Hi,
This is a trivial question and I am surprised I could not find it anywhere else...
How can you map an intergenic SNP to a unique gene? I mean, is there any "canonical good way" to do it? Several ways to do it come to my mind: the closest in distance, the one with the higher R² value between the SNP and the first gene polymorphic position, etc... But I would like to know if any previous reference of someone doing it somehow do actually exist. GWAS usually report both genes (upstream & downstream), but I'd rather like to have a single hit.
Does anyone know a good way to do it?
I don't have time to write a full answer now, but have a look at this paper: Habegger et al, 2012. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
In this recent paper Raj et al, 2013, Common Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection they assigned SNPs to the closest gene inside the LD block.
I know... & you know we are doing a journal club on it soon... ;) hehehe...