Variant Browser
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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 | ||||||
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| Input Type: |
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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. |
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| 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. |
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| Chromosomal position: |
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Please click on a variant in the browser window to get detailed annotations.