Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT, the Genomic Regions Enrichment of Annotations Tool, assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes.
One of the natural applications of GREAT is to infer biological meaning from regions identified by a chromatin immunoprecipitation (ChIP) experiment. To hypothesize the biological processes in which a transcription factor is relevant, you can perform a ChIP experiment to identify regions where the transcription factor binds and then use GREAT to find annotations enriched among the genes near the binding sites.
Using the GREAT web server, you can determine annotation enrichments for your regions of interest.