Isn't this the usual situation for GWAS? I don't follow this area closely, but from what I see in publications, most of the suspect SNPs appear to be at some place where they don't make any obvious sense.
But seriously, wow can you be so sure that there is no influence on transcription or splicing? Do you have one set of RNA-seq data per allele? Or many of them? I'm not an expert for RNA-seq, but with microarrays I would like to see dozens of replicates before drawing any conclusions.
I am not a GWAS expert either, but here is another thought: Having something as the 'top hit' doesn't mean that it is meaningful. I assume that you have sufficient statistical evidence for the SNP-to-phenotype association.
Finally, can you exclude that some other variant (that you did not test for) is causing the phenotype and that your intronic SNP is just linked to it?
Please excuse if these suggestions are rubbish, I am way out of my league here.
7.6 years ago by
Lyco • 2.3k