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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.
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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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