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

rs562946814
Alleles:
reference
G
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 10   position  31,677,401  (GRCh37) Explore rs562946814 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.1%
0.9%
AFR 94.3%
5.7%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
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 SGDP4,442.3 generations 104  =  7  +  971.000
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_Ju_hoan_North-3A + S_Khomani_San-2A Concordant SGDP 31,092,468 – 31,824,938 732,470.0 0.30228466 75 594.4133 2,523.5
S_Ju_hoan_North-1A + S_Khomani_San-1B Concordant SGDP 31,107,575 – 32,162,772 1,055,197.0 0.71285433 60 1,077.7780 1,113.4
S_Khomani_San-2A + S_Khomani_San-1B Concordant SGDP 30,998,177 – 31,824,938 826,760.5 0.47080762 51 774.4911 1,317.0
S_Ju_hoan_North-1A + S_Khomani_San-2A Concordant SGDP 31,107,575 – 31,824,938 717,363.0 0.29153703 95 578.5639 3,284.0
S_Ju_hoan_North-3B + S_Khomani_San-1B Concordant SGDP 31,477,943 – 31,910,782 432,839.0 0.33634360 14 477.8376 586.0
S_Ju_hoan_North-3A + S_Khomani_San-1B Concordant SGDP 31,092,468 – 31,870,414 777,946.0 0.33267586 35 640.5548 1,092.8
S_Ju_hoan_North-3A + S_Ju_hoan_North-1A Concordant SGDP 31,444,035 – 31,870,414 426,379.0 0.16908465 16 340.9296 938.6
S_Khomani_San-2A + S_Papuan-9A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + B_Australian-3A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + B_French-3A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Jordanian-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_French-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Sindhi-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Papuan-3A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + B_Australian-4A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Mala-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Brahui-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Burusho-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Czech-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Georgian-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_BedouinB-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Hungarian-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Yemenite_Jew-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Icelandic-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-1B + S_Papuan-12A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Chechen-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Ami-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3A + S_Spanish-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Maori-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Mozabite-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Kapu-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + B_Australian-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Brahmin-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Papuan-5B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Pathan-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Khonda_Dora-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Armenian-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Brahmin-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Saami-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Iranian-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Iranian-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Kyrgyz-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Sardinian-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Russian-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Turkish-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Lezgin-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Yemenite_Jew-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + S_Turkish-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Pima-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-3B + B_Sardinian-3A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-1B + S_Kalash-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Tubalar-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Burmese-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Maori-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Thai-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Papuan-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Dusun-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Papuan-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Bougainville-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Papuan-4B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Chukchi-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Papuan-7A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Relli-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Papuan-9B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Mala-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Mansi-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Madiga-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Finnish-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Makrani-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_French-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Kalash-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + S_Polish-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Abkhasian-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Ju_hoan_North-1A + B_Papuan-15A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Bulgarian-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Mixe-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_English-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Mongola-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Saami-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Tubalar-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Icelandic-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Even-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Druze-1B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Even-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Bergamo-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Yakut-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Tuscan-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Aleut-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Orcadian-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Cambodian-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Yemenite_Jew-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Naxi-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Yemenite_Jew-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Han-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + B_Dai-4B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Tu-2B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + B_French-3B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Oroqen-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-1B + S_Papuan-14B Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Uygur-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-1B + S_Papuan-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_She-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-1B + S_Sardinian-1A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
S_Khomani_San-2A + S_Korean-2A Discordant SGDP 31,677,400 – 31,677,403 3.0 0.00000001 4 1.0014 79,884.3
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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