Looking for non-coding SNPs that may be associated with phenotypes

One way to look for phenotype-associated SNPs in non-coding areas is to use the ENCODE segmentations. These are available at the UCSC table browser and mirrors. Click on BX table browser, choose group regulation, and track Broad ChromHMM. This is a composite track with many tables with coordinates (shown in bubble below). Clicking on describe table schema (green arrow) we can get more information on this track.