While much attention has been focused on chromatin at promoters and exons, human 
genes are mostly composed of intronic sequences. Analyzing published surveys of 
nucleosomes and 41 chromatin marks in humans, we identified histone 
modifications specifically associated with 5' intronic sequences, 
distinguishable from promoter marks and bulk nucleosomes. These intronic marks 
were spatially reciprocal to trimethylated histone H3 Lys36 (H3K36me3), 
typically transitioning near internal exons. Several marks transitioned near 
bona fide exons, but not near nucleosomes at exon-like sequences. Therefore, we 
examined whether splicing affects histone marking. Even with considerable 
changes in regulated alternative splicing, histone marks were stable. Notably, 
these findings are consistent with exon definition influencing histone marks. In 
summary, we show that the location of many intragenic marks in humans can be 
distilled into a simple organizing principle: association with 5' intronic or 3' 
exonic regions.