I've performed a candidate gene association study and my top SNPs are all intronic SNPs. I've run them through a couple of basic annotation software online, checking for the usual stuff as well as some of the more recent things like miRNA binding sites etc. Two of my top hits are very close to each other ( <1000 bases) but aren't in high LD. The only thing I can think of, that could possibly result in the intronic SNPs causing a change in the phenotype, is that they are in LD with some other variant, but a trawl through the normal databases hasn't proven fruitful. Does anyone know how I can check for variants that are in LD with my SNPs? Any ideas on how else I can functionally annotate my SNPs ?
Secondly, all my top SNPs are in repeat-rich regions. Apart from the fact that repeat rich regions are recombination hotspots, any other idea of how this might be significant? Any software that I can use to examine this further?