y., Dey, K. K., & Leslie, C. S. (2024) · Nature Genetics · doi:10.1038/s41588-024-01689-8 · Cited by 67 · see citing works
A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine
Ye, Y., Zhang, Z., Liu, Y., Diao, L., & Han, L. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.01.009 · Cited by 64 · see citing works
Xu, Y., Au, N. P. B., & Ma, C. H. E. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.896852 · Cited by 63 · see citing works
Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis
Aygün, N., Elwell, A. L., Liang, D., Lafferty, M. J., Cheek, K. E., Courtney, K. P., Mory, J. T., Hadden-Ford, E., Krupa, O., de la Torre-Ubieta, L., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.07.011 · Cited by 54 · see citing works
Wu, Y., Broadaway, K. A., Raulerson, C. K., Scott, L. J., Pan, C., Ko, A., He, A., Tilford, C. A., Fuchsberger, C., Locke, A. E., et al. (2019) · Human Molecular Genetics · doi:10.1093/hmg/ddz263 · Cited by 52 · see citing works
Patrick, M. T., Stuart, P. E., Zhang, H., Zhao, Q., Yin, X., He, K., Zhou, S., Mehta, N. N., Voorhees, J. J., Boehnke, M., et al. (2020) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2020.11.025 · Cited by 56 · see citing works
Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs
van Dongen, J., Ehli, E. A., Jansen, R., van Beijsterveldt, C. E. M., Willemsen, G. A. H. M., Hottenga, J., Kallsen, N. A., Peyton, S. A., Breeze, C. E., Kluft, C., et al. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0225-x · Cited by 55 · see citing works
Zhang, P., Kitchen-Smith, I., Xiong, L., Stracquadanio, G., Brown, K. A., Richter, P., Wallace, M. D., Bond, E. E., Sahgal, N., Moore, S., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-20-0177 · Cited by 45 · see citing works
Zolotareva, O. I., Saik, O. V., Königs, C., Bragina, E. Y., Goncharova, I. A., Freidin, M. B., Dosenko, V., Иванисенко, В. А., & Hofestädt, R. (2019) · Scientific Reports · doi:10.1038/s41598-019-52762-w · Cited by 50 · see citing works
Shang, L., Zhao, W., Wang, Y.-Z., Li, Z., Choi, J. J., Kho, M., Mosley, T. H., Kardia, S. L. R., Smith, J. A., & Zhou, X. (2023) · Nature Communications · doi:10.1038/s41467-023-37961-4 · Cited by 47 · see citing works
Zhu, A., Matoba, N., Wilson, E., Tapia, A. L., Li, Y., Ibrahim, J. G., Stein, J. L., & Love, M. I. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009455 · Cited by 32 · see citing works
Arthur, T. D., Nguyen, J., Henson, B. A., D’Antonio‐Chronowska, A., Jaureguy, J., Silva, N., Arias, A. D., Benaglio, P., Berggren, W. T., Borja, V., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100775 · Cited by 39 · see citing works
Leveraging allelic imbalance to refine fine-mapping for eQTL studies
Zou, J., Hormozdiari, F., Jew, B., Castel, S. E., Lappalainen, T., Ernst, J., Sul, J. H., & Eskin, E. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008481 · Cited by 39 · see citing works
Evidence for DNA Methylation Mediating Genetic Liability to Non-Syndromic Cleft Lip/Palate
Howe, L. J., Richardson, T. G., Arathimos, R., Alvizi, L., Passos‐Bueno, M. R., Stanier, P., Nohr, E. A., Ludwig, K. U., Mangold, E., Knapp, M., et al. (2019) · Epigenomics · doi:10.2217/epi-2018-0091 · Cited by 37 · see citing works
Sieberts, S. K., & Schadt, E. E. (2019) · Wiley eBooks · doi:10.1002/9781119487845.ch25 · Cited by 37 · see citing works
Kunkle, B., Grenier-Boley, B., Sims, R., Bis, J., Naj, A., Boland, A., Vronskaya, M., van der Lee, S., Amlie-Wolf, A., Bellenguez, C., et al. (2018) · doi:10.1101/294629 · Cited by 35 · see citing works
