Re: maximum distance for positional mapping

[Tanya Phung]

Hi Karen, 

What is your FUMA jobID? 
Could you also please be more specific about the issue? For example, from which file do you see that your variant of interest is mapped to which gene? 

Thank you,
Tanya

On Tuesday, April 1, 2025 at 2:08:40 PM UTC+2 Alcohol-BP wrote:

Hi - I am selecting 500kb as my maximum distance for positional mapping under 3.1 Gene Mapping, but when I look at the genes that are selected, many of them appear to be >500KB from my SNP.  I am only including a small number of SNPs in my FUMA run, and there is one (and only one) IndSigSNP per locus in my input file.

For example, when I am using rs3820201 at chr1:53115998, I am getting a long list of genes >500KB from my variant, including  CPT2 (53662101-53679869), LRP8 (53711217-53793742), GLIS1 (53971910-54199877), and so on.

Does anyone know why this is happening?

Thanks,

Karen Schwander

[Alcohol-BP]

Hi Tanya - I am withdrawing my question.  I was accidentally comparing FUMA positions (hg19) against my hg38 positions. 

Thanks,

Karen