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Linkage Disequilibrium
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Association Maps
Here you can create association maps (karyograms) containing all genome-wide significant (P < 5×10-8) SNP associations as listed in the GWAS Catalog. Please refer to www.genome.gov/gwastudies/ for further information including citation guide. Last updated: 11/2020 .
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.
Association map settings
Input Type:
Select a trait from the NHGRI GWAS Catalog or create your own association map.
Phenotypes: Choose as many traits as you like (the more, the longer it will take to render the plot). The variants with significant associations to these traits are plotted in the karyogram.

To select multiple traits, hold the "CTRL" key (Apple: "cmd ⌘") while clicking on the entries.
Filter: Use this field to search for traits in the list above or to display a set of related traits.
Variants: Please input one rs-identifier per line. Optionally, you can also enter your association p-values together with the rs-identifiers in the following format:
For example:

rs12345 0.0001
rs241456 3.21e-12
rs543221 1e-82

Mixing lines of rs-numbers with and without p-values is also possible. Where a p-value is given, it will show up in the association map if you hover over the respective variant.
Trait: Use this field to enter the trait in your study (optional).
Association map


Click on a GWAS hit on the association map. Detailed annotations for this variant will be displayed in this section.