Single Locus

Overview

The Single Locus mode allows you to select two studies (e.g. an eQTL and a GWAS study) and a single region to create an interactive LocusCompare plot.

Usage

1. Select the first study with the Study Name drop-down menu. Note: you can type to search for the study. You can also choose to upload your own study by clicking on the Browse button. Your file should have 2 columns: a rsid and a pval column. An example file can be downloaded through Example file link.

2. Once a study has been selected, the Trait drop-down menu will update according to the study. Select a trait from the drop-down menu. Most studies have one trait while some studies have multiple traits. If you choose to upload a custom study, you will need to type in an axis label.

3. Repeat Steps 1-2 for study 2.

4. Specify a genomic region in one of the three ways.

   • Reference SNP and flanking window size
   • Reference gene and flanking window size
   • Chromosome, start, and end.

   The flanking window size will be extended in both directions. For instance, if you use a reference SNP and 100 Kb, a 100 Kb window towards both direction from the reference SNP will be plotted. If you use a reference gene, the TSS will be used as the center. Note: you should choose only one of the three options.

5. Click plot.

Now, you will be taken to the LocusCompare page. If you would like to know more on how to interact with the LocusCompare plots, click here.