Aberrant RNA Splicing Is a Primary Link between Genetic Variation and Pancreatic Cancer Risk
Tian, J., Chen, C., Rao, M., Zhang, M., Lu, Z., Cai, Y., Ying, P., Li, B., Wang, H., Wang, L., et al. (2022) · Cancer Research · doi:10.1158/0008-5472.can-21-4367 · Cited by 29 · see citing works
Baranski, T., Kraja, A. T., Fink, J. L., Feitosa, M. F., Lenzini, P. A., Borecki, I. B., Liu, C., Cupples, L. A., North, K. E., & Province, M. A. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007222 · Cited by 32 · see citing works
Discovery of novel hepatocyte eQTLs in African Americans
Zhong, Y., De, T., Alarcón, C., Park, C. S., Lec, B., & Perera, M. A. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008662 · Cited by 28 · see citing works
Qi, G.-H., Strober, B., Popp, J. M., Keener, R., Ji, H., & Battle, A. (2022) · bioRxiv · doi:10.1038/s41467-023-42016-9 · Cited by 29 · see citing works
Lin, B. D., Carnero‐Montoro, E., Bell, J. T., Boomsma, D. I., de Geus, E. J. C., Jansen, R., Kluft, C., Mangino, M., Penninx, B. W. J. H., Spector, T. D., et al. (2017) · Journal of Human Genetics · doi:10.1038/jhg.2017.76 · Cited by 31 · see citing works
Ortiz‐Fernández, L., Carmona, F. D., López-Mejías, R., González‐Escribano, M. F., Lyons, P., Morgan, A. W., Sawalha, A. H., Merkel, P. A., Smith, K. G. C., González-Gay, M. Á., et al. (2018) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2017-212372 · Cited by 30 · see citing works
Gene Interactions in Human Disease Studies—Evidence Is Mounting
Singhal, P., Verma, S. S., & Ritchie, M. D. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-102022-120818 · Cited by 26 · see citing works
Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas
Khan, R. R., Guerrero, R. F., Wapner, R. J., Hahn, M. W., Raja, A., Salleb-Aouissi, A., Grobman, W. A., Simhan, H. N., Silver, R. M., Chung, J. M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-61218-9 · Cited by 25 · see citing works
Lin, J. J., & Musunuru, K. (2018) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.117.001946 · Cited by 26 · see citing works
Hou, R., Cole, S. A., Graff, M., Haack, K., Laston, S., Comuzzie, A. G., Mehta, N. R., Ryan, K. A., Cousminer, D. L., Zemel, B. S., et al. (2019) · Bone · doi:10.1016/j.bone.2019.115175 · Cited by 25 · see citing works
New role of fat-free mass in cancer risk linked with genetic predisposition
Harris, B. H. L., Di Giovannantonio, M., Zhang, P., Harris, D. A., Lord, S. R., Allen, N. E., Maughan, T. S., Bryant, R. J., Harris, A. L., Bond, G. L., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-54291-7 · Cited by 24 · see citing works
Fine-mapping causal tissues and genes at disease-associated loci
Strober, B. J., Zhang, M. J., Amariuta, T., Rossen, J., & Price, A. L. (2025) · Nature Genetics · doi:10.1038/s41588-024-01994-2 · Cited by 22 · see citing works
Brotman, S. M., Moustafa, J. S. E.-S., Guan, L., Broadaway, K. A., Wang, D., Jackson, A., Welch, R., Currin, K. W., Tomlinson, M., Vadlamudi, S., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-01982-6 · Cited by 24 · see citing works
Danila, M. I., Laufer, V. A., Reynolds, R. J., Yan, Q., Liu, N., Gregersen, P. K., Lee, A., Kern, M., Langefeld, C. D., Arnett, D. K., et al. (2017) · Molecular Medicine · doi:10.2119/molmed.2017.00081 · Cited by 23 · see citing works
From North Asia to South America: Tracing the longest human migration through genomic sequencing
