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

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 Mutation clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP194.3 generations 96  =  3  +  930.333
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_BantuTswana-1B + S_Madiga-1A Concordant SGDP 136,537,504 – 136,603,542 66,037.5 0.01252909 3 32.6980 1,835.0
S_Mozabite-1B + S_Madiga-1A Concordant SGDP 135,757,046 – 136,603,542 846,496.0 0.11331060 7 407.3181 343.7
S_Mozabite-1B + S_BantuTswana-1B Concordant SGDP 136,537,504 – 136,787,770 250,265.5 0.06380881 9 121.1274 1,486.0
S_Mozabite-1B + S_Norwegian-1B Discordant SGDP 136,080,619 – 137,032,475 951,855.5 0.40798207 30 457.8906 1,310.4
S_Mozabite-1B + S_Bergamo-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_Icelandic-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 21 611.7410 686.6
S_Madiga-1A + S_Eskimo_Naukan-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Piapoco-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 481.9379 1,535.5
S_Mozabite-1B + S_Yemenite_Jew-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 33 481.9379 1,369.5
S_Mozabite-1B + S_Tlingit-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Tubalar-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Mongola-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 9 481.9379 373.5
S_Mozabite-1B + S_Mixtec-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Mixtec-1A Discordant SGDP 135,597,516 – 136,821,414 1,223,898.0 0.32984843 31 588.4710 1,053.6
S_Mozabite-1B + S_Mixe-3B Discordant SGDP 135,760,098 – 136,761,879 1,001,781.5 0.08799281 27 481.8551 1,120.7
S_Mozabite-1B + S_Lezgin-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 481.9379 1,535.5
S_Mozabite-1B + S_Spanish-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_Aleut-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 13 611.7410 425.0
S_Mozabite-1B + B_Mixe-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 38 510.4317 1,488.9
S_Mozabite-1B + S_Naxi-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Madiga-1A + S_Eskimo_Sireniki-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 481.9379 1,618.5
S_Mozabite-1B + S_Dai-3A Discordant SGDP 135,597,516 – 136,762,052 1,164,536.0 0.24705801 58 559.9773 2,071.5
S_Madiga-1A + S_North_Ossetian-2A Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 15 405.8531 739.2
S_Mozabite-1B + S_Miao-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 481.9379 1,535.5
S_Mozabite-1B + S_Georgian-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Uygur-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Iranian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 42 683.2046 1,229.5
S_Mozabite-1B + S_Xibo-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 32 481.9379 1,328.0
S_Mozabite-1B + S_Jordanian-3B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Yi-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 34 481.9379 1,411.0
S_Mozabite-1B + S_Orcadian-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 11 611.7410 359.6
S_Mozabite-1B + S_Xibo-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 36 481.9379 1,494.0
S_Mozabite-1B + S_Lezgin-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_Thai-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Tajik-2A Discordant SGDP 135,760,098 – 136,538,417 778,319.5 0.05991390 58 374.5934 3,096.7
S_Mozabite-1B + S_Kinh-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 33 481.9379 1,369.5
S_Mozabite-1B + B_Crete-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 28 481.9379 1,162.0
S_Mozabite-1B + S_Dusun-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Surui-2B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 28 510.4317 1,097.1
S_Mozabite-1B + S_Maori-1A Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 11 510.4317 431.0
S_Madiga-1A + S_Mixe-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 39 481.9379 1,618.5
S_Mozabite-1B + S_Maori-1B Discordant SGDP 135,760,098 – 136,821,414 1,061,316.0 0.17130701 18 510.4317 705.3
S_Madiga-1A + S_Oroqen-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 43 481.9379 1,784.5
S_Mozabite-1B + S_Chukchi-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 11 611.7410 359.6
S_Madiga-1A + S_Czech-2A Discordant SGDP 135,384,127 – 136,603,542 1,219,415.0 0.35233943 26 586.3192 886.9
S_Mozabite-1B + S_Mozabite-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Madiga-1A + S_Chane-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 43 481.9379 1,784.5
