 Either you position the primers very close to either side of the SNP in question (small amplicon genotyping, Liew, 2004) or amplify a larger region (100-400bp in length) for scanning purposes.For simple genotyping of an SNP, it is easier to just make the amplicon small to minimize the chances you mistake one SNP for another.The melting temperature (Tm) of the entire amplicon is determined and most homozygotes are sufficiently different (in the better instruments) in Tm to genotype.