HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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TGP
1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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SGDP
Simons Genome Diversity Project
Populations: 130
Individuals: 278
Ancestry analyses:6,800,992
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Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

rs374301338
Alleles:
reference
G
ancestral
alternate
A
derived
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
How was the ancestral/derived state determined?Chromosome 2   position  109,571,975  (GRCh37) Explore rs374301338 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 97.7%
2.3%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
SAS 100.0%
0.0%
WEA 100.0%
0.0%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Joint clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,600.8 generations 94  =  1  +  930.989
Pairwise results table Joint clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_BantuHerero-2A + S_Biaka-1B Concordant SGDP 109,556,534 – 109,583,531 26,996.5 0.02320276 4 32.5205 2,460.0
S_Biaka-1B + B_Mbuti-4B Discordant SGDP 109,558,177 – 109,581,776 23,599.5 0.01198719 12 21.9175 10,950.1
S_Biaka-1B + S_Ju_hoan_North-1B Discordant SGDP 108,954,234 – 109,572,000 617,765.5 0.29227743 124 531.3494 4,667.4
S_Biaka-1B + S_Lezgin-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Jordanian-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + B_Sardinian-3A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Hazara-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Surui-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mbuti-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Burmese-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mbuti-3B Discordant SGDP 109,320,672 – 109,572,000 251,328.0 0.15447411 80 245.2167 6,524.8
S_Biaka-1B + S_Biaka-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Tlingit-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Tubalar-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_BantuTswana-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Saharawi-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mende-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mbuti-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_BantuTswana-1B Discordant SGDP 108,954,234 – 109,572,000 617,765.5 0.29227743 50 531.3494 1,882.0
S_Biaka-1B + S_Gambian-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Basque-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_BantuKenya-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Mende-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mansi-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Russian-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Bengali-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Adygei-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Yadava-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Yoruba-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Irula-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + B_Yoruba-3A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Somali-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mandenka-2A Discordant SGDP 109,558,177 – 109,581,776 23,599.5 0.01198719 11 21.9175 10,037.6
S_Biaka-1B + S_Brahmin-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Dinka-2A Discordant SGDP 109,567,339 – 109,579,056 11,717.5 0.00341312 6 9.3549 12,827.5
S_Biaka-1B + S_Kusunda-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Piapoco-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Luhya-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Gambian-2A Discordant SGDP 108,954,234 – 109,572,000 617,765.5 0.29227743 57 531.3494 2,145.5
S_Biaka-1B + S_Brahui-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Finnish-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Brahui-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Iranian-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Luo-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Mandenka-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Sindhi-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mozabite-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Punjabi-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Orcadian-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Punjabi-4A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Saharawi-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Luhya-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_North_Ossetian-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Bulgarian-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Ju_hoan_North-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_BantuKenya-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + B_Crete-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Estonian-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + B_Mbuti-4A Discordant SGDP 109,132,345 – 109,579,056 446,711.0 0.18519622 123 363.5783 6,766.1
S_Biaka-1B + S_Estonian-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + B_Ju_hoan_North-4A Discordant SGDP 109,151,036 – 109,572,000 420,963.5 0.18095297 117 347.8249 6,727.5
S_Biaka-1B + S_Finnish-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + B_Dinka-3A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Finnish-3B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Esan-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_French-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Mende-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Georgian-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Khomani_San-1A Discordant SGDP 109,552,851 – 109,572,000 19,149.0 0.01261965 22 20.2872 21,688.5
S_Biaka-1B + S_Georgian-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Surui-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Greek-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Piapoco-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Hungarian-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_BantuHerero-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Hungarian-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Gambian-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Icelandic-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Khonda_Dora-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Iranian-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Finnish-2A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Masai-1A Discordant SGDP 108,954,234 – 109,572,000 617,765.5 0.29227743 118 531.3494 4,441.5
S_BantuHerero-2A + S_French-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Druze-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Masai-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Palestinian-3B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Abkhasian-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_BedouinB-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Yoruba-2B Discordant SGDP 108,826,342 – 109,572,000 745,658.0 0.49633307 46 755.9823 1,217.0
S_Biaka-1B + S_Luo-1A Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Mandenka-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Bergamo-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_BantuHerero-2A + S_Saharawi-2B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
S_Biaka-1B + S_Tuscan-1B Discordant SGDP 109,571,973 – 109,572,000 26.5 0.00000650 4 1.0179 78,591.9
View as figure
Data shown in this table can be downloaded from this page.
α Shape parameter of the Gamma distribution, calculated from the number of pairwise differences along the sequence of the inferred shared haplotype segment (mutation clock), or the breakpoints detected (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
β Rate parameter of the Gamma distribution, calculated from the physical length of the inferred shared haplotype segment and the mutation rate (mutation clock), or the genetic length given the variable recombination rate (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
Mean TMRCA Calculated as the mean of the Gamma distribution with parameters α and β, multiplied by 2 x Ne, where Ne = 10,000 by default.
 

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