S_Mozabite-1B + S_Mansi-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 33 481.9379 1,369.5
S_Mozabite-1B + S_Basque-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 11 611.7410 359.6
S_Mozabite-1B + S_Brahmin-2B Discordant SGDP 135,778,044 – 136,976,283 1,198,239.5 0.31058545 49 576.1550 1,700.9
S_Mozabite-1B + S_Greek-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 22 510.8754 861.3
S_Mozabite-1B + S_Balochi-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_Icelandic-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 12 611.7410 392.3
S_Mozabite-1B + S_Brahui-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 14 510.8754 548.1
S_Mozabite-1B + S_Bergamo-2A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 9 510.8754 352.3
S_Mozabite-1B + S_Makrani-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Tuscan-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Pathan-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Norwegian-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 17 510.8754 665.5
S_Mozabite-1B + S_Burusho-2A Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 40 473.3238 1,690.2
S_Mozabite-1B + S_Orcadian-1A Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 14 584.7690 478.8
S_Mozabite-1B + S_Hazara-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Polish-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 7 510.8754 274.0
S_Mozabite-1B + S_Sindhi-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 12 611.7410 392.3
S_Mozabite-1B + S_Lezgin-2B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_Punjabi-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 13 611.7410 425.0
S_Mozabite-1B + S_North_Ossetian-1B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 15 611.7410 490.4
S_Mozabite-1B + S_Punjabi-4B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 9 510.8754 352.3
S_Mozabite-1B + S_Spanish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 41 481.9379 1,701.5
S_Mozabite-1B + S_Bulgarian-1B Discordant SGDP 136,021,995 – 136,555,141 533,146.0 0.04543018 24 256.9101 1,868.4
S_Mozabite-1B + S_Turkish-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Atayal-1A Discordant SGDP 136,489,176 – 136,762,052 272,875.5 0.03482260 10 131.9802 1,515.4
S_Mozabite-1B + S_Yemenite_Jew-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 481.9379 1,660.0
S_Mozabite-1B + S_English-1A Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + B_French-3B Discordant SGDP 135,760,098 – 136,822,338 1,062,240.5 0.17379654 11 510.8754 430.6
S_Mozabite-1B + S_English-2A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 24 611.7410 784.6
S_Mozabite-1B + S_Saharawi-2A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_BantuKenya-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Karitiana-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Estonian-2B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 12 611.7410 392.3
S_Mozabite-1B + S_Pima-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 481.9379 1,577.0
S_Mozabite-1B + S_Estonian-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 18 611.7410 588.5
S_Madiga-1A + S_Mongola-2B Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 18 405.8531 887.0
S_Mozabite-1B + S_Estonian-1B Discordant SGDP 135,597,516 – 137,032,475 1,434,959.0 0.58652654 30 689.7803 869.8
S_Madiga-1A + S_Eskimo_Chaplin-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Finnish-1A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 18 611.7410 588.5
S_Madiga-1A + S_Itelman-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 40 481.9379 1,660.0
S_Mozabite-1B + S_Finnish-3B Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 9 611.7410 294.2
S_Madiga-1A + S_Burusho-1B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Mozabite-1B + S_Saami-1A Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Madiga-1A + S_Kyrgyz-2A Discordant SGDP 135,760,098 – 136,603,542 843,444.0 0.07235683 18 405.8531 887.0
S_Mozabite-1B + S_Saami-2B Discordant SGDP 136,538,275 – 136,538,417 142.0 0.00001343 2 1.0682 37,447.6
S_Madiga-1A + B_Karitiana-3B Discordant SGDP 136,489,176 – 136,603,542 114,365.5 0.01866284 4 55.8954 1,431.2
S_Mozabite-1B + S_French-2A Discordant SGDP 135,760,098 – 137,032,475 1,272,377.0 0.42798512 12 611.7410 392.3
S_Madiga-1A + S_Piapoco-2A Discordant SGDP 135,597,516 – 136,603,542 1,006,026.0 0.23089825 20 483.8925 826.6
S_Mozabite-1B + S_French-2B Discordant SGDP 135,536,371 – 137,032,475 1,496,104.0 0.66723804 18 719.1299 500.6
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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