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Abundant associations with gene expression complicate GWAS follow-up

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Fig. 1: Distinguishing candidates from false-positive genes by using LocusCompare.

Data availability

A bash script to download all GWAS datasets is available at GTEx eQTL data can be accessed via Data for coronary artery smooth muscle cells are available at Data for retinal pigment epithelium cells are available at Methylation QTL data for brain and blood are available at

Code availability

LocusCompare is hosted at and is also available as open source software at LocusCompareR is open source and is available at Our pipeline for running colocalization tests is available at The LocusCompareR package was built with R version 3.2.3.


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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.

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Authors and Affiliations



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

Correspondence to Boxiang Liu or Stephen B. Montgomery.

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Competing interests

S.B.M. is on the SAB of Prime Genomics.

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Supplementary Information

Supplementary Methods and Supplementary Figs. 1–6

Reporting Summary

Supplementary Tables 1 and 2

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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).

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