We identified 825 putative SNPs. Of these, 245 were either present in the CEU HapMap or had been genotyped by us in that sample, leaving 580 potential variants whose LD relationships were unknown. We were able to design assays for 34% of these SNPs (n=198). The remaining 66% putative SNPs were comprised mainly of sites in repetitive elements (49%), with the rest (17%) in unique sequence. We attempted to confirm 19 of those SNPs that were in repetitive elements by more routine sequencing methods (BigDye chemistry, Applied Biosystems). Of these, 16 (85%) were not confirmed suggesting that the vast majority of the sites in highly repetitive elements were sequencing artefacts.
