How can chromatin state be measured?
Starting out with RNA data is great, since you already have fully spliced entities, despite  being in a different dynamic regime.

As the chromatin landscape itself is dynamic and High throughput data exploration has only begun in the last decade, consider the following tools and results with care...

You may find the following tools helpful:


Archalign , Publication (didn't work well during my day of trials)
Ensembl chromatin-state map data (See the database layout, Regulatory Build, and the lincRNA
genes in the web-interface of the Ensembl databases)
HaploReg, Publication (the most recent)