Linkage disequilibrium (LD) is the non-random association of alleles at two or more loci on a chromosome. It describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies and genetic distances. In population genetics, linkage disequilibrium is said to characterize the haplotype distribution at two or more loci. It has been suggested that this article or section be merged with gene. ... The word locus (plural loci) is Latin for place. In biology, a locus is the position of a gene (or other significant sequence) on a chromosome. ... Figure 1: Chromosome. ... A haplotype, a contraction of the phrase haploid genotype, is the genetic constitution of an individual chromosome. ... It has been suggested that this article or section be merged with gene. ... Population genetics is the study of the distribution of and change in allele frequencies under the influence of the five evolutionary forces: natural selection, genetic drift, mutation, migration and nonrandom mating. ... A haplotype, a contraction of the phrase haploid genotype, is the genetic constitution of an individual chromosome. ... This page deals with mathematical distributions. ...

Formally, if we define pair-wise LD, we consider indicator variables on alleles at two loci, say I₁,I₂. We define the LD parameter δ as: In the mathematical subfield of set theory, the indicator function is a function defined on a set X which is used to indicate membership of an element in a subset A of X. Remark. ... It has been suggested that this article or section be merged with gene. ...

δ: = Cov(I₁,I₂) = p₁p₂ − h₁₂

Here p₁,p₂ denote the marginal allele frequencies at the two loci and h₁₂ denotes the haplotype frequency in the joint distribution of both alleles. Various derivatives of this parameter have been developed. In the genetic literature the wording "two alleles are in LD" usually means to imply . Contrariwise, linkage equilibrium, denotes the case δ = 0. Allele frequency is a term of population genetics that is used in characterizing the genetic diversity of a species population, or equivalently the richness of its gene pool. ...

The International HapMap Project allows to study the LD of human populations online. The goal of the International HapMap Project is to develop a haplotype map of the human genome, also referred to as the HapMap, which will describe the common patterns of human genetic variation. ...