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

rs373267093
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  136,585,219  (GRCh37) Explore rs373267093 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.9%
1.1%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 88.0%
12.0%
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 Recombination clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP73.8 generations 105  =  11  +  940.091
Pairwise results table Recombination clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Papuan-5B + S_Papuan-12B Concordant SGDP 135,758,336 – 136,646,325 887,989.0 0.09856159 3 79.8493 751.4
S_Papuan-5A + S_Papuan-4A Concordant SGDP 135,758,336 – 136,762,052 1,003,716.0 0.10634626 3 86.0770 697.1
S_Papuan-5B + S_Papuan-5A Concordant SGDP 135,758,336 – 136,646,325 887,989.0 0.09856159 3 79.8493 751.4
S_Papuan-6A + S_Papuan-4A Concordant SGDP 135,758,336 – 136,762,052 1,003,716.0 0.10634626 3 86.0770 697.1
S_Papuan-6A + S_Papuan-12B Concordant SGDP 135,758,336 – 136,788,485 1,030,149.5 0.15304406 3 123.4353 486.1
S_Papuan-6A + S_Papuan-5B Concordant SGDP 135,758,336 – 136,646,325 887,989.0 0.09856159 3 79.8493 751.4
S_Papuan-3A + S_Papuan-12B Concordant SGDP 135,757,046 – 136,976,448 1,219,402.0 0.36788382 3 295.3071 203.2
S_Papuan-3A + S_Papuan-4A Concordant SGDP 135,282,355 – 136,762,052 1,479,697.0 0.49506966 3 397.0557 151.1
S_Papuan-4A + S_Papuan-12B Concordant SGDP 135,758,336 – 136,762,052 1,003,716.0 0.10634626 3 86.0770 697.1
S_Papuan-3A + S_Papuan-5B Concordant SGDP 135,339,363 – 136,631,099 1,291,736.0 0.38765847 3 311.1268 192.8
S_Papuan-3A + S_Papuan-6A Concordant SGDP 135,758,336 – 136,789,046 1,030,710.0 0.16203451 3 130.6276 459.3
S_Papuan-4A + S_Estonian-2A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Chukchi-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Punjabi-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Mozabite-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Ami-2A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Kyrgyz-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Saharawi-2A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-3A + S_Adygei-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-3A + S_Surui-1B Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 3 316.9687 189.3
S_Papuan-3A + S_Papuan-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 3 343.3881 174.7
S_Papuan-3A + S_Mala-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-3A + S_Thai-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-3A + S_Cambodian-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Papuan-3A + S_Tubalar-2B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 3 256.4575 234.0
S_Papuan-4A + S_Saami-1A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-3A + S_Karitiana-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Icelandic-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-6A + S_Even-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Adygei-2A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-6A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Papuan-3A + S_Zapotec-2A Discordant SGDP 136,489,176 – 136,976,283 487,107.0 0.26562788 3 213.5023 281.0
S_Papuan-6A + S_Tujia-1A Discordant SGDP 135,760,098 – 136,784,585 1,024,487.5 0.10077474 3 81.6198 735.1
S_Papuan-4A + S_Dai-1B Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 3 50.5939 1,185.9
S_Papuan-6A + S_Eskimo_Sireniki-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Papuan-4A + S_Dusun-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-6A + B_Crete-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Khonda_Dora-1A Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 3 305.2259 196.6
S_Papuan-5B + S_Lezgin-2B Discordant SGDP 136,489,176 – 136,646,325 157,148.5 0.02703793 3 22.6303 2,651.3
S_Papuan-4A + S_English-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5B + S_Piapoco-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Finnish-3A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-4A + S_Mozabite-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_French-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-4A + S_Even-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Papuan-4A + S_Iranian-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Aleut-2A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Orcadian-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Oroqen-1B Discordant SGDP 136,489,176 – 136,590,087 100,911.0 0.01679429 3 14.4354 4,156.4
