Association signal missing in the results?

[Daiki Tomidokoro]

Dear FUMA team,

I successfully completed running job ID:627960 but am having trouble identifying an association signal in the results of SNP2GENE module.

There clearly seems to be a signal (P<1e-5) at around chr6:30775017 but in my Results there are no SNPs tagged as lead SNP/independent significant SNP near the region.

Checking my original input data I noticed that the lead SNP(s) at the locus are the following SNPs with identical P values. Could this (having identical P-values for the two sentinel SNPs) have caused a bug? I believe I haven't specified any criteria (ie MAF) that would lead to exclusion of ALL SNPs at the locus. 

CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA P

6:30775017 G A 0.40438 26668 ADD 0.284408 0.0564197 24.7416 6.1834 NA 6.56E-07  6:30775033 C G 0.40438 26668 ADD 0.284408 0.0564197 24.7416 6.1834 NA 6.56E-07

I appreciate your help and look forward to your response.

Thank you,

Daiki Tomidokoro

[Tanya Phung]

Hi Daiki, 

Your SNP of interest falls within the MHC region (defined as 6:29614758 - 6:33170276 on hg19 coordinates). You specified that MHC is removed in your SNP2GENE job: 

Therefore, this SNP is filtered out. You can uncheck removal of MHC if you want to include this SNP. 

Best,
Tanya