If you have a VCF dataset with variant calls, the tool VCFfilter could be used.
If you have a BAM dataset of mapped reads, the tool DeepTools: computeGCBias could be used.
If you have genome coordinates and want to find out known CpG sites, examine the tracks at UCSC (http://genome.ucsc.edu) or your data source of choice. Once the data is loaded to Galaxy, filter it by region. Which tool to use for filtering depends on that data's format.
Reference Galaxy tutorials: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team