Have a look at Ensembl VEP, the Variant Effect Predictor. As the name says VEP predicts the effect of your variants on a given genome (whether it's deleterious or not; whether it falls in regulatory regions or not). The input data can be in VCF (plus many others). There is an online version of it (watch the tutorial video) in addition to a standalone Perl script and the REST API. It's worth having a look at the BioStars post by my colleague Emily.