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Ensembl Variation - Variant sets

We use the concept of variant sets to group variants that share some property together. For example, we have grouped the variants identified in the 1000 Genomes phase 3 sets, these are divided into subsets based on population. For example, the set representing variants identified in the 1000 Genomes phase 3 study is named '1000 Genomes 3 - All' and has several subsets like: '1000 Genomes 3 - AFR', '1000 Genomes 3 - AMR', '1000 Genomes 3 - EAS', '1000 Genomes 3 - EUR' and '1000 Genomes 3 - SAS'. The variant sets can be displayed as separate tracks on the location view. This behaviour is controlled from the 'Variation' section on the configuration panel which is accessed by clicking the 'Configure this page' link in the left hand side navigation.

The sets are constructed during production and are stored in the database. The table below lists the available variant sets in the Ensembl variation database (subsets are indicated by bullet points).

Name Short name Description Examples
1000 Genomes 3 - All 1kg_3 Variants genotyped by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - AFR
1kg_3_afr Variants genotyped in African individuals by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - AFR - common
1kg_3_afr_com Variants genotyped in African individuals by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
  • 1000 Genomes 3 - AMR
1kg_3_amr Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - AMR - common
1kg_3_amr_com Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
  • 1000 Genomes 3 - All - common
1kg_3_com Variants genotyped by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
  • 1000 Genomes 3 - EAS
1kg_3_eas Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - EAS - common
1kg_3_eas_com Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
  • 1000 Genomes 3 - EUR
1kg_3_eur Variants genotyped in European individuals by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - EUR - common
1kg_3_eur_com Variants genotyped in European individuals by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
  • 1000 Genomes 3 - SAS
1kg_3_sas Variants genotyped in South Asian individuals by the 1000 Genomes project (phase 3) Link trackLink variant
  • 1000 Genomes 3 - SAS - common
1kg_3_sas_com Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 3) with frequency of at least 1% Link trackLink variant
All LSDB-associated variants lsdb_variants Variants association from one or several Locus Specific DataBase (LSDB) Link trackLink variant
  • HbVar
HbVar Variants for the Human Hemoglobin Variants and Thalassemias database Link trackLink variant
  • Infevers
Infevers Variants from the registry of Hereditary Auto-inflammatory Disorders Mutations Link trackLink variant
  • KAT6BDB
KAT6BDB Variants from the K(lysine) acetyltransferase 6B database, BCM Link trackLink variant
  • LMDD
LMDD Variants from the Leiden Muscular Dystrophy Database Link trackLink variant
  • LSDB
LSDB Variants dbSNP annotates as being from LSDBs Link trackLink variant
  • OIVD
OIVD Variants from the Osteogenesis Imperfecta Variant Database Link trackLink variant
  • PAHdb
PAHdb Variants from the Phenylalanine hydroxylase database Link trackLink variant
  • dbPEX
dbPEX Variants from the PEX Gene Database Link trackLink variant
All phenotype/disease-associated variants ph_variants Variants that have been associated with a phenotype or a disease Link trackLink variant
  • All ClinVar
ClinVar Variants with ClinVar annotation Link trackLink variant
  • COSMIC phenotype variants
ph_cosmic Phenotype annotations of somatic mutations found in human cancers from the COSMIC project Link trackLink variant
  • Clinically associated variants
clin_assoc Variants described by ClinVar as being probable-pathogenic, pathogenic, drug-response or histocompatibility Link trackLink variant
  • HGMD-PUBLIC variants
ph_hgmd_pub Variants annotated by HGMD Link trackLink variant
  • NHGRI-EBI catalog phenotype variants
ph_nhgri Variants associated with phenotype data from the NHGRI-EBI GWAS catalog [http://www.ebi.ac.uk/gwas/] Link trackLink variant
  • OMIM phenotype variants
ph_omim Variants linked to entries in the Online Mendelian Inheritance in Man (OMIM) database Link trackLink variant
  • PhenCode
phencode Variants from the PhenCode Project Link trackLink variant
ESP_6500 esp_6500 Variants from the NHLBI Exome Sequencing Project (investigating heart, lung and blood disorders) Link trackLink variant
ExAC exac Variants identified by the Exome Aggregation Consortium (ExAC) - release 0.3 Link trackLink variant
Genotyping chip variants all_chips Variants which have assays on commercial chips held in ensembl Link trackLink variant
  • Affy GeneChip 500K
Affy_500K Variants from the Affymetrix GeneChip Human Mapping 500K Array Set Link trackLink variant
  • Affy GenomeWideSNP_6.0
Affy_SNP6 Variants from the Affymetrix Genome-Wide Human SNP Array 6.0 Link trackLink variant
  • HumanCoreExome-12
HumanCoreExome Variants from the Illumina HumanCoreExome-12 v1 genotyping chip. Link trackLink variant
  • HumanOmniExpress
HumanOmniExpress Variants from the Illumina HumanOmniExpress 12v1-1_a whole genome genotyping array Link trackLink variant
  • Illumina_1M-duo
Illumina_1M-duo Variants from the Illumina Human1M-duo v3 whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_Cardio-Metabo_Chip
Cardio-Metabo_Chip Variants from the Illumina Cardio-Metabo_Chip genotyping array designed to target variants of interest for metabolic and cardiovascular disease traits Link trackLink variant
  • Illumina_CytoSNP12v1
Illumina_CytoSNP12v1 Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis Link trackLink variant
  • Illumina_ExomeChip
ExomeChip Variants from the Illumina ExomeChip genotyping array designed to target variants within exons Link trackLink variant
  • Illumina_Human610_Quad
Human610_Quad Variants from the Illumina Human610_Quad v1_B whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_Human660W-quad
Illumina_660Q Variants from the Illumina Human660W-quad whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_HumanHap550
HumanHap550 Variants from the Illumina Human550 v3.0 whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_HumanHap650Y
HumanHap650Y Variants from the Illumina HumanHap650Y v3.0 whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_HumanOmni1-Quad
HumanOmni1-Quad Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_HumanOmni2.5
HumanOmni2.5 Variants from the Illumina HumanOmni2.5 4v1 whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_HumanOmni5
HumanOmni5 Variants from the Illumina HumanOmni5v1 whole genome genotyping array designed for association studies Link trackLink variant
  • Illumina_ImmunoChip
ImmunoChip Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases Link trackLink variant
gnomAD gnomAD Variants reported by the Genome Aggregation Database Link trackLink variant
Uniprot variants ph_uniprot Variants with annotations provided by UniProt Link trackLink variant
Failed variations fail_all Variations that have failed the Ensembl QC checks - -