LocusFocus: A Colocalization Tool to Prioritize Genes and Tissues from GWAS and eQTL Integration

You may upload up to 3 files:

.txt or .tsv (required): tab-separated primary summary statistics (eg. GWAS)
.ld (optional): PLINK-generated LD matrix -- must have the same number of SNPs as primary file
.html (optional): Secondary datasets to test colocalization. Each data table must be preceded by an <h3> title tag describing the table

Refer to the documentation on how to generate the HTML file.
You may use the merge_and_convert_to_html.py script, or merge_and_convert_to_html_coloc2.py.
You may use provided sample datasets as a guide to formatting your files.

File size limit is 500 MB for all 3 files

Marker Column Name:

Use marker ID column to infer variant position and alleles

Chromosome Column Name:

Position Column Name:

Reference Allele Column Name:

Alternate Allele Column Name:

Add required inputs for COLOC2

Coordinates

Lead Marker Name:

Coordinates:

Select GTEx (V7) Tissues

Select Genes (enter coordinates above to populate)

Stage one set-based p-value threshold

LocusFocus