lead SNPs do not map to Genes in FUMA

[nitesh e]

Hi,

for the Job Id: 178747, the lead SNP (11:47232038) do not match to results in Mapped Genes tab, but maps to Gene in Annovar method. why is this discrepancy?

[d.p.wi...@vu.nl]

Hi, 

It looks like from the parameters file from your job that you only chose chromatin interaction mapping and not positional mapping. These parameters do not apply to ANNOVAR, only to the gene mapping performed by FUMA. The ANNOVAR results rely on separate input files where the gene-mapping has already been performed based on position.

Based on the chromatin datasets you selected, these regions overlap with 11:47232038: 

chr1    start1  end1    chr2    start2  end2    FDR

11    47230000    47240000    11    46360000    46370000    0

11    47230000    47240000    11    47190000    47200000    0
11    47230000    47240000    11    47400000    47410000    0
11    47200001    47240000    11    47600001    47640000    0.02217364

and the 2 regions for each interaction do not overlap with DDB2 (11:47236493-47260767) or RN7SL772P (11:47227396-47227672).

Cheers,

Doug

[nitesh e]

Hi Doug,

I still see these kind of results with positional mapping JOB ID:  180624

lead SNP chr8:  7466315 found the nearest Gene CLU in ANNOVAR, but not in the Mapped Genes section.

I selected ALL gene type . can you explain why this happened?

thanks,

Nitesh.

On Thursday, April 21, 2022 at 4:14:22 PM UTC-5 nitesh e wrote:

thanks Doug.

[d.p.wi...@vu.nl]

Hi, 

The parameters of this job show that you selected to use variants with CADD>12.37 for positional gene mapping. All of the variants which map to CLU in your data have CADD<12.37.

Cheers,

Doug