Minor allele frequency threshold risk loci and MAGMA

[Siyi Liu]

Dear FUMA developers,

Thanks for developing and maintaining this wonderful tool.

I would like to ask if only common variants (MAF>5%) in the summary statistics were able to be annotated. I submitted a SNP2GENE job (ID:655637) in which there are 4 genome-wide significant SNPs located in 4 chromosomes. However, in the summary of SNPs and mapped genes, only  2 lead SNPs/genomic risk loci were identified.  The other 2 significant hits were 16:84439569:A:G (rs748058632, MAF=0.00012) and 3:27622123:C:T (rs58017843, MAF=4.49e-5). The minimum MAF in Parameters for lead SNPs has been set to 0. Were they not identified as lead SNPs because they were rare? Similarly, would these rare variants be included in the MAGMA analysis? I'd really appreciate your help.

Best regards,

Siyi

[Tanya Phung]

Hi Siyi, 

These 2 SNPs ( rs748058632 and  rs58017843) do not exist in the reference database that is utilized by FUMA. You can check that here: https://fuma.ctglab.nl/tutorial#refpanel

Best,
Tanya

[Siyi Liu]

Hi Tanya,

Thanks for your response. It's been helpful. I'll try looking for these SNPs in the ALL reference database.

Best regards,

Siyi