S_Papuan-4A + S_Yemenite_Jew-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Xibo-1B Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 3 50.5939 1,185.9
S_Papuan-5A + S_Tubalar-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-3A + S_Zapotec-1A Discordant SGDP 136,489,176 – 137,032,475 543,298.5 0.37429113 3 300.4329 199.7
S_Papuan-5B + B_Sardinian-3A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5A + S_Naxi-2A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-5B + S_Pima-2A Discordant SGDP 136,489,176 – 136,642,620 153,443.5 0.02626792 3 22.0143 2,725.5
S_Papuan-5A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Papuan-4A + S_Mongola-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5A + S_Xibo-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Tlingit-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5A + S_Mansi-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Miao-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5A + S_Sindhi-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Xibo-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Yi-2B Discordant SGDP 136,489,176 – 136,590,087 100,911.0 0.01679429 3 14.4354 4,156.4
S_Papuan-5A + S_English-2B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Uygur-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5A + S_Estonian-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Burmese-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Papuan-5A + S_Basque-1A Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Kinh-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5A + S_Norwegian-1B Discordant SGDP 136,489,176 – 136,785,841 296,664.5 0.04950107 3 40.6009 1,477.8
S_Papuan-4A + S_Papuan-13A Discordant SGDP 135,343,836 – 137,188,964 1,845,128.0 1.07760872 3 863.0870 69.5
S_Papuan-5A + S_Spanish-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_Papuan-4A + S_Eskimo_Naukan-1A Discordant SGDP 135,340,792 – 136,631,099 1,290,307.0 0.36989600 3 296.9168 202.1
S_Papuan-5A + S_Yemenite_Jew-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-4A + S_Brahmin-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_Papuan-5A + S_Pima-1A Discordant SGDP 136,489,176 – 136,585,227 96,050.5 0.01506635 3 13.0531 4,596.6
S_Papuan-4A + S_Bulgarian-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5B + S_Mixtec-2A Discordant SGDP 136,489,176 – 136,642,620 153,443.5 0.02626792 3 22.0143 2,725.5
S_Papuan-4A + S_English-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5B + S_Altaian-1B Discordant SGDP 135,760,098 – 136,646,325 886,227.0 0.08073192 3 65.5855 914.8
S_Papuan-4A + S_Finnish-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5B + S_Cambodian-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_BantuKenya-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5B + S_Cambodian-2A Discordant SGDP 135,760,098 – 136,646,325 886,227.0 0.08073192 3 65.5855 914.8
S_Papuan-4A + S_Saami-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5B + S_Naxi-3A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Basque-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5B + S_Uygur-1A Discordant SGDP 136,489,176 – 136,646,325 157,148.5 0.02703793 3 22.6303 2,651.3
S_Papuan-4A + S_Icelandic-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5B + S_Xibo-2A Discordant SGDP 135,760,098 – 136,642,620 882,522.0 0.07996192 3 64.9695 923.5
S_Papuan-4A + S_Tuscan-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5B + S_Japanese-1A Discordant SGDP 135,760,398 – 136,646,325 885,927.0 0.08009265 3 65.0741 922.0
S_Papuan-4A + S_Orcadian-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 3 20.5490 2,919.9
S_Papuan-5B + S_Dusun-2B Discordant SGDP 136,489,176 – 136,642,620 153,443.5 0.02626792 3 22.0143 2,725.5
S_Papuan-4A + S_North_Ossetian-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5B + S_Burusho-2B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-4A + S_Turkish-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-5B + S_French-2B Discordant SGDP 136,489,176 – 136,646,325 157,148.5 0.02703793 3 22.6303 2,651.3
S_Papuan-4A + S_Yemenite_Jew-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 3 28.8581 2,079.1
S_Papuan-5B + S_Samaritan-1B Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
S_Papuan-12B + S_Yadava-2A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 3 256.4575 234.0
S_Papuan-5B + S_Kyrgyz-1A Discordant SGDP 136,585,210 – 136,585,227 17.0 0.00000849 3 1.0068 59,595.2
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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