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.
Linkage Disequilibrium Calculator
Calculate Linkage Disequilibrium (LD) between variants using genotypes from a selected population.
Translate a variant identifier or HGVS notation to all possible variant IDs and HGVS
Computes observed transcript haplotype sequences based on phased genotype data
Generate all single base substitutions for protein coding genes given a specific species or chromosome or gene.