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:
| Name |
Size |
Description |
| 1000GENOMES:phase_3:ALL |
2504 |
All phase 3 individuals |
| 1000GENOMES:phase_3:AFR |
661 |
African |
|
96 |
African Caribbean in Barbados |
|
61 |
African Ancestry in Southwest US |
|
99 |
Esan in Nigeria |
|
113 |
Gambian in Western Division, The Gambia |
|
99 |
Luhya in Webuye, Kenya |
|
85 |
Mende in Sierra Leone |
|
108 |
Yoruba in Ibadan, Nigeria |
| 1000GENOMES:phase_3:AMR |
347 |
American |
|
94 |
Colombian in Medellin, Colombia |
|
64 |
Mexican Ancestry in Los Angeles, California |
|
85 |
Peruvian in Lima, Peru |
|
104 |
Puerto Rican in Puerto Rico |
| 1000GENOMES:phase_3:EAS |
504 |
East Asian |
|
93 |
Chinese Dai in Xishuangbanna, China |
|
103 |
Han Chinese in Bejing, China |
|
105 |
Southern Han Chinese, China |
|
104 |
Japanese in Tokyo, Japan |
|
99 |
Kinh in Ho Chi Minh City, Vietnam |
| 1000GENOMES:phase_3:EUR |
503 |
European |
|
99 |
Utah residents with Northern and Western European ancestry |
|
99 |
Finnish in Finland |
|
91 |
British in England and Scotland |
|
107 |
Iberian populations in Spain |
|
107 |
Toscani in Italy |
| 1000GENOMES:phase_3:SAS |
489 |
South Asian |
|
86 |
Bengali in Bangladesh |
|
103 |
Gujarati Indian in Houston, TX |
|
102 |
Indian Telugu in the UK |
|
96 |
Punjabi in Lahore, Pakistan |
|
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 
.
Population from GEM-J
| Name |
Size |
Description |
| GEM-J |
- |
GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel |
| 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 |
| 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 .
| 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 .
