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

Set-based Test

Upload a summary statistics dataset (eg. GWAS) to perform a simple set-based test. Results will include the P-value from the test.

You may provide your own LD matrix, so long as it is the same length as your provided dataset. If no LD matrix is provided, LocusFocus will generate one for you given your dataset and a selected population from the 1000 Genomes datasets.

Select coordinate system

Select files to upload

You must upload 1 file:

One of (.txt, .tsv) (required): Summary statistics file to perform set-based test (eg. GWAS). .txt files will be interpreted the same as .tsv files.
.ld (optional): PLINK-generated LD matrix with your dataset(s). LD matrix length must be equal your dataset length.

File size limit is 500 MB total for 2 files

Marker Column Name:

Chromosome Column Name:

Position Column Name:

P-value Column Name:

Coordinate Region(s)

Specify one or more regions in your dataset

Please specify your region(s) of interest here with the following format: {CHROM}:{START}-{END} Each region must be typed on a separate line as shown.

If no LD is provided, LocusFocus will generate an LD matrix for each provided region, and regions within 2 Mbps of each other will be combined. Regions may not be greater than 2,000,000 BPs in size.

If no regions are provided, LocusFocus will infer the regions from the provided GWAS dataset (1 region per chromosome in dataset).

SNPs that are outside of these regions will be removed before LD calculation and before the set-based test.
More information: Set-based test documentation

Run separate tests for each region?

Set-based Test

Select coordinate system

Select files to upload

Specify one or more regions in your dataset

Select Populations for LD

By hitting submit, you understand that you are uploading your dataset to a public server