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Population frequencies & genotypes

Ensembl Variation - Population allele frequencies & genotypes

We provide allele frequency data from a range of different projects including the 1000 Genomes Project and the genome Aggregation Database (gnomAD).
Genotype data is also available for a number of studies including the 1000 Genomes Project and NextGen livestock project. Frequencies displayed (to three decimal places) may not add up to one due to rounding.

Minor Alleles

Minor alleles and their frequencies are available for variants discovered in the 1000 Genomes Project.
These are calculated by dbSNP. If there are more than two alleles, the second most common is reported (See example: rs200077393).
This allows common variants to be distinguished from rare variants in situations where deep sequencing has identified a third rare allele.

Populations

Below we list the populations associated with the larger variant discovery projects available in Ensembl:

Populations from the 1000 Genomes Project

Name Size Description
1000GENOMES:phase_3:ALL 2504 All phase 3 individuals
1000GENOMES:phase_3:AFR 661 African
  • 1000GENOMES:phase_3:ACB
96 African Caribbean in Barbados
  • 1000GENOMES:phase_3:ASW
61 African Ancestry in Southwest US
  • 1000GENOMES:phase_3:ESN
99 Esan in Nigeria
  • 1000GENOMES:phase_3:GWD
113 Gambian in Western Division, The Gambia
  • 1000GENOMES:phase_3:LWK
99 Luhya in Webuye, Kenya
  • 1000GENOMES:phase_3:MSL
85 Mende in Sierra Leone
  • 1000GENOMES:phase_3:YRI
108 Yoruba in Ibadan, Nigeria
1000GENOMES:phase_3:AMR 347 American
  • 1000GENOMES:phase_3:CLM
94 Colombian in Medellin, Colombia
  • 1000GENOMES:phase_3:MXL
64 Mexican Ancestry in Los Angeles, California
  • 1000GENOMES:phase_3:PEL
85 Peruvian in Lima, Peru
  • 1000GENOMES:phase_3:PUR
104 Puerto Rican in Puerto Rico
1000GENOMES:phase_3:EAS 504 East Asian
  • 1000GENOMES:phase_3:CDX
93 Chinese Dai in Xishuangbanna, China
  • 1000GENOMES:phase_3:CHB
103 Han Chinese in Bejing, China
  • 1000GENOMES:phase_3:CHS
105 Southern Han Chinese, China
  • 1000GENOMES:phase_3:JPT
104 Japanese in Tokyo, Japan
  • 1000GENOMES:phase_3:KHV
99 Kinh in Ho Chi Minh City, Vietnam
1000GENOMES:phase_3:EUR 503 European
  • 1000GENOMES:phase_3:CEU
99 Utah residents with Northern and Western European ancestry
  • 1000GENOMES:phase_3:FIN
99 Finnish in Finland
  • 1000GENOMES:phase_3:GBR
91 British in England and Scotland
  • 1000GENOMES:phase_3:IBS
107 Iberian populations in Spain
  • 1000GENOMES:phase_3:TSI
107 Toscani in Italy
1000GENOMES:phase_3:SAS 489 South Asian
  • 1000GENOMES:phase_3:BEB
86 Bengali in Bangladesh
  • 1000GENOMES:phase_3:GIH
103 Gujarati Indian in Houston, TX
  • 1000GENOMES:phase_3:ITU
102 Indian Telugu in the UK
  • 1000GENOMES:phase_3:PJL
96 Punjabi in Lahore, Pakistan
  • 1000GENOMES:phase_3:STU
102 Sri Lankan Tamil in the UK

Variants which have been discovered in this project have the "evidence status" 1000Genomes. On the website this corresponds to the icon .

Populations from the NHLBI Exome Sequencing Project

Name Size Description
ESP6500:AA - African American
ESP6500:EA - European American

Population from TOPMed

Name Size Description
TOPMed - Trans-Omics for Precision Medicine (TOPMed) Program

Variants which have been discovered in this project have the "evidence status" TOPMed. On the website this corresponds to the icon .

Populations from UK10K

Name Size Description
UK10K:ALSPAC - ALSPAC cohort
UK10K:TWINSUK - TWINSUK cohort excluding 67 samples where a monozygotic or dyzygotic twin was included in the release

Populations from gnomAD exomes

Name Size Description
gnomADe:ALL - All gnomAD exomes individuals
gnomADe:afr - African/African American
gnomADe:amr - Latino
gnomADe:asj - Ashkenazi Jewish
gnomADe:eas - East Asian
gnomADe:fin - Finnish
gnomADe:nfe - Non-Finnish European
gnomADe:oth - Other
gnomADe:sas - South Asian

Variants which have been discovered in this project have the "evidence status" gnomAD. On the website this corresponds to the icon .

Populations from gnomAD genomes

Name Size Description
gnomADg:ALL - All gnomAD genomes individuals
gnomADg:afr - African/African American
gnomADg:amr - Latino
gnomADg:asj - Ashkenazi Jewish
gnomADg:eas - East Asian
gnomADg:fin - Finnish
gnomADg:nfe - Non-Finnish European
gnomADg:oth - Other

Variants which have been discovered in this project have the "evidence status" gnomAD. On the website this corresponds to the icon .