Gusareva, E. S., Ghosh, A. G., Харьков, В. Н., Khor, S., Зарубин, А. А., Moshkov, N., Kalsi, N., Ratan, A., Heinle, C. E., Cooke, N. P., et al. (2025) · Science · doi:10.1126/science.adk5081 · Cited by 22 · see citing works
Lee, T., Lee, H., & Initiative, T. A. D. N. (2021) · Biomedicines · doi:10.3390/biomedicines9111525 · Cited by 22 · see citing works
Jeng, M. Y., Mumbach, M. R., Granja, J. M., Satpathy, A. T., Chang, H. Y., & Chang, A. L. S. (2018) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2018.09.011 · Cited by 21 · see citing works
Limited evidence for blood eQTLs in human sexual dimorphism
Porcu, E., Claringbould, A., Weihs, A., Lepik, K., Richardson, T. G., Völker, U., Santoni, F. A., Teumer, A., Franke, L., Reymond, A., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01088-w · Cited by 20 · see citing works
Tree-based QTL mapping with expected local genetic relatedness matrices
Link, V., Schraiber, J. G., Fan, C., Dinh, B. L., Mancuso, N., Chiang, C. W. K., & Edge, M. D. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.10.017 · Cited by 21 · see citing works
Lee, K.-Y., Leung, K., Ma, S.-L., So, C., Huang, D., Tang, N., & Wong, M. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.01003 · Cited by 20 · see citing works
Heritability and GWAS Studies for Monocyte–Lymphocyte Ratio
Lin, B. D., Willemsen, G. A. H. M., Fedko, I. O., Jansen, R., Penninx, B. W. J. H., de Geus, E. J. C., Kluft, C., Hottenga, J., & Boomsma, D. I. (2017) · Twin Research and Human Genetics · doi:10.1017/thg.2017.3 · Cited by 20 · see citing works
Singh, B., Maiti, G. P., Zhou, X., Fazel‐Najafabadi, M., Bae, S., Sun, C., Terao, C. C., Okada, Y., Chua, K. H., Kochi, Y., et al. (2021) · Arthritis & Rheumatology · doi:10.1002/art.41799 · Cited by 19 · see citing works
Removing unwanted variation between samples in Hi-C experiments
Fletez‐Brant, K., Qiu, Y., Gorkin, D. U., Hu, M., & Hansen, K. D. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae217 · Cited by 18 · see citing works
Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits
Giovannantonio, M. D., Harris, B. H. L., Zhang, P., Kitchen-Smith, I., Xiong, L., Sahgal, N., Stracquadanio, G., Wallace, M. D., Blagden, S. P., Lord, S., et al. (2020) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2019-106799 · Cited by 18 · see citing works
Genetic coupling of enhancer activity and connectivity in gene expression control
Ray-Jones, H. F., Sung, C. K., Chan, L. T., Haglund, A., Artemov, P., Rosa, M. D., Ruje, L., Burden, F., Kreuzhuber, R., Litovskikh, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-55900-3 · Cited by 17 · see citing works
Shan, J., Chouchane, A., Mokrab, Y., Saad, M., Boujassoum, S., Sayaman, R. W., Ziv, E., Bouaouina, N., Remadi, Y., Gabbouj, S., et al. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.01328 · Cited by 17 · see citing works
Lim, L. J., Lim, A. J. W., Ooi, B. N. S., Tan, J. W. L., Koh, E. T., TTSH Rheumatoid Arthritis Study Group, Ang, A. E. L., Chan, G. Y. L., Chan, M. T.-L., Chia, F. L., et al. (2022) · Lara D. Veeken · doi:10.1093/rheumatology/keac032 · Cited by 16 · see citing works
Nguyen, J., Arthur, T. D., Fujita, K., Salgado, B. M., Donovan, M. K. R., Aguiar, L. R., Arias, A. D., Benaglio, P., Berggren, W. T., Belmonte, J. C. I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42560-4 · Cited by 16 · see citing works
