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Ensembl LDView

Introduction

The Ensembl 'LDView' page displays detailed information about linkage disequilibrium (LD) that measures the correlation between two alleles (neighbouring genetic variations) in a specific population. Two values have been calculated:

• r²
• D'

By default, the r² value is displayed, but it is possible to switch between r² and D' by selecting a different value in the 'LD parameter' radio button. Only LDs having r² values larger than 0.05 are available.

The display is centred in the genomic position given by the SNP, and shows all LD values that are contained in the region. It is possible to zoom in or zoom out of the region by selecting a different value from the drop-down list "Zoom". By default, the region has 50 Kb.

The default population is PERLEGEN:AFD_CHN_PANEL, but it is possible to view the LD values corresponding to a different population by selecting the relevant population amongst the options available from 'Choose population' drop-down list.

To select a different region in the LDView page, it is necessary to enter a new SNP in the "Centre the display on this SNP" textbox. Doing that, the new LD displayed will take the SNP genomic coordinates to be displayed in the page.

LD values between two variants are graphically displayed using inverted coloured triangles going from white (low LD) to red (high LD). Scrolling over the inverted triangle, it is possible to view the value between the two variants.

At the bottom of the page, there is a table that can be dumped as a tab delimited text file that contains all the LD information for the variations displayed in the region.

• Genomic Region - This section lists the chromosome name or more generally the sequence region name followed by a physical map location as the centre of a 50 bp genome sequence window. Following the link leads to the corresponding Ensembl 'ContigView' page.

• SNP - The SNP accession number and the source database version. A link leads to the corresponding Ensembl 'SNPView' page, which displays more detailed information on this particular genetic variation.

• Population - This section provides more details about the population such as the relevant identifier, the population size and a supplementary description.

• Super-Population - This section provides the name of the super-population.

• Display Options - The Display Options sections allows up dating of several display parameters at once.

The search box at the top of the page allows you to search for any identifier present in Ensembl. For detailed instructions see the Ensembl 'TextView' page.