Ensembl Variation - Variant tools

Ensembl provides several tools related to variant data:

Variant Effect Predictor (VEP)

Determines the effect of your variants on genes, transcripts, and protein sequence, as well as regulatory regions.

Availability:

Linkage Disequilibrium Calculator

Calculate Linkage Disequilibrium (LD) between variants using genotypes from a selected population.

Availability:

Variant Recoder

Translate a variant identifier or HGVS notation to all possible variant IDs and HGVS

Availability:

Haplosaurus

Computes observed transcript haplotype sequences based on phased genotype data

Availability:

Variant Simulator

Generate all single base substitutions for protein coding genes given a specific species or chromosome or gene.

Availability:
Available as a web tool
Available as a REST API
Available as a Perl standalone script