Ip, H. F., Jansen, R., Abdellaoui, A., Bartels, M., Boomsma, D. I., & Nivard, M. G. (2018) · Behavior Genetics · doi:10.1007/s10519-018-9914-2 · Cited by 17 · see citing works
Madan, N., Ghazi, A. R., Kong, X., Chen, E. S., Shaw, C. A., & Edelstein, L. C. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008287 · Cited by 16 · see citing works
A powerful and versatile colocalization test
Deng, Y., & Pan, W. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007778 · Cited by 15 · see citing works
Brandt, J., Borgquist, S., Almgren, P., Försti, A., Huss, L., Melander, O., & Manjer, J. (2017) · International Journal of Cancer · doi:10.1002/ijc.31156 · Cited by 15 · see citing works
Alasoo, K., Rodrigues, J., Mukhopadhyay, S., Knights, A. J., Mann, A. L., Kundu, K., Hale, C., Dougan, G., & Gaffney, D. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/102392 · Cited by 15 · see citing works
Vyse, T. J., & Graham, D. S. C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218383 · Cited by 14 · see citing works
A variant in PPP4R3A protects against alzheimer‐related metabolic decline
Christopher, L., Napolioni, V., Khan, R. R., Han, S. S., Greicius, M. D., & Initiative, A. D. N. (2017) · Annals of Neurology · doi:10.1002/ana.25094 · Cited by 14 · see citing works
Yang, D., Chung, T., & Kim, D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac373 · Cited by 13 · see citing works
Rare variants regulate expression of nearby individual genes in multiple tissues
Li, J., Kong, N., Han, B., & Sul, J. H. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009596 · Cited by 13 · see citing works
Mai, H., Chen, J., Chen, H., Liu, Z., Huang, G., Wang, J., Xiao, Q., Ren, W., Zhou, B., Hou, J., et al. (2021) · Journal of Hepatocellular Carcinoma · doi:10.2147/jhc.s321919 · Cited by 11 · see citing works
Jayarathna, D. K., Rentería, M. E., Malik, A., Sauret, E., Batra, J., & Gandhi, N. S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.716236 · Cited by 10 · see citing works
Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease
Yavuz, Ş., Pucholt, P., Sandling, J. K., Bianchi, M., Leonard, D., Bolin, K., Imgenberg‐Kreuz, J., Eloranta, M., Kozyrev, S. V., Lanata, C. M., et al. (2022) · Lupus Science & Medicine · doi:10.1136/lupus-2022-000752 · Cited by 11 · see citing works
Farries, G., Gough, K. F., Parnell, A. C., McGivney, B. A., McGivney, C. L., McGettigan, P., MacHugh, D. E., Katz, L. M., & Hill, E. W. (2019) · Animal Genetics · doi:10.1111/age.12848 · Cited by 11 · see citing works
Brotman, S. M., Moustafa, J. S. E.-S., Guan, L., Broadaway, K. A., Wang, D., Jackson, A., Welch, R., Currin, K. W., Tomlinson, M., Vadlamudi, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.26.563798 · Cited by 11 · see citing works
Prince, C., Mitchell, R. E., & Richardson, T. G. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.10.003 · Cited by 10 · see citing works
Innocenti, F., Jiang, C., Sibley, A. B., Denning, S., Etheridge, A. S., Watson, D. M., Niedzwiecki, D., Hatch, A. J., Hurwitz, H. I., Nixon, A. B., et al. (2019) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000375 · Cited by 10 · see citing works
De, T., Zhang, H., Alarcon, C., Lec, B., Avitia, J., Smithberger, E., Chen, C., Horvath, M., Kwan, S., Young, M., et al. (2021) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000445 · Cited by 9 · see citing works
Wang, X. T., Mo, X., Zhang, H., Zhang, Y., & Shen, Y. (2019) · Current Molecular Medicine · doi:10.2174/1566524019666190828151540 · Cited by 9 · see citing works
