HelmholtzZentrum munich
Linkage Disequilibrium
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Variant Browser
The variant browser visualizes the functional annotation of variants within a 200 kb window. The position on the y-axis represents the estimated function of a variant, ranging from unknown (bottom) to direct transcript effects (top). Use the karyogram to quickly navigate to a chromosomal region. Blue spikes in the karyogram indicate regions containing a high proportion of functional variants.
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.
Variant / Transcript / Chromosomal Position
Input Type:
Enter the variant, gene or chromosomal position, to which the variant browser window should be centered.
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.

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.

Chromosomal position:

Please click on a variant in the browser window to get detailed annotations.