There are segmentations that use various datasets as input to an HMM (chromHMM or segway) and output a bed file that lists open-chromatin, enhancer, etc (http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHmm) . Those are for each cell-type.

Is there a segmentation anywhere that has done this across cell-types, to delineate, for example sites that are classified as be promoters in all cell types?

If not, are there any things to keep in mind when using something like this:

?

And are the files that Aaron uses there the most up-to-date?