Integrated analysis of single nucleotide polymorphisms (SNPs) and structure variations showed that the extent of linkage disequilibrium is common across different types of genetic variants. A subset of SNPs (called tag SNPs) is sufficient for capturing alleles of bi-allelic and even multi-allelic variants. However, accuracy and power of tag SNPs are affected by several factors, including genotyping failure, errors and tagging bias of certain alleles. In addition, different sets of tag SNPs should be selected for fulfilling requirements of various genotyping platforms and projects.