[galaxy-user] stuck

I'm sure this is a silly question, but I have been stuck since yesterday. I have some whole genome sequencing data - What was given to me is an enormous XL file with all the single base changes identified in 4 people. I don't want to track down all the changes, yet I've noticed some of them labeled as "novel" are in fact SNPs - particularly if I use build 130. I imported just chr, start, end using same base number for start/end from part of my file (chr 1) and then pulled down all the SNPs from UCSC for Chr. 1. What I would like to do is label the lines in my file that are snps. I have tried intersect, join, subtract, all to no avail. What am I doing wrong? Any help would be appreciated. thanks - Amy Hsu