How to identify positions by gene

[penolove]

Hi,I'm new here.
I'm going to do rare variant analysis(CAST CMC)

now I have a vcf file(only snp) which contains case and control group

but there are too many positions

are there any way to make them as gene set like MAP4,FLNB,ABTB1

forgive me for my poor english,thx

[GenoMax]

Have you tried snpeff: http://snpeff.sourceforge.net/