Issue uploading chrX QTL summary statistics in FUMA QTLs Analysis (Job ID: 756646 and 756359)

[Wu Bangsheng]

Dear FUMA team,

I am trying to perform a QTLs Analysis in FUMA using GWAS summary statistics from a chrX locus, but the upload jobs have repeatedly failed. I have tried different chromosome annotations (using both "X" and "23"), but neither format resolved the issue.

The job IDs are:

• 756646
• 756359

The input file is based on the GRCh38 genome build and contains summary statistics only for a specific chrX locus (i.e., variants within a defined start and end position range), rather than genome-wide summary statistics.

The first few lines of my input file are shown below:

CHR POS REF ALT N BETA P MAF
23 19565353 T C 839901 0.0166 0.6501 0.003
23 19827963 G A 839901 -0.0142 0.2166 0.0292
23 20686705 T A 839901 -0.0089 0.257 0.0641
23 19713204 A G 839901 0.04 0.6588 0.0035
23 20036305 T C 839901 -0.0568 0.3927 0.0011
23 20897841 A T 839901 -0.0049 0.5816 0.0478
23 19175401 T C 839901 0.0167 0.6222 0.0038
23 20858810 C T 839901 0.1171 0.05542 0.0012
23 20373305 A G 839901 0.0191 0.4304 0.0075

For the analysis settings, I selected:

• Perform colocalization analysis
• Perform LAVA analysis

I would like to ask:

1. Does FUMA currently support chrX QTL/GWAS summary statistics for QTLs Analysis?
2. Should chrX variants be encoded as "X" or "23" in the CHR column for GRCh38 data?
3. Are there any additional required columns or formatting requirements for chrX data, especially when performing colocalization and LAVA analyses?

Thank you very much for your help. I would appreciate any suggestions on how to correctly format the input file or configure the analysis.

Best regards,

Bangsheng

[Tanya Phung]

Hi Bangsheng, 

Currently only the autosomes are supported for this analysis: 



Best,
Tanya