LocusCompare

Interactively visualize the colocalization of two association datasets (e.g. a GWAS and an eQTL) at a single locus.

LocusCompare

Introduction

LocusCompare is an interactive tool for visualizing the colocalization of two genetic association datasets (for example, a GWAS and an eQTL) at a single locus. Upload two sets of summary statistics, choose a region by SNP, gene, or coordinate, and explore the shared association signal with a LocusCompare scatter plot and two LocusZoom panels, colored by linkage disequilibrium (1000 Genomes Phase 3).

Plots are produced by the locuscomparer R package.

Looking for genome-wide colocalization?

For an ensemble of colocalization, TWAS, and Mendelian randomization methods across hundreds of pre-loaded eQTL datasets, see LocusCompare2.

The LocusCompare family

Citation

Liu B, Gloudemans MJ, Rao AS, Ingelsson E, Montgomery SB. Abundant associations with gene expression complicate GWAS follow-up. Nature Genetics (2019).

License

GPL v3 or later

Developers

Boxiang Liu, Mike Gloudemans, Abhiram Rao, Stephen Montgomery

Upload two association datasets

Each file must be tab- or comma-delimited with two columns: rsid and pval .

Study 1

Study 2

Select a region (maximum window = 1Mb)

SNP

Or Gene

Or Coordinate




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


SNP information


                  
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LD SNPs