Dear list, Using the same imputed HapMap SNP set, for a specific gene hg18 region, I got a set of SNPs with hg18 position. Then if I use the hg19 location for the same gene, am I supposed to get the same set of SNPs with hg19 position? The HapMap SNP locations were obtained using the liftover tools. The Gene 19 locations were retrieved from NCBI/UCSC. Here I am not interested in the SNP position. What I would like to know is, starting with the same set of HapMap SNPs, for a specific gene region, whether I get the same set of SNPs located in this gene using either hg18 or hg19 (hg19 positions for both SNPs and gene, vs. hg18 locations for both SNPs and gene). My guess is if the position between hg18 and hg19 is just shifted by a certain range for both SNPs and genes, then I should get the same set of SNPs for the gene of my interest, right? Thanks in advance, Shirley [[alternative HTML version deleted]]