Linkage disequilibrium (LD)
The top panel gives details on a given variant such as source, class, clinical significance and others. See 'Explore this variant' for more details.
A table is shown with links to find out about the linkage disequilibrium in the different 1000 genomes sub-populations, grouped by super-population. Click on the populations to find out more about them. Click on the links in the table to view a Manhattan plot, a list of variants in LD, an LD plot and a table of local variants indicating level of linkage.
Click on "Configure this page" at the left to select populations to be displayed, or to change the distance over which linked variants are shown.
Linked variants
You can see variants in high LD by clicking on Show in the Variants in high LD column for a population. This will open up a table below the original one, listing all the variants. Note the values are calculated for the comparison of the variant of interest with nearby variants, from the 1000 Genomes individuals.
The linked variant tables show the distance between the linked variant and the variant on which the view is focused, any overlapping genes, phenotypes associated with the linked variant and overlapping genes and the D' and r2 values.
D' is the difference between the observed and the expected frequency of a given haplotype. If two loci are independent (i.e. in linkage equilibrium and therefore not coinherited at all), the D' value will be 0. r2 is the correlation between a pair of loci. It varies from 0 (loci are in complete linkage equilibrium) to 1 (loci are in complete linkage disequilibrium and coinherited). Note that only LDs with r2 values larger than 0.05 are shown in Ensembl.