Losing two lead SNP in result table

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chang cheng

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Dec 7, 2024, 11:37:10 PM12/7/24

to FUMA GWAS users

Dear FUMA team,

I have a recent job ( 564645 ). There are 12 lead SNPs in my input file . 8:21583792_TATTA_T and rs769102116 were missing from the results even if I include MHC region. I also checked other resources and found that these variants exist in gnomAD database.

The entire GWAS summary data was in job 561301.

Could you help me understand why this happens and how to solve this?

Thank you very much.

Tanya Phung

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Dec 8, 2024, 3:38:37 PM12/8/24

to FUMA GWAS users

Hello,

Previously there was a similar question, and it was already answered there:

https://groups.google.com/g/fuma-gwas-users/c/NuJEn_6xWIw/m/oVOnWTGhAgAJ

FUMA uses a reference panel to filter data. Because both of your SNP do not exist in the FUMA database it it not considered. Currently there is not a solution for this in FUMA.

We shared the reference data for the 1000G dataset in the Download tab on FUMA:
https://fuma.ctglab.nl/downloadPage

So you can check if your variant is present in the reference. However, you selected UKB dataset and it is not available to be shared due to data restriction.