Do you have a VCF dataset of the SNPs or a list of rs numbers? And do you wish to compare these to other known annotations or something different?
If you have a list of rs numbers, these can be compared to a dbSNP dataset to obtain the genomic position and other details. Extract the dbSNP table from UCSC (under "Get Data"), then use the tool Join or Compare in the tool group Join, Subtract and Group. From there you can compare the data using genomic coordinates to any other dataset also mapped to the same genome.
For other manipulations involving VCF datasets, including specialized tools that perform comparisons to functional predictions, see the tool groups VCF Manipulation and NGS: Variant Analysis.
Best, Jen, Galaxy team