HelmholtzZentrum munich
Linkage Disequilibrium
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Block Annotation
The block annotation provides a summary of the annotations for a set of variants within a chromosomal region.
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.
Variants / LD / Genetic Locus / Chromosomal Region
Input Type:
Enter a variant's rs-identifier to get a summary for this variant and all variants in linkage disequilibrium.
Alternatively, enter a list of variants, a gene identifier or a chromosomal region.
Variants: Note that all variants have to be on the same chromosome. Other variants will be ingnored for annotation.

Enter one rs-identifier per line.

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

Sentinel variant: Enter a variant's rs-identifier (e.g. rs174547).
If you have already added variants to SNiPA's clipboard, these are available as a preselection.

LD threshold:
Set the threshold for the minimum correlation coefficient between the variant given above and its proxy variants. Lower values will give you more proxies, but will also slow down the processing of your job. We recommend a value above 0.5.
Gene: 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.

SNP selection:
Select "Gene region" for retrieving the annotations of variants located within the gene. "Gene association" will retrieve the annotations of variants that are located within the gene or in its proximity (+-5kb), as well as variants that are associated with the gene by eQTL data or regulatory elements.
Chromosomal region:
Maximum window size is 1 Mb.