Now that we've had a week or so to digest the ENCODE publications (nice summary here), this is a question for those groups engaged in next-gen sequencing projects for gene discovery in human disorders. Most of you have probably focused on whole exome.
What elements of the ENCODE data set are ready or near-ready to include in future experiments that capture the "exome-plus"? Are groups designing targets for some of these regions for capture? Which ones? Enhancers? Promotors? Other long-range functional elements? Or do you suspect it's more efficient to just target the whole genome, so that data can be re-analyzed as functional annotations of the non-coding regions continue to improve? Interested in your responses.