I wonder if an annotation database exists which contains all known feature across the whole genom hg19 using keywords from [sequence ontology][1] ? 


  [1]: http://www.sequenceontology.org/
You can use Variant Effect Predictor or SnpEff to annotate Sequence Ontology features.

http://www.ensembl.org/info/genome/variation/predicted_data.html

http://snpeff.sourceforge.net/