Summaries of Linkage Disequilibrum in the Genome

This page includes summaries of the linkage disequilibrium data used in the following paper:

Smith AV, Thomas DJ, Munro HM and Abecasis GR (2005). Sequence features in regions of weak and strong linkage disequilibrium. Genome Res 15:1519-34 [Abstract] [PDF]

If you use any of this information in a published work or presentation, please cite appropriately.

Sliding Window Summaries of Linkage Disequilibrium

This set of files contains fitted r² values for sliding windows of different sizes. For each window, fitted r² values are tabulated for markers separated by 10kb, 30kb and 100kb in each of the three HapMap sample sets (CEU, YRI, CHB+JPT).

100kb.txt.gz              0.95 Mb  (4.5 Mb Unzipped)
500kb.txt.gz              0.19 Mb  (0.9 Mb Unzipped)
1000kb.txt.gz             0.09 Mb  (0.5 Mb Unzipped)

Quartile Classification of the Genome

This file classifies each 100kb window in the genome into one of 4 quartiles, according to the degree of linkage disequilibrium among the markers it contains.

quartiles.txt.gz           0.25 Mb  (1.5 Mb Unzipped)

Spanning r² Analysis

This set of files provides a summary of the data used for the spanning r² analysis. Specifically, a spanning r² value for each intermarker interval we examined is provided and intervals with the lowest spanning r² are classified as potential recombination hotspots.

ceu.spots.txt.gz          5.8 Mb   (22 Mb Unzipped)
yri.spots.txt.gz          6.5 Mb   (24 Mb Unzipped)
chb+jpt.spots.txt.gz       5.1 Mb   (19 Mb Unzipped)

For additional information, including detailed descriptions of the algorithms used to generate these data, please see the published manuscript. For questions or comments regarding these data please e-mail Goncalo Abecasis or Daryl Thomas.