HelmholtzZentrum munich
Linkage Disequilibrium
Variant clipboard (0) reset
Proxy Search
Here you can query for variants that are in linkage disequilibriums to other variants within a 500 kb window. 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.
Sentinel variants / Genetic Locus / Chromosomal Region
Input Type:
You can either manually input one or more sentinels or use all available variants in a gene or a chromosomal region.
Variants: Enter one rs-identifier per line.

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

Gene locus: Enter an ENSEMBL gene identifier (e.g. ENSG00000015532).
You may also enter identifiers from other gene resources and then select the appropriate ENSEMBL gene identifier from the list.
SNiPA will perform a proxy search for all sentinel SNPs covered by that gene.

Chromosomal region:
The maximum range is 1 Mb.

Output options
LD threshold:
Set the threshold for the minimum correlation coefficient between sentinels and proxies. Lower values will give you more proxies, but will also slow down the processing of your job. We suggest that you keep the threshold above 0.5.
Select "Yes" if you want to include functional annotations in the query results.
This option will significantly increase the amount of time it takes to process your job, especially when you input many individual sentinels.
Include sentinels:
When enabled, the sentinel variants are included in the results table.
Interactive table:
By default, SNiPA presents the results in sortable and searchable tables. 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 file in the "Report" tab.

Click on the arrow () next to a proxy SNP in the results table. Detailed annotations for this SNP will then be displayed in this section.