A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. However, there are other uses of this term. First, it is used to mean a collection of specific alleles (that is, specific DNA sequences) in a cluster of tightly linked genes on a chromosome that are likely to be inherited together—that is, they are likely to be conserved as a sequence that survives the descent of many generations of reproduction. A second use is to mean a set of linked single-nucleotide polymorphism (SNP) alleles that tend to always occur together (i.e., that are associated statistically). It is thought that identifying these statistical associations and few alleles of a specific haplotype sequence can facilitate identifying all other such polymorphic sites that are nearby on the chromosome. Such information is critical for investigating the genetics of common diseases; which in fact have been investigated in humans by the International HapMap Project. Thirdly, many human genetic testing companies use the term in a third way: to refer to an individual collection of specific mutations within a given genetic segment; (see short tandem repeat mutation).
The term 'haplogroup' refers to the SNP/unique-event polymorphism (UEP) mutations that represent the clade to which a collection of particular human haplotypes belong. (Clade here refers to a set of haplotypes sharing a common ancestor.) A haplogroup is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. Mitochondrial DNA passes along a maternal lineage that can date back thousands of years.