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Linkage Disequilibrium
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Pairwise LD
You can check whether two or more neighbouring variants (distance < 250 kb) are in linkage disequilibrium. To get functional annotations for the variants listed in the results table, click on the symbol.
Genome Assembly, Variant Set, Population, and Genome Annotation
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.
Sentinels: Enter one rs-identifier per line.

If you have already added variants to SNiPA's clipboard, these are available as a preselection.

Output options
LD threshold:
Set the threshold for the minimum correlation coefficient between variants.
Select "Yes" if you want the query results to include functional annotations.
WARNING: This option will significantly increase the amount of time it takes to process your job, especially when you input many individual sentinels!
Include sentinel(s):
When enabled, the sentinels are included as a proxy for themselves in the results list.
Interactive table:
By default, SNiPA presents the results in tables that are sortable and searchable. Select "no" if you experience performance issues. If the result of your query exceeds 25,000 lines, this option will automatically be disabled.
Select "Yes" if you want SNiPA to provide the results as a comma-separated text file. You can download the files in the "Report" tab.

Click on a variant in the results table. Detailed annotations for this variant will then be shown in this tab.