Changes

: This option allows you to plot results for all markers within a specific distance (e.g. 500kb) of an index SNP. To use this option, set column 1 to have the name of the index SNP (e.g. ''rs2'' below) and set column 5 to specify the width of the region of interest (e.g. 500kb below). Here is an example:

: This option allows you to plot results for all markers within a specific distance (e.g. 500kb) of an index SNP. To use this option, set column 1 to have the name of the index SNP (e.g. ''rs2'' below) and set column 5 to specify the width of the region of interest (e.g. 500kb below). Here is an example:

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Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

rs1     na     na       na      500kb        yes      rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”  

rs1     na     na       na      500kb        yes      rfrows=3 weightCol=”N” snpset=”HapMap” metalRug=”Our SNPs”  

: This option is similar to the previous option, but allows you to specify an assymetric region of interest. For example, perhaps you interested in a plot that extends a bit further to the right of the SNP of interest. In this case, specify the coordinates of the region to be plotted in columns 2, 3, and 4. Here is an example:

: This option is similar to the previous option, but allows you to specify an assymetric region of interest. For example, perhaps you interested in a plot that extends a bit further to the right of the SNP of interest. In this case, specify the coordinates of the region to be plotted in columns 2, 3, and 4. Here is an example:

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Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

rs2     1     540000  580000  na     yes      rfrows=4 legend=”right” showAnnot=T  

rs2     1     540000  580000  na     yes      rfrows=4 legend=”right” showAnnot=T  

: This option allows you to focus on a particular gene, rather than a specific SNP. It is similar to the first option. You should set column 1 to be the name of the gene of interest and column 5 to be the desired window width. When you use this option, LocusZoom will automatically select an index SNP for each region; the SNP will be the site with the smallest p-value. Here is an example:

: This option allows you to focus on a particular gene, rather than a specific SNP. It is similar to the first option. You should set column 1 to be the name of the gene of interest and column 5 to be the desired window width. When you use this option, LocusZoom will automatically select an index SNP for each region; the SNP will be the site with the smallest p-value. Here is an example:

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Feature    chr    start    end      flank        plot    arguments

Feature    chr    start    end      flank        plot    arguments

CETP     na     na       na      200kb        yes      rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”

CETP     na     na       na      200kb        yes      rfrows=6 showAnnot=T annotPch=”1,24,24,25,22,21,8,7”