What resources, algorithms, or tools are available for analyzing non-coding variants? I'm aware of tools like SIFT and PolyPhen, but they're applicable only to changes within coding regions. I'm looking for something to analyze (potential) regulatory variants and predict an impact on phenotype, possibly using other functional or conservation data.
Update from a quick search before posting: I've found GWAS3D, which seems promising. Are there other similar tools?