The Galaxy 101 tutorials demonstrate how to calculate SNP density for coding exons. This analysis could be modified to calculate density for full genes and intergenic regions by swapping in BED datasets representing those regions. Both can be extracted from the UCSC table browser or you can upload/create your own BED file for regions of interest.
Galaxy tutorials: https://galaxyproject.org/learn/
- Galaxy 101 https://galaxyproject.org/tutorials/g101/
Thanks! Jen, Galaxy team