[Term] id: SO:0000188 name: intron def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region
[Term] id: SO:0000198 name: noncoding_exon def: "An exon that does not contain any codons." [SO:ke] subset: SOFA synonym: "noncoding exon" EXACT  is_a: SO:0000147 ! exon
I suppose the real answer is that it depends on what format of gene annotation data you're working with. Anything goes, so long as people agree to use your standard.
From the top my head: promoters, enhancers, chromatin states, DNA modifications (e.g. methylation), variations (SNPs, CNVs), gene type (e.g. coding/non-coding ...). There's probably more. Just look at annotated genomes in Ensembl to get ideas.