I have found ~ 200 significant associations at a specific p-value threshold by running a GWAS between SNPs and a phenotype. I can map the significant SNPs to human genes, but I would like to find the independent signals associated with the phenotype, i.e. if the genes where the SNPs map to are nearby and there is LD between these genes, then I would like to consider the associations as a unique signal. I think this is a normal step to find the independent signals in post-GWAS processing.
My question is, is there a way to do this in R or any software, so retrieving the LD between a list of SNPs (something like BiomaRt) and then using this information to find independent signals, maybe creating LD clusters? I don't know if this is the usual way of finding independent signals in a GWAS, if not, could you tell me how this is normally done?
Thank you for any advice/help/suggestion!
EDIT by Michael: This boils down to the question if there is a tool like SNAP but for local installation.