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

rs537707375
Alleles:
reference
C
ancestral
alternate
T
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  136,616,752  (GRCh37) Explore rs537707375 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 96.0%
4.0%
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 Mutation clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP703.6 generations 96  =  1  +  951.000
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_Papuan-3A + S_Papuan-4A Concordant SGDP 135,282,355 – 136,762,052 1,479,697.0 0.49506966 19 711.2546 534.3
S_Papuan-4A + S_English-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Punjabi-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Khonda_Dora-1A Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 58 683.2046 1,697.9
S_Papuan-3A + S_Zapotec-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Turkish-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 131.9802 3,333.8
S_Papuan-4A + S_Kyrgyz-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_French-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 9 69.1230 2,604.1
S_Papuan-3A + S_Jordanian-3A Discordant SGDP 136,493,766 – 136,785,841 292,075.0 0.04838542 19 141.1960 2,691.3
S_Papuan-3A + S_Mala-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 35 493.3566 1,418.9
S_Papuan-3A + S_Yadava-2A Discordant SGDP 135,343,836 – 136,976,283 1,632,447.0 0.60553821 133 784.5746 3,390.4
S_Papuan-3A + S_Papuan-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-3A + S_Papuan-12B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 81 584.7690 2,770.3
S_Papuan-3A + S_Tubalar-2B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 88 584.7690 3,009.7
S_Papuan-3A + S_Zapotec-2A Discordant SGDP 136,489,176 – 136,976,283 487,107.0 0.26562788 69 234.8114 5,877.1
S_Papuan-4A + S_Estonian-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
S_Papuan-4A + S_Finnish-3A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Mozabite-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 131.9802 3,333.8
S_Papuan-4A + S_Iranian-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
S_Papuan-4A + S_Mixe-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 44 481.9379 1,826.0
S_Papuan-4A + S_Lezgin-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 7 69.1230 2,025.4
S_Papuan-4A + S_Mixtec-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Saharawi-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Mongola-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 18 131.9802 2,727.7
S_Papuan-4A + S_Mansi-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 131.9802 3,030.8
S_Papuan-4A + S_Mongola-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Burusho-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
S_Papuan-4A + S_Altaian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 481.9379 1,535.5
S_Papuan-4A + S_Atayal-1A Discordant SGDP 135,782,261 – 136,631,099 848,838.0 0.06829744 32 408.4422 1,566.9
S_Papuan-4A + S_Tubalar-1B Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 2 1.0084 39,666.8
S_Papuan-4A + S_English-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Even-3B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Estonian-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Tlingit-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 131.9802 3,182.3
S_Papuan-4A + S_Saami-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Aleut-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Basque-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Even-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 481.9379 1,660.0
S_Papuan-4A + S_Tuscan-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Cambodian-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 131.9802 3,333.8
S_Papuan-4A + S_Orcadian-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 69.1230 2,893.4
S_Papuan-4A + S_Cambodian-2B Discordant SGDP 135,340,792 – 136,631,099 1,290,307.0 0.36989600 55 620.3474 1,773.2
S_Papuan-4A + S_Adygei-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 131.9802 3,333.8
S_Papuan-4A + S_Naxi-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 52 481.9379 2,158.0
S_Papuan-4A + S_Yemenite_Jew-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 6 69.1230 1,736.0
S_Papuan-4A + S_Miao-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 12 69.1230 3,472.1
S_Papuan-4A + S_Pima-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 131.9802 3,485.4
S_Papuan-4A + S_Dai-3B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Eskimo_Naukan-1A Discordant SGDP 135,340,792 – 136,631,099 1,290,307.0 0.36989600 44 620.3474 1,418.6
S_Papuan-4A + S_Miao-2A Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 28 314.2806 1,781.8
S_Papuan-4A + S_Eskimo_Sireniki-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Miao-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 69.1230 2,893.4
S_Papuan-4A + S_Brahmin-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Oroqen-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Sindhi-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 11 69.1230 3,182.7
S_Papuan-4A + S_Uygur-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
S_Papuan-4A + S_Bulgarian-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 131.9802 3,030.8
S_Papuan-4A + S_Xibo-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 18 131.9802 2,727.7
S_Papuan-4A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 131.9802 3,030.8
S_Papuan-4A + S_Xibo-1B Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 31 314.2806 1,972.8
S_Papuan-4A + S_English-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 481.9379 1,577.0
S_Papuan-4A + S_BantuKenya-1A Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 2 1.0084 39,666.8
S_Papuan-4A + S_Yi-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 131.9802 3,182.3
S_Papuan-4A + S_Estonian-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 49 481.9379 2,033.5
S_Papuan-4A + S_Finnish-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Mozabite-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 24 131.9802 3,636.9
S_Papuan-4A + S_Finnish-3B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 131.9802 3,030.8
S_Papuan-4A + S_Uygur-2A Discordant SGDP 135,760,398 – 136,762,052 1,001,654.0 0.08787732 49 481.7939 2,034.1
S_Papuan-4A + S_Saami-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 131.9802 3,182.3
S_Papuan-4A + S_Xibo-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 131.9802 3,182.3
S_Papuan-4A + S_French-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Dai-1A Discordant SGDP 136,556,402 – 136,762,052 205,650.0 0.02360275 15 99.7120 3,008.7
S_Papuan-4A + S_Icelandic-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 69.1230 2,314.7
S_Papuan-4A + S_Japanese-1B Discordant SGDP 135,978,431 – 136,762,052 783,620.5 0.07237876 45 377.1378 2,386.4
S_Papuan-4A + S_Samaritan-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
S_Papuan-4A + S_Burmese-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 49 481.9379 2,033.5
S_Papuan-4A + S_Kyrgyz-2B Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 2 1.0084 39,666.8
S_Papuan-4A + S_Ami-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Norwegian-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 9 69.1230 2,604.1
S_Papuan-4A + S_Ami-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Orcadian-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 131.9802 3,030.8
S_Papuan-4A + S_Kinh-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 131.9802 3,485.4
S_Papuan-4A + S_North_Ossetian-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Dusun-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 131.9802 3,485.4
S_Papuan-4A + S_Spanish-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 22 129.7773 3,390.4
S_Papuan-4A + S_Dusun-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Yemenite_Jew-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Papuan-6A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 26 481.9379 1,079.0
S_Papuan-4A + B_Crete-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 15 131.9802 2,273.1
S_Papuan-4A + S_Papuan-5A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 36 481.9379 1,494.0
S_Papuan-4A + S_Piapoco-1A Discordant SGDP 136,489,176 – 136,632,444 143,267.5 0.02479693 8 69.7684 2,293.3
S_Papuan-4A + S_Papuan-13A Discordant SGDP 135,343,836 – 137,188,964 1,845,128.0 1.07760872 83 886.6614 1,872.2
S_Papuan-4A + S_Pima-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 2 2.2206 18,012.8
S_Papuan-4A + S_Chukchi-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 19 131.9802 2,879.2
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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