Annotation of Genomes

[Firebird]

Hi,

I have expierence with exome annotaion, which is quite simple as you are only looking into coding sequences. That make interpretation of the results much easier.
But how do I annotate the non-coding region I get from whole genome sequenicng. Does it make sense to annotate with Encode data or are there better databanks available to make sense of variants in non-coding regions?

Thanks