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LocusCompare: Visualizing the colocalization of association summary statistics


LocusCompare is a suite of tools and datasets to visualize the colocalization of summary statistics from pairs of association datasets (e.g. GWAS and eQTL). These tools and datasets include:

  • Colocalization statistics between more than 200 GWAS and 48 GTEx (version 7) tissues
  • Interactive LocusCompare plot to visualize a single locus
  • Bash script to download summary statistics of more than 200 GWAS


For instructions please follow these links:

To download stand-alone version:


GPL v3 or later


  • Boxiang Liu (author, maintainer)
  • Mike Gloudemans (author, maintainer)
  • Abhiram Rao (author)
  • Stephen Montgomery (author)


If you use locuscompare, please cite the following paper:

Boxiang Liu, Michael J. Gloudemans, Abhiram S. Rao, Erik Ingelsson & Stephen B. Montgomery (2019) Abundant associations with gene expression complicate GWAS follow-up, Nature Genetics

Select Studies

Select GWAS

Select eQTL



Select Studies

Study 1

Select Published

Or Upload

Study 2

Select Published

Or Upload

Select a region (maximum window = 1Mb)


Or Gene

Or Coordinate


[INSTRUCTIONS] 1. Click on a point to select the corresponding SNP; 2. Drag and double-click on plots on the right-hand side to zoom in; 3. Double-click again to zoom out.

SNP information


Download options



Downloading GWAS and QTL datasets

LocusCompare current hosts more than 200 GWAS datasets and 48 eQTL datasets. We provide a convenient bash script for you to download these data.

Link to bash script:


We are grateful to the individuals and organizations who have made their data publically available. Below is a list of studies we included in LocusCompare. If we missed a reference to your study, please email Boxiang Liu <> or Mike Gloudemans <>.

Share your study

Current GWAS datasets are distributed across various websites, making them difficult to find and download. LocusCompare provides a platform for sharing GWAS and QTL datasets. If you would like to contribute your data to LocusCompare, please fill out the following form. Alternatively, you can email Boxiang Liu or Mike Gloudemans to add your study. (* = mandatory)

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