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).

Variant sets common to all species

Name	Short name	Description
Failed variations	fail_all	Variations that have failed the Ensembl QC checks

Human (Homo sapiens)

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

Variant sets for the non-human species

Cattle (Bos taurus)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
Illumina BovineHD BeadChip	BovineHD	Variants from the Illumina BovineHD BeadChip genotyping array	track	variant
Illumina BovineLD BeadChip	BovineLD	Variants from the Illumina BovineLD BeadChip genotyping array	track	variant
Illumina BovineSNP50 BeadChip	BovineSNP50	Variants from the Illumina BovineSNP50 BeadChip genotyping array	track	variant

Chicken (Gallus gallus)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
Affymetrix Chicken600K Array	Chicken600K	Variants from the Affymetrix Chicken600K genotyping array	track	variant

Goat (Capra hircus)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
Illumina_GoatSNP50	GoatSNP50	Variants from the Illumina GoatSNP50 genotyping array	track	variant

Horse (Equus caballus)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
Illumina EquineSNP50 BeadChip	Illumina_EquineSNP50	Variants from the Illumina EquineSNP50 BeadChip genotyping array	track	variant

Mouse (Mus musculus)

Name	Short name	Description	Examples
Mouse Genomes Project	MGP	Variants genotyped by the Mouse Genomes Project	track	variant

Pig (Sus scrofa)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
Axiom Genotyping Array	Affy_PorcineHD	Axiom Porcine Genotyping Array from Affymetrix	track	variant
GGP Porcine HD	PorcineHD	GeneSeek Genomic Profiler Porcine - HD	track	variant
GGP Porcine LD	PorcineLD	GeneSeek Genomic Profiler Porcine - LD BeadChip	track	variant
Illumina_PorcineSNP60	PorcineSNP60	PorcineSNP60 BeadChip	track	variant

Sheep (Ovis aries)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
IlluminaOvineHDSNP	OvineHDSNP	Illumina Ovine Infinium HD SNP BeadChip	track	variant
IlluminaOvineSNP50	OvineSNP50	Illumina OvineSNP50 BeadChip	track	variant

Sheep - Texel (Ovis aries texel)

Name	Short name	Description	Examples
Genotyping chip variants	all_chips	Variants which have assays on commercial chips held in ensembl	track	variant
IlluminaOvineHDSNP	OvineHDSNP	Illumina Ovine Infinium HD SNP BeadChip	track	variant
IlluminaOvineSNP50	OvineSNP50	Illumina OvineSNP50 BeadChip	track	variant