The COJO app performs regional conditional and joint association analysis using GCTA-COJO on a harmonised GWAS study.
Use COJO to determine whether an association signal remains after accounting for one or more variants in the same region. This helps identify potentially independent association signals at a locus.
Before you begin
You will need:
- A harmonised GWAS study
- A gene or genomic region to investigate
- A destination project for your results
- Optionally, a list of SNPs to condition on
Name your job
Enter a descriptive name in the Prefix field. This is required.
[Screenshot 1: Red box around the Prefix field.]
For example:
LDL_APOE_COJOCAD_9p21_conditionalBMI_FTO_regional
Select the GWAS study
Use the Study dropdown to select the harmonised GWAS study you want to analyse.
[Screenshot 2: Red box around the Study dropdown.]
COJO runs the regional analysis using association data from this selected study.
Select a gene or genomic region
Enter the target in the Gene or Region field.
[Screenshot 3: Red box around the Gene or Region field.]
You can use this field to focus the analysis on a gene or a defined genomic locus.
Define the regional window
Enter the size of the surrounding area to analyse in Region Window. The default value is 100kb.
[Screenshot 4: Red box around the Region Window field.]
The regional window defines how far around the selected gene or region the analysis should extend. A larger window includes more nearby variants; a smaller window provides a more focused view of the locus.
Optionally condition on selected SNPs
The Condition SNP List is optional. Use it when you want to test the association of regional variants after accounting for one or more known or lead SNPs.
[Screenshot 5: Highlight the Condition SNP List section and its three source options.]
You can provide the SNP list in one of three ways:
- Upload New — Upload a new SNP list from your computer.
- Select Existing — Choose a SNP list already available in the portal.
- From Jobs Output — Use a SNP list generated by a previous job.
Uploaded files must be in .snplist or .txt format and no larger than 1 MB.
[Screenshot 6: Red box around the upload area, including the supported file formats.]
Leave this section blank if you want to run the regional COJO analysis without conditioning on pre-specified SNPs.
Select the LD reference panel
Choose an LD Reference Panel. This is required.
[Screenshot 7: Red box around the LD Reference Panel dropdown, showing the default “auto” selection.]
- Select auto to allow the platform to select a suitable LD panel automatically.
- Select a specific LD panel when your analysis plan requires an explicit reference choice.
Where possible, use an LD reference that is appropriate for the ancestry represented in the GWAS study.
Select a project
Choose a destination project in the Project dropdown. This is required.
[Screenshot 8: Red box around the Project dropdown.]
Your COJO job and output files will be saved to this project.
Launch the analysis
Check your study, region, window, conditioning list, LD reference panel, and project. Then select Launch App.
[Screenshot 9: Red box and arrow pointing to “Launch App”.]
When the job is complete, access the results from the selected project or the job results area.
Tips
- Use COJO when you want to assess whether multiple signals at one locus are independent.
- Start with the default
100kbwindow for a focused locus-level analysis, then increase it if you need broader regional coverage. - Include a condition SNP list when you want to test whether additional variants remain associated after adjusting for an established lead signal.
- Ensure the LD reference panel is appropriate for the study population, as LD patterns differ across ancestries.