A haplotype, a contraction of the phrase "haploid genotype", is the genetic constitution of an individual with respect to one member of a pair of allelic genes. A haplotype can refer to only one locus or to an entire genome. A genome-wide haplotype would comprise half of a diploid genome, including one allele from each allelic gene pair.

In a second meaning it refers to a set of single nucleotide polymorphisms found to be statistically associated on a single chromatid. With this knowledge, the identification of a few alleles of a haplotype block unambiguously identifies all other polymorphic sites in this region. Such information is most valuable to investigate the genetics behind common diseases and collected by the International HapMap Project.

A genotype is distinct from a haplotype because an individual's genotype may not uniquely define that individual's haplotype. As an example, consider two loci, each with two possible alleles, the first locus being either A or a, the second locus being B or b. If the genotype of an individual was found to be AaBb, there are two possible sets of haplotypes, corresponding to which pairs happen to occur on the same chromosome:

In this case, more information would be required to determine which particular set of haplotypes occur in the individual (i.e. which alleles appear on the same chromosome).

See also

• International HapMap Project