In this PDF, there is a quick definition of haplotype blocks.

A haplotype block is a set of closely linked alleles/markers on a chromosome that, over evolutionary time, tend to be inherited together.

Also look at this definition:

We defined a haplotype block as a region over which a very small proportion (<5%) of comparisons among informative SNP pairs show strong evidence of historical recombination. [We allow for 5% because many forces other than recombination (both biological and artifactual) can disrupt haplotype patterns, such as recurrent mutation, gene conversion, or errors of genome assembly or genotyping.]

Although in the abstract they say:

haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed.

But the first definition confuses me because it really looks like the definition of linkage disequilibrium:

linkage disequilibrium is the non-random association of alleles at different loci in a given population.

Which means that they are inherited together (non-randomly inherited). The other definitions don't seem to agree in the same paper...

Just as a reminder a haplotype is: "The set of alleles found on a single sequence is referred to as a haplotype." (Hahn, M. W. 2018. Molecular Population Genetics. Sinauer Associates, Incorporated, Sunderland, Massachusetts.)


  1. What are haplotypes blocks precisely and compared to LD? How to estimate haplotypes blocks?

  2. Why is this an important concept (what is it informing us, why would want to study that specifically)?

  3. What influences haplotypes blocks and how is it useful to get some information when doing genomic analysis (can we account for that)?

Here are 2 relevant resources on the subject:

  • Daly, M. J., J. D. Rioux, S. F. Schaffner, T. J. Hudson, and E. S. Lander. 2001. High-resolution haplotype structure in the human genome. Nature Genetics 29:229–232.
  • Patil, N., A. J. Berno, D. A. Hinds, W. A. Barrett, J. M. Doshi, C. R. Hacker, C. R. Kautzer, D. H. Lee, C. Marjoribanks, D. P. McDonough, B. T. N. Nguyen, M. C. Norris, J. B. Sheehan, N. Shen, D. Stern, R. P. Stokowski, D. J. Thomas, M. O. Trulson, K. R. Vyas, K. A. Frazer, S. P. A. Fodor, and D. R. Cox. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719–1723.

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