BACKGROUND: Deciphering the most common modes by which chromatin regulates 
transcription, and how this is related to cellular status and processes is an 
important task for improving our understanding of human cellular biology. The 
FANTOM5 and ENCODE projects represent two independent large scale efforts to map 
regulatory and transcriptional features to the human genome. Here we investigate 
chromatin features around a comprehensive set of transcription start sites in 
four cell lines by integrating data from these two projects.
RESULTS: Transcription start sites can be distinguished by chromatin states 
defined by specific combinations of both chromatin mark enrichment and the 
profile shapes of these chromatin marks. The observed patterns can be associated 
with cellular functions and processes, and they also show association with 
expression level, location relative to nearby genes, and CpG content. In 
particular we find a substantial number of repressed inter- and intra-genic 
transcription start sites enriched for active chromatin marks and Pol II, and 
these sites are strongly associated with immediate-early response processes and 
cell signaling. Associations between start sites with similar chromatin patterns 
are validated by significant correlations in their global expression profiles.
CONCLUSIONS: The results confirm the link between chromatin state and cellular 
function for expressed transcripts, and also indicate that active chromatin 
states at repressed transcripts may poise transcripts for rapid activation 
during immune response.