According to Cardon et al. 2003, a haplotype block is

A discrete chromosome region of high linkage disequilibrium and low haplotype diversity. It is expected that all pairs of polymorphisms within a block will be in strong linkage disequilibrium, whereas other pairs will show much weaker association. Blocks are hypothesized to be regions of low recombination flanked by recombination hotspots.

It seems obvious that the parts of the genome that compose genes will have a somewhat similar behavior.

So what are the differences between haplotype blocks and genes? Are genes a kind of haplotype block?

Cardon, L. R., and G. R. Abecasis. 2003. Using haplotype blocks to map human complex trait loci. Trends in Genetics 19:135–140.


1 Answer 1


Haplotype blocks may cover more than just one gene.

While positions within a gene are also in high linkage disequilbrium (or well correlated) with each other, this phenomena of high LD may extend beyond the gene body and overlap with the next gene. A good visual representation of this comes from Jeffreys et al. in the figure below:

haplotype blocks

Red means more LD, black means zero LD. Each point in the heatmap is essentially a pairwise correlation between two points in the genome. Therefore regions of red represent regions of high LD or haplotype blocks. Going from left to right we can see that each gene appears to be in its own block of high LD. However, the genes PSMB9 and TAP1 appear to be in the same block. Other examples exist as well, a great source is this review.

  • $\begingroup$ OK! Cool! But in the end, is a gene a haplotype block? I guess there are cases where there are haplotype blocks that span many genes, but genes themselves seem to have the same characteristics of a haplotype block. $\endgroup$ May 15, 2019 at 2:25
  • 1
    $\begingroup$ Yes genes could likely be considered haplotype blocks, although this distinction does not add any understanding about genes. Perhaps similar to calling a square a rectangle, the distinction is true but rather redundant. $\endgroup$
    – user42909
    May 16, 2019 at 11:43

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