Haplotype Structure in the Human Genome

HAPLOTYPE STRUCTURE IN THE HUMAN GENOME 3.1. Haplotype Classification 

If the human genome is partitioned into haplotype blocks, the definition of LD can be refined. Because a given local haplotype block has multiple variants, the probability that SNPs that are in LD but are not located on the same haplotype block will be in phase (i.e., part of the same local haplotype structure) is a function of increasing distance. For instance, in a hypothetical situation in which two variants or forms are available for every haplotype block, the probability that pairwise SNPs in LD will not be part of the same local haplotype (in phase) is 0.5 +1, where n represents the number of haplotype blocks that separate the two SNPs. For example, if the SNPs are on adjacent blocks (zero block separation), the probability that they will be part of the same local haplotype is 0.5 or 50%. This is the upper limit for SNPs not present on the same haplotype block in this situation. If SNPs are separated by four blocks, the probability that they are part of the same local haplotype falls to 0.03 or 3%, because now there are more blocks and hence more possibilities for variation between the SNPs. 

Because LD is defined as the occurrence of two SNPs on an allele at a frequency greater than that predicted by chance, which for two SNPs is 0.51+1 = 0.25 or 25%, we can modify the definition of LD LD is the 

---

Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet 2001 29(2) 229-232. 

---