The majority of sequence variants in Ensembl are Single Nucleotide Polymorphisms (SNPs), insertions, and deletions imported from NCBI dbSNP. For human SNPs in particular, we aim to keep current with dbSNP, updating these with every Ensembl release (every 2-3 months). Projects submitting their variants to dbSNP include individual labs and the 1000 genomes project. Small sequence variants are mapped onto the reference genome, and effects on Ensembl transcripts are determined. Larger structural variations (such as copy number variation) are also viewable on the genomic sequence. These include structural variants from dGVA and somatic mutations.
Genotype information for human variants is imported from dbSNP, and reflects data from individual submissions, HapMap, and the 1000 Genomes project. Disease and phenotype associations are imported from projects such as the NHGRI GWAS catalogue and EGA.