Where can I get consequence annotations for the 1000 genome variants?

The final 1000 Genomes phase 3 analysis calculated consequences based on GENCODE annotation and this can be found in the directory: release/20130502/supporting/functional_annotation/

Ensembl can also provides consequence information for the variants. The variants that are loaded into the Ensembl database and have consequence types assigned and displayed on the Variation view. Ensembl can also offer consequence predictions using their Variant Effect Predictor (VEP).

Please note the phase 3 annotations and the Ensembl annotations visible via the browser due to using different versions of gene and non coding annotation.

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