Linkage Disequilibrium Datasets
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Linkage disequilibrium was run separately for each super population and sub population within 1,000 Genomes phase 3 variants using the method defined in Box 1 of:
Nature Reviews Genetics, Volume 9, Issue 6, 477 - 485
LD was computed for all pairs of variants within a window of 1,000,000 bp (1 megabase) and all pairs with absolute allelic correation of 0.4 are retained. See Compute Linkage Disequilibrium on a Variant Set for more detail.
The output files were split by chromosome with output columns indicating the identity of each pair of values and the resulting LD value. The output files have also been loaded into BigQuery with the same columns. Examples of using BigQuery to analyze LD are available as Datalab notebooks.
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