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

rs893295820
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  136,538,395  (GRCh37) Explore rs893295820 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
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 98.7%
1.3%
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 SGDP177.5 generations 96  =  3  +  930.333
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_BantuTswana-1B + S_Madiga-1A Concordant SGDP 136,537,504 – 136,603,542 66,037.5 0.01252909 5 42.7213 2,340.8
S_Mozabite-1B + S_Madiga-1A Concordant SGDP 135,757,046 – 136,603,542 846,496.0 0.11331060 9 497.9666 361.5
S_Mozabite-1B + S_BantuTswana-1B Concordant SGDP 136,537,504 – 136,787,770 250,265.5 0.06380881 11 172.1745 1,277.8
S_Mozabite-1B + S_Norwegian-1B Discordant SGDP 136,080,619 – 137,032,475 951,855.5 0.40798207 32 784.2763 816.0
S_Mozabite-1B + S_Bergamo-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_Icelandic-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 23 954.1291 482.1
S_Madiga-1A + S_Eskimo_Naukan-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Piapoco-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 552.7512 1,411.1
S_Mozabite-1B + S_Yemenite_Jew-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 35 552.7512 1,266.4
S_Mozabite-1B + S_Tlingit-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Tubalar-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Mongola-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 11 552.7512 398.0
S_Mozabite-1B + S_Mixtec-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Mixtec-1A Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 33 852.3498 774.3
S_Mozabite-1B + S_Mixe-3B Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 29 552.2494 1,050.3
S_Mozabite-1B + S_Lezgin-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 552.7512 1,411.1
S_Mozabite-1B + S_Spanish-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_Aleut-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 15 954.1291 314.4
S_Mozabite-1B + B_Mixe-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 40 647.4773 1,235.6
S_Mozabite-1B + S_Naxi-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Madiga-1A + S_Eskimo_Sireniki-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 41 552.7512 1,483.5
S_Mozabite-1B + S_Dai-3A Discordant SGDP 135,597,516 – 136,762,052 1,164,536.0 0.24705801 60 757.6237 1,583.9
S_Madiga-1A + S_North_Ossetian-2A Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 17 463.7386 733.2
S_Mozabite-1B + S_Miao-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 552.7512 1,411.1
S_Mozabite-1B + S_Georgian-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Uygur-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Iranian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 44 987.4305 891.2
S_Mozabite-1B + S_Xibo-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 34 552.7512 1,230.2
S_Mozabite-1B + S_Jordanian-3B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Yi-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 36 552.7512 1,302.6
S_Mozabite-1B + S_Orcadian-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 13 954.1291 272.5
S_Mozabite-1B + S_Xibo-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 552.7512 1,374.9
S_Mozabite-1B + S_Lezgin-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_Thai-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Tajik-2A Discordant SGDP 135,760,098 – 136,538,417 778,319.5 0.05991390 60 422.5245 2,840.1
S_Mozabite-1B + S_Kinh-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 35 552.7512 1,266.4
S_Mozabite-1B + B_Crete-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 30 552.7512 1,085.5
S_Mozabite-1B + S_Dusun-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Surui-2B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 30 647.4773 926.7
S_Mozabite-1B + S_Maori-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 13 647.4773 401.6
S_Madiga-1A + S_Mixe-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 41 552.7512 1,483.5
S_Mozabite-1B + S_Maori-1B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 20 647.4773 617.8
S_Madiga-1A + S_Oroqen-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Mozabite-1B + S_Chukchi-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 13 954.1291 272.5
S_Madiga-1A + S_Czech-2A Discordant SGDP 135,384,127 – 136,603,542 1,219,415.0 0.35233943 28 868.1907 645.0
S_Mozabite-1B + S_Mozabite-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Madiga-1A + S_Chane-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Mozabite-1B + S_Mansi-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 35 552.7512 1,266.4
S_Mozabite-1B + S_Basque-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 13 954.1291 272.5
S_Mozabite-1B + S_Brahmin-2B Discordant SGDP 135,778,044 – 136,976,283 1,198,239.5 0.31058545 51 824.6233 1,236.9
S_Mozabite-1B + S_Greek-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 24 649.9127 738.6
S_Mozabite-1B + S_Balochi-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_Icelandic-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 14 954.1291 293.5
S_Mozabite-1B + S_Brahui-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 16 649.9127 492.4
S_Mozabite-1B + S_Bergamo-2A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 649.9127 338.5
S_Mozabite-1B + S_Makrani-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Tuscan-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Pathan-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Norwegian-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 19 649.9127 584.7
S_Mozabite-1B + S_Burusho-2A Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 42 537.1480 1,563.8
S_Mozabite-1B + S_Orcadian-1A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 16 840.2265 380.8
S_Mozabite-1B + S_Hazara-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Polish-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 9 649.9127 277.0
S_Mozabite-1B + S_Sindhi-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 14 954.1291 293.5
S_Mozabite-1B + S_Lezgin-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_Punjabi-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 15 954.1291 314.4
S_Mozabite-1B + S_North_Ossetian-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 17 954.1291 356.3
S_Mozabite-1B + S_Punjabi-4B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 649.9127 338.5
S_Mozabite-1B + S_Spanish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 43 552.7512 1,555.9
S_Mozabite-1B + S_Bulgarian-1B Discordant SGDP 136,021,995 – 136,555,141 533,146.0 0.04543018 26 293.2542 1,773.2
S_Mozabite-1B + S_Turkish-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Atayal-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 12 159.8383 1,501.5
S_Mozabite-1B + S_Yemenite_Jew-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 42 552.7512 1,519.7
S_Mozabite-1B + S_English-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + B_French-3B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 13 649.9127 400.1
S_Mozabite-1B + S_English-2A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 26 954.1291 545.0
S_Mozabite-1B + S_Saharawi-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_BantuKenya-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Karitiana-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Estonian-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 14 954.1291 293.5
S_Mozabite-1B + S_Pima-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 552.7512 1,447.3
S_Mozabite-1B + S_Estonian-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 20 954.1291 419.2
S_Madiga-1A + S_Mongola-2B Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 20 463.7386 862.6
S_Mozabite-1B + S_Estonian-1B Discordant SGDP 135,597,516 – 137,032,475 1,434,959.0 0.58652654 32 1,159.0016 552.2
S_Madiga-1A + S_Eskimo_Chaplin-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Finnish-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 20 954.1291 419.2
S_Madiga-1A + S_Itelman-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 42 552.7512 1,519.7
S_Mozabite-1B + S_Finnish-3B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 11 954.1291 230.6
S_Madiga-1A + S_Burusho-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Mozabite-1B + S_Saami-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Madiga-1A + S_Kyrgyz-2A Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 20 463.7386 862.6
S_Mozabite-1B + S_Saami-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 4 1.0789 74,149.0
S_Madiga-1A + B_Karitiana-3B Discordant SGDP 136,489,176 – 136,603,542 114,365.5 0.01866284 6 70.8257 1,694.3
S_Mozabite-1B + S_French-2A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 14 954.1291 293.5
S_Madiga-1A + S_Piapoco-2A Discordant SGDP 135,597,516 – 136,603,542 1,006,026.0 0.23089825 22 668.6111 658.1
S_Mozabite-1B + S_French-2B Discordant SGDP 135,536,371 – 137,032,475 1,496,104.0 0.66723804 20 1,252.9204 319.3
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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