A tag SNP is a representative single nucleotide polymorphisms (SNPs) in a region of the genome with high linkage disequilibrium (the non-random association of alleles at two or more loci). It is possible to identify genetic variation without genotyping every SNP in a chromosomal region. Tag SNPs are significant in whole-genome SNP association studies which hundreds of thousands of SNPs across the entire genome are genotyped. For this reason, the HapMap Project hopes to use tag SNPs to discover genes responsible for certain disorders.
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