Linkage disequilibrium plots show the amount of correlation between a sentinel variant and its surrounding variants. The y-axis shows the correlation coefficient (r2), the x-axis shows chromosomal position of each SNP. The plot symbol of each variant indicates its functional annotation.
Interactive plots allow you to zoom into the plot and to get annotations when you hover your mouse pointer over them. Click on a variant to show detailed annotations or to copy it to SNiPA's clipboard. See the documentation for a list of features.
Linkage Disequilibrium Plot
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| Genome Assembly, Variant Set, Population, and Genome Annotation | ||
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| Genome assembly: | Chromosome coordinates (and thus all genetic elements) are mapped to the selected human reference assembly. | |
| Variant set: | Linkage disequilibrium data and allele frequencies are computed for the selected variant set (and population where applicable). | |
| Population: | If a variant set contains more than one population, select the one that fits your study population best. | |
| Genome annotation: | Genetic elements are annotated based on data of the selected annotation dataset. | |
| Sentinel Variant | ||
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| Sentinel: |
SNiPA looks for genetic variants in linkage disequilibrium (r2 > 0.1) with the sentinel. If you have already added variants to SNiPA's clipboard, these are available as a preselection.
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| Plot options | ||
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| Highlight variants: |
You can optionally enter variants that you want to highlight in the LD plot. Only variants that are in LD (r2 > 0.1) with the sentinel and present in the selected variant set and/or population will be highlighted. Please enter one rs identifier per line. |
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| Highlight mode: |
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If you have specified any variants to be highlighted, you can select how any other variants in LD with the sentinel should be plotted. Set this option to "hide" and SNiPA will omit those variants from the plot. If you chose "show", SNiPA will plot those variants at reduced opacity. |
| Interactive plot: |
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Interactive plots offer detailed variant annotations as well as zooming and other features. However, this will only work on modern browsers.
If you have no interest in these features or if you are using a legacy browser, disable this option to speed up data processing. |
| Download plot: |
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When enabled, SNiPA generates high-resolution PNG and PDF versions of the static plot. You can download the plots in the "Report" section. |