4.12 Visualizing LD blocks

LDproxy, another LDlink tool, finds all SNPs in strong LD with a SNP of interest.

Open LDproxy and use it to search for one of the SNPs from today (it may take the webpage a minute to load the results).

Fig. 6. LDproxy results for rs28574812.

To generate this plot, LDproxy calculated \(r^2\) between our SNP of interest and all other SNPs in a 500kb window. As expected, we can see that LD is strongest for variants that are closest to the SNP.

LDproxy also provides even more information than just LD – it also includes regulatory annotations for all the variants in this region (the numbers within each dot), as well as gene annotations and a list of nearby variants (below the plot).