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Conditional eQTL analysis reveals allelic heterogeneity of gene expression
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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.
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“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
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Metadata
- 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
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