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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

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SNP FAQ Archive [Internet].

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Linkage Disequilibrium Data

Do you have an LD report where I can get a table of pairwise r-squared values for a set of SNPs in some region?

dbSNP doesn't have a LD report in table format but we will look into providing one in the future. For now, download the files to open in Haploview and then export out as a tab-delimited table:

1.

Search either by SNP, position, or gene

2.

Select a population and click on "Display Results"

3.

Select "Download HaploView Files" (the links for the Haploview files are in blue text and located to the right of the genotype results).

4.

Open the files in HaploView, generate the LD Plot, and export as tab-delimited text

(08/11/08)

rs4680 is only 1kbp downstream of rs6267, yet rs4680 has an allele frequency of >0.5 in our population. How do I find linkage disequilibrium information for these two SNPs?

To get LD data page for rs6267:

1.

Go to the refSNP page for rs6267

2.

Scroll down to the "GeneView" section.

3.

Select the "cSNP" radio button located below the blue GeneView section header and click the “Go” button at the end of the same line to open the "SNP linked to Gene" page.

4.

Click the blue picture icon called "Gene Genotype Report" that is located near the top left hand side of the page to see LD analysis data and results using (R^2).

5.

Click on one of the the LD thumbnail views located on the right side of the page to see details of the LD calculation.

You can also download the raw data in html, xml, or gzip format and perform your own linkage analysis. (9/05:08/09)

PubReader format: click here to try

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