A phenomenon found in linkage mapping of genes whereby a certain combination of alleles at two or more marker loci occurs more frequently than expected. This happens when there is a relatively low level of recombination in the chromosomal region containing the loci, so that the alleles tend to be inherited as a set, or haplotype. Linkage disequilibrium is more common in some parts of the human genome than in others, corresponding to recombination ‘cold spots’. In these chromosomal regions, large DNA stretches (haplotype blocks) are transmitted through many generations with the same allelic combinations. This is very useful in mapping disease-related genes because a marker, such as a single nucleotide polymorphism (SNP), can be used to tag an entire haplotype block containing a particular set of alleles. This makes it much easier to scan the genome for markers that are associated with a disease and is the rationale underlying the International HapMap Project.