HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
Shared Ancestry Database
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 Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP591.5 generations 96  =  1  +  951.000
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_Papuan-3A + S_Papuan-4A Concordant SGDP 135,282,355 – 136,762,052 1,479,697.0 0.49506966 21 1,107.3103 379.3
S_Papuan-4A + S_English-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Punjabi-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Khonda_Dora-1A Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 60 987.4305 1,215.3
S_Papuan-3A + S_Zapotec-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Turkish-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 24 159.8383 3,003.0
S_Papuan-4A + S_Kyrgyz-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_French-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 11 88.6720 2,481.1
S_Papuan-3A + S_Jordanian-3A Discordant SGDP 136,493,766 – 136,785,841 292,075.0 0.04838542 21 179.9043 2,334.6
S_Papuan-3A + S_Mala-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 37 575.9127 1,284.9
S_Papuan-3A + S_Yadava-2A Discordant SGDP 135,343,836 – 136,976,283 1,632,447.0 0.60553821 135 1,269.0051 2,127.7
S_Papuan-3A + S_Papuan-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-3A + S_Papuan-12B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 83 840.2265 1,975.7
S_Papuan-3A + S_Tubalar-2B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 90 840.2265 2,142.3
S_Papuan-3A + S_Zapotec-2A Discordant SGDP 136,489,176 – 136,976,283 487,107.0 0.26562788 71 447.3137 3,174.5
S_Papuan-4A + S_Estonian-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
S_Papuan-4A + S_Finnish-3A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Mozabite-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 24 159.8383 3,003.0
S_Papuan-4A + S_Iranian-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
S_Papuan-4A + S_Mixe-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 46 552.7512 1,664.4
S_Papuan-4A + S_Lezgin-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 9 88.6720 2,030.0
S_Papuan-4A + S_Mixtec-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Saharawi-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Mongola-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 159.8383 2,502.5
S_Papuan-4A + S_Mansi-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 159.8383 2,752.8
S_Papuan-4A + S_Mongola-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Burusho-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
S_Papuan-4A + S_Altaian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 552.7512 1,411.1
S_Papuan-4A + S_Atayal-1A Discordant SGDP 135,782,261 – 136,631,099 848,838.0 0.06829744 34 463.0802 1,468.4
S_Papuan-4A + S_Tubalar-1B Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 4 1.0085 79,322.3
S_Papuan-4A + S_English-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Even-3B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Estonian-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Tlingit-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 159.8383 2,877.9
S_Papuan-4A + S_Saami-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Aleut-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Basque-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Even-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 42 552.7512 1,519.7
S_Papuan-4A + S_Tuscan-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Cambodian-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 24 159.8383 3,003.0
S_Papuan-4A + S_Orcadian-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 12 88.6720 2,706.6
S_Papuan-4A + S_Cambodian-2B Discordant SGDP 135,340,792 – 136,631,099 1,290,307.0 0.36989600 57 916.2642 1,244.2
S_Papuan-4A + S_Adygei-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 24 159.8383 3,003.0
S_Papuan-4A + S_Naxi-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 54 552.7512 1,953.9
S_Papuan-4A + S_Yemenite_Jew-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 8 88.6720 1,804.4
S_Papuan-4A + S_Miao-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 14 88.6720 3,157.7
S_Papuan-4A + S_Pima-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 25 159.8383 3,128.2
S_Papuan-4A + S_Dai-3B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Eskimo_Naukan-1A Discordant SGDP 135,340,792 – 136,631,099 1,290,307.0 0.36989600 46 916.2642 1,004.1
S_Papuan-4A + S_Miao-2A Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 30 363.8746 1,648.9
S_Papuan-4A + S_Eskimo_Sireniki-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Miao-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 12 88.6720 2,706.6
S_Papuan-4A + S_Brahmin-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Oroqen-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Sindhi-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 13 88.6720 2,932.2
S_Papuan-4A + S_Uygur-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
S_Papuan-4A + S_Bulgarian-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 159.8383 2,752.8
S_Papuan-4A + S_Xibo-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 20 159.8383 2,502.5
S_Papuan-4A + S_Atayal-1B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 159.8383 2,752.8
S_Papuan-4A + S_Xibo-1B Discordant SGDP 135,978,431 – 136,631,099 652,668.0 0.06199239 33 363.8746 1,813.8
S_Papuan-4A + S_English-2A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Yi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 552.7512 1,447.3
S_Papuan-4A + S_BantuKenya-1A Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 4 1.0085 79,322.3
S_Papuan-4A + S_Yi-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 159.8383 2,877.9
S_Papuan-4A + S_Estonian-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Tujia-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 51 552.7512 1,845.3
S_Papuan-4A + S_Finnish-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Mozabite-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 26 159.8383 3,253.3
S_Papuan-4A + S_Finnish-3B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 159.8383 2,752.8
S_Papuan-4A + S_Uygur-2A Discordant SGDP 135,760,398 – 136,762,052 1,001,654.0 0.08787732 51 552.0958 1,847.5
S_Papuan-4A + S_Saami-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 159.8383 2,877.9
S_Papuan-4A + S_Xibo-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 23 159.8383 2,877.9
S_Papuan-4A + S_French-2B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Dai-1A Discordant SGDP 136,556,402 – 136,762,052 205,650.0 0.02360275 17 118.5942 2,866.9
S_Papuan-4A + S_Icelandic-1B Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 10 88.6720 2,255.5
S_Papuan-4A + S_Japanese-1B Discordant SGDP 135,978,431 – 136,762,052 783,620.5 0.07237876 47 435.0408 2,160.7
S_Papuan-4A + S_Samaritan-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
S_Papuan-4A + S_Burmese-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 51 552.7512 1,845.3
S_Papuan-4A + S_Kyrgyz-2B Discordant SGDP 136,616,736 – 136,616,753 17.5 0.00000018 4 1.0085 79,322.3
S_Papuan-4A + S_Ami-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Norwegian-1A Discordant SGDP 136,489,176 – 136,631,099 141,923.0 0.02443623 11 88.6720 2,481.1
S_Papuan-4A + S_Ami-2A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Orcadian-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 22 159.8383 2,752.8
S_Papuan-4A + S_Kinh-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 25 159.8383 3,128.2
S_Papuan-4A + S_North_Ossetian-1A Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Dusun-2B Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 25 159.8383 3,128.2
S_Papuan-4A + S_Spanish-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 24 156.7428 3,062.3
S_Papuan-4A + S_Dusun-1B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Yemenite_Jew-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Papuan-6A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 28 552.7512 1,013.1
S_Papuan-4A + B_Crete-2A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 17 159.8383 2,127.1
S_Papuan-4A + S_Papuan-5A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 552.7512 1,374.9
S_Papuan-4A + S_Piapoco-1A Discordant SGDP 136,489,176 – 136,632,444 143,267.5 0.02479693 10 89.6059 2,232.0
S_Papuan-4A + S_Papuan-13A Discordant SGDP 135,343,836 – 137,188,964 1,845,128.0 1.07760872 85 1,748.7484 972.1
S_Papuan-4A + S_Pima-2B Discordant SGDP 136,616,736 – 136,619,279 2,543.0 0.00113296 4 3.1270 25,583.5
S_Papuan-4A + S_Chukchi-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 21 159.8383 2,627.7
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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