Interpreting Results from FUMA - mapped genes

[Avni Kaur]

Hi all,

This isn't so much a question regarding carrying out the analysis using the online database tool but a question regarding the interpretation  of my results. 

I have uploaded my GWAS results onto FUMA (total sample size of ~ 1500 participants) JOB ID 169758.  I have defined a less stringent p value for identification of lead SNPs/independent significant SNPs and carried out three strategies to map SNPs to genes (positional, eqtl and chromatin interaction mapping). I have also filtered using CADD score, RDB score and for 15-core chromatin state (in the relevant tissues). 

I am having  trouble interpreting these results.

I have a list of 12 mapped genes in the genes.txt excel spreadsheet. I have all 0 values in the posMapSNPs and eqtlMapSNPs columns meaning that none of these SNPs were mapped to the genes based on eQTL mapping or via positional mapping. I have YES in all the fields for Chromatin interaction so am I right in saying all the genes were mapped using chromatin interaction? In the column IndSigSNPs, I only have one SNP which is the exact same across all fields in this column. Does this mean only this SNP was used to map to genes. I am not sure why no other SNPs were used to map to genes and just this particular SNP? 

I would appreciate any help and I am sorry for any confusion. 

Kind Regards,

Avni

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

Hi Avni, 

Yes in the chromatin interaction columns means that the genes were mapped by chromatin interaction. The README says this about the IndSigSNPs column

"IndSigSNPs : rsID of the independent significant SNPs that are in LD with the mapped SNPs.
        Note that this column does not represent SNPs that are mapped to the gene.
        The actual mapped SNPs are available in gene_snps.txt file."

Cheers,

Doug