Ooi, B. N. S., Raechell, R., Ying, A. F., Koh, Y. Z., Jin, Y., Yee, S. W. L., Lee, J. H. S., Chong, S. S., Tan, J. W. C., Liu, J., et al. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.605764 · Cited by 8 · see citing works
Ramírez-Sánchez, A. D., Zühlke, S., Aguirre‐Gamboa, R., Vochteloo, M., Franke, L., Lundin, K. E. A., Withoff, S., & Jonkers, I. H. (2025) · Genes and Immunity · doi:10.1038/s41435-025-00356-0 · Cited by 7 · see citing works
Simpson, C. E., Griffiths, M., Yang, J., Nies, M., Vaidya, D. M., Brandal, S., Martin, L. J., Pauciulo, M. W., Lutz, K. A., Coleman, A. W., et al. (2022) · ERJ Open Research · doi:10.1183/23120541.00725-2021 · Cited by 6 · see citing works
Effect of all-but-one conditional analysis for eQTL isolation in peripheral blood
Brown, M. A., Greenwood, E., Zeng, B., Powell, J. E., & Gibson, G. C. (2022) · Genetics · doi:10.1093/genetics/iyac162 · Cited by 7 · see citing works
Purdue, M. P., Song, L., Scélo, G., Houlston, R. S., Wu, X., Sakoda, L. C., Thai, K. K., Graff, R. E., Rothman, N., Brennan, P., et al. (2020) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-20-0472 · Cited by 7 · see citing works
Co-localization of Conditional eQTL and GWAS Signatures in SchizophreniaPreprint
Dobbyn, A. L., Huckins, L. M., Boocock, J., Sloofman, L. G., Glicksberg, B. S., Giambartolomei, C., Hoffman, G. E., Perumal, T. M., Girdhar, K., Jiang, Y. P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/129429 · Cited by 7 · see citing works
Pallares, L. F., Melo, D., Wolf, S., Cofer, E. M., Abhyankar, V., Peng, J., & Ayroles, J. F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.20.541576 · Cited by 7 · see citing works
- Authors
- Jansen, R., Hottenga, J.-J., Nivard, M. G., Abdellaoui, A., Laport, B., de Geus, E. J., Wright, F. A., Penninx, B. W. J. H., & Boomsma, D. I.
- Affiliations
- Amsterdam Neuroscience (NL)
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam Public Health, Amsterdam, The Netherlands
- North Carolina State University (US)
- Corresponding author
- Jansen, Rick
- ORCID
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-02-06
- Volume
- 26
- Issue
- 8
- Pages
- 1444-1451
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- PMC
- PMC6075455
- OpenAlex
- W2587589680
- Cited by
- 141
- References
- 38
- Citations by year
- 2026: 5 · 2025: 13 · 2024: 10 · 2023: 12 · 2022: 15 · 2021: 23 · 2020: 17 · 2019: 19 · 2018: 17 · 2017: 10
- FWCI
- 11.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Molecular Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- Pure Amsterdam UMC (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- National Institute of Mental Health (RC2 MH089951)
- Netherlands Organization for Scientific Research (904-61-090, 985-10-002,904-61-193,480-04-004, 400-05-717, 912-100-20;)
- Spinozapremie (56-464-14192)
- Geestkracht program (10-000-1002)
- Neuroscience Campus Amsterdam and the European Science Council (230374)
- BBMRI-NL, NWO (184.021.007)
- 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 › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- expression quantitative trait loci, cis-eQTL, allelic heterogeneity, gene expression regulation, single nucleotide polymorphisms, whole blood gene expression
- MeSH terms
- Alleles, Blood, Gene Expression Regulation, Humans, Phenotype, Genetic Heterogeneity, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Genome-Wide Association Study, Transcriptome
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
