Ranking And Prioritizing Non-Coding Variants

Question

[matted]

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?

Answer 1

[jxchong]

Determining functionality (or lack thereof) of non-coding variants is an open area of research, so finding a ranking/prediction algorithm similar to Polyphen/SIFT is probably unlikely at this point in time.

You can check out GREAT: http://bejerano.stanford.edu/great/public/html/index.php

Answer 2

[Ashutosh Pandey]

Recent tool for ranking non-coding variants in human

http://funseq.gersteinlab.org/

Answer 3

[rbagnall]

A scoring tool for all 8.6 billion possible single nucleotide variants (SNVs) of the reference genome. This does not predict impact on phenotype though..

http://cadd.gs.washington.edu/home