A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium that represents a group of SNPs called a haplotype. It is possible to identify genetic variation and association to phenotypes without genotyping every SNP in a chromosomal region. This reduces the expense and time of mapping genome areas associated with disease, since it eliminates the need to study every individual SNP. Tag SNPs are useful in whole-genome SNP association studies in which hundreds of thousands of SNPs across the entire genome are genotyped. Introduction Linkage Disequilibrium Two loci are said to be in linkage equilibrium (LE) if their inheritance is an independent event. If the alleles at those loci are non-randomly inherited then we say that they are at linkage disequilibrium (LD). LD is most commonly caused by physical linkage of genes. When two genes are inherited on the same chromosome, depending on their distance and the likelihood of recombination between the loci they can be at high LD. However, LD can be also observed due to functional interactions where even genes from different chromosomes can jointly confer an evolutionarily selected phenotype or can affect the viability of potential offspring. In families LD is highest because of the lowest numbers of recombination events (fewest meiosis events). This is especially true between inbred lines. In populations LD exists because of selection, physical closeness of the genes that causes low recombination rates or due to recent crossing or migration. On a population level, processes that influence linkage disequilibrium include genetic linkage, epistatic natural selection, rate of recombination, mutation, genetic drift, random mating, genetic hitchhiking and gene flow. When a group of SNPs are inherited together because of high LD there tends to be redundant information. The selection of a tag SNP as a representative of these groups reduces the amount of redundancy when analyzing parts of the genome associated with traits/diseases. The regions of the genome in high LD that harbor a specific set of SNPs that are inherited together are also known as haplotypes. Therefore, tag SNPs are representative of all SNPs within a haplotype. Haplotypes The selection of tag SNPs is dependent on the haplotypes present in the genome. Most sequencing technologies provide the genotypic information and not the haplotypes i.e. they provide information on the specific bases that are present but do not provide phasic information (at which specific