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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs12257591
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 10   position  31,822,106  (GRCh37) Explore rs12257591 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.4%
1.6%
AFR 90.9%
9.1%
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 99.3%
0.7%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP18,841.8 generations 136  =  36  +  1000.980
Pairwise results table Mutation clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Saharawi-2A + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Saharawi-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Saharawi-2A + S_Esan-1B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 3 3.6189 16,579.7
S_Esan-1B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Saharawi-2A + S_Luhya-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 2 3.6189 11,053.1
S_Yoruba-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Esan-1B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Luhya-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 1 2.3622 8,466.5
S_Luhya-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 2 2.3622 16,933.1
S_Biaka-2A + S_Esan-2B Concordant SGDP 31,822,100 – 31,841,841 19,741.5 0.00198474 10 10.4759 19,091.4
S_Biaka-2A + S_Khomani_San-2B Concordant SGDP 31,693,149 – 31,822,112 128,963.0 0.00457854 47 62.9022 14,943.8
S_Biaka-2A + S_Esan-1B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Biaka-2A + S_Yoruba-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Biaka-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Esan-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Luhya-2B + S_Yoruba-2B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 36 67.5345 10,661.2
S_Khomani_San-2B + S_Georgian-2B Concordant SGDP 31,822,025 – 31,822,112 87.0 0.00000145 1 1.0418 19,198.3
S_Luhya-2B + S_Esan-1B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 37 67.5345 10,957.4
S_Esan-1B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Luhya-2B + S_Esan-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 2 2.3622 16,933.1
S_Esan-1B + S_Esan-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 3 3.6189 16,579.7
S_Luhya-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Saharawi-2A + S_Biaka-2A Concordant SGDP 31,820,336 – 31,841,841 21,505.0 0.00222725 11 11.3224 19,430.5
S_Georgian-2B + B_Mbuti-4A Concordant SGDP 31,821,907 – 31,822,112 204.5 0.00000342 1 1.0982 18,212.3
S_Saharawi-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Yoruba-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Saharawi-2A + S_Yoruba-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 1 2.2624 8,840.2
S_Yoruba-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 32,051,343 229,243.0 0.33866899 49 111.0366 8,825.9
S_Saharawi-2A + S_Esan-2B Concordant SGDP 31,614,944 – 31,965,047 350,103.0 0.24796352 13 169.0494 1,538.0
S_Yoruba-2B + S_Esan-1B Concordant SGDP 31,536,157 – 31,874,064 337,906.5 0.12244606 12 163.1951 1,470.6
S_Esan-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Yoruba-2B + S_Esan-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 1 2.2624 8,840.2
S_Esan-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Khomani_San-2B + B_Mbuti-4A Concordant SGDP 31,485,956 – 31,824,938 338,982.0 0.02792865 165 163.7114 20,157.4
S_Biaka-2A + S_Luhya-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.3622 25,399.6
S_Biaka-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 1 1.0058 19,885.5
S_Esan-1B + S_North_Ossetian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Jordanian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Palestinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Punjabi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Czech-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Palestinian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Georgian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_French-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Chane-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Jordanian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Orcadian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Brahmin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Spanish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Albanian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + B_Sardinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Finnish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Zapotec-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Iraqi_Jew-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Quechua-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Even-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Orcadian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Aleut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + B_French-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Burmese-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Piapoco-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Abkhasian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Bulgarian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Atayal-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Biaka-2A + S_Polish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_English-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Georgian-2B + S_Saharawi-2B Discordant SGDP 31,484,549 – 31,841,841 357,292.0 0.03021478 8 172.5002 927.5
S_Yoruba-2B + S_Saami-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Tubalar-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Georgian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Yakut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Greek-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Tu-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Iraqi_Jew-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Uygur-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_She-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Tuscan-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Korean-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Kyrgyz-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Thai-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Chechen-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Maori-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Maori-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Pima-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Bougainville-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Mixtec-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Ulchi-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_BantuTswana-1B Discordant SGDP 31,536,157 – 32,453,323 917,166.0 0.54162157 20 441.2397 906.5
S_Yoruba-2B + S_Papuan-10B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Burmese-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Bougainville-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-14A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Mala-3A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-7A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Madiga-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-7B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Luhya-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-9B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Albanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-12A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Finnish-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Papuan-12B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Basque-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Chukchi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Iraqi_Jew-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Mansi-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Samaritan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Bengali-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Bergamo-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Kapu-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Relli-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Jordanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Irula-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Lezgin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Mala-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Pathan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + B_Papuan-15B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Hazara-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Esan-1B + S_Karitiana-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Kalash-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Saharawi-2A + S_Mende-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
S_Yoruba-2B + S_Kalash-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 2 1.0058 39,770.9
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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