This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Investigating potential biomarkers of acute pancreatitis in patients with a BMI>30 using Mendelian randomization and transcriptomic analysis
Lipids in Health and Disease Open Access 22 April 2024
-
Integrative multi-omics analysis identifies genetically supported druggable targets and immune cell specificity for myasthenia gravis
Journal of Translational Medicine Open Access 24 March 2024
-
Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation
Nature Communications Open Access 18 March 2024
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Data availability
A bash script to download all GWAS datasets is available at https://github.com/mikegloudemans/gwas-download. GTEx eQTL data can be accessed via https://gtexportal.org/home/datasets. Data for coronary artery smooth muscle cells are available at https://stanford.app.box.com/s/e6e8hyft5u7wix1nzg5mjfqa084c4tin. Data for retinal pigment epithelium cells are available at https://stanford.box.com/s/asrxy0o66xxe1j7mfj56p3z3d405gijj. Methylation QTL data for brain and blood are available at https://cnsgenomics.com/software/smr/#DataResource.
Code availability
LocusCompare is hosted at http://locuscompare.com and is also available as open source software at https://github.com/boxiangliu/locuscompare. LocusCompareR is open source and is available at https://github.com/boxiangliu/locuscomparer. Our pipeline for running colocalization tests is available at https://bitbucket.org/mgloud/production_coloc_pipeline/. The LocusCompareR package was built with R version 3.2.3.
References
MacArthur, J. et al. Nucleic Acids Res. 45, D896–D901 (2017).
Farh, K. K.-H. et al. Nature 518, 337–343 (2015).
Battle, A., Brown, C. D., Engelhardt, B. E. & Montgomery, S. B. Nature 550, 204–213 (2017).
Zhao, W. et al. Nat. Genet. 49, 1450–1457 (2017).
Nica, A. C. et al. PLoS Genet. 6, e1000895 (2010).
Hormozdiari, F. et al. Am. J. Hum. Genet. 99, 1245–1260 (2016).
Zhu, Z. et al. Nat. Genet. 48, 481–487 (2016).
Giambartolomei, C. et al. PLoS Genet. 10, e1004383 (2014).
Liu, B. et al. Am. J. Hum. Genet. 103, 377–388 (2018).
Liu, B. et al. Preprint at bioRxiv https://doi.org/10.1101/446799 (2018).
Qi, T. et al. Nat. Commun. 9, 2282 (2018).
Hannon, E. et al. Nat. Neurosci. 19, 48–54 (2016).
McRae, A. F. et al. Sci. Rep. 8, 17605 (2018).
Pruim, R. J. et al. Bioinformatics 26, 2336–2337 (2010).
Benner, C. et al. Bioinformatics 32, 1493–1501 (2016).
Acknowledgements
B.L. is supported by the Stanford Center for Evolution and Human Genomics fellowship and National Key R&D Program of China, 2016YFD0400800 and Baidu Research. M.J.G. is funded by NLM training grant T15 LM 007033 and a Stanford Graduate Fellowship. E.I. is supported by R01DK106236. S.B.M. is supported by R33HL120757 (NHLBI), U01HG009431 (NHGRI; ENCODE4), R01MH101814 (NIH Common Fund; GTEx Program), R01HG008150 (NHGRI; Non-Coding Variants Program), R01HL142015 (NHLBI; TOPMED), U01HG009080 (NHGRI; GSPAC) and the Edward Mallinckrodt Jr. Foundation. We acknowledge A. Shcherbina for support in this project and N. Cyr for support with graphical illustration.
Author information
Authors and Affiliations
Contributions
B.L. and S.B.M. designed the study. B.L., M.J.G. and A.S.R. performed analyses. E.I. provided study support and feedback. B.L., M.J.G. and S.B.M. wrote the paper. B.L. and M.J.G. contributed equally to this work.
Corresponding authors
Ethics declarations
Competing interests
S.B.M. is on the SAB of Prime Genomics.
Supplementary information
Supplementary Information
Supplementary Methods and Supplementary Figs. 1–6
Rights and permissions
About this article
Cite this article
Liu, B., Gloudemans, M.J., Rao, A.S. et al. Abundant associations with gene expression complicate GWAS follow-up. Nat Genet 51, 768–769 (2019). https://doi.org/10.1038/s41588-019-0404-0
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41588-019-0404-0
This article is cited by
-
Sex-biased genetic regulation of inflammatory proteins in the Dutch population
BMC Genomics (2024)
-
Integrative multi-omics analysis identifies genetically supported druggable targets and immune cell specificity for myasthenia gravis
Journal of Translational Medicine (2024)
-
Investigating potential biomarkers of acute pancreatitis in patients with a BMI>30 using Mendelian randomization and transcriptomic analysis
Lipids in Health and Disease (2024)
-
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits
Nature Genetics (2024)
-
Integration of multi-omics summary data reveals the role of N6-methyladenosine in neuropsychiatric disorders
Molecular Psychiatry (2024)