Across a human chromosome, neighboring single-nucleotide polymorphisms often show substantial linkage disequilibrium, while average allelic correlation tends to decline with increasing genetic distance. A new mutation starts on one ancestral haplotype; repeated genetic recombination separates it from progressively more distant markers. In an ideal randomly mating two-locus population without further mutation, migration or selection, gamete formation gives , where is the recombination fraction. The marginal allele frequencies remain fixed, soHere the prime means the next-generation value, not a separately standardized LD statistic. This simple decay explains the distance trend, rather than asserting an exact deterministic law for real finite populations.
The local pattern is heterogeneous. Many regions have haplotype blocks with strong LD and a small number of common haplotypes, separated by intervals showing more historical recombination, often recombination hotspots. A hotspot can therefore cause a rapid drop in LD between markers that are close in physical distance. Block lengths and boundaries are not uniform, perfectly sharp or independent of the population and the statistical block definition. These empirical features are documented in the HapMap data.
Population history also matters. Population bottlenecks can reduce the number of ancestral haplotypes and increase the extent of LD; population stratification or admixture can create longer-range associations, including between distant loci. Different populations can consequently have different haplotype frequencies and LD patterns at the same genomic interval. Raw also varies with allele frequency, so comparing LD across markers requires attention to the chosen measure. The typical pattern is locally strong, block-like and highly variable LD, with a broad decline over genetic distance rather than a uniform chromosome-wide decay.
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