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

rs531493580
Alleles:
reference
A
ancestral
alternate
G
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  31,616,945  (GRCh37) Explore rs531493580 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 Recombination clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,921.1 generations 109  =  9  +  1001.000
Pairwise results table Recombination clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Ju_hoan_North-1A + S_Khomani_San-1B Concordant SGDP 31,107,575 – 32,162,772 1,055,197.0 0.71285433 3 571.2835 105.0
S_Ju_hoan_North-3B + S_Khomani_San-1B Concordant SGDP 31,477,943 – 31,910,782 432,839.0 0.33634360 3 270.0749 222.2
S_Ju_hoan_North-1A + S_Khomani_San-2A Concordant SGDP 31,107,575 – 31,824,938 717,363.0 0.29153703 3 234.2296 256.2
S_Ju_hoan_North-3B + S_Khomani_San-2A Concordant SGDP 31,477,943 – 31,824,938 346,995.0 0.11827066 3 95.6165 627.5
S_Ju_hoan_North-3B + S_Ju_hoan_North-1A Concordant SGDP 31,477,943 – 31,910,782 432,839.0 0.33634360 3 270.0749 222.2
S_Ju_hoan_North-3A + S_Khomani_San-1B Concordant SGDP 31,092,468 – 31,870,414 777,946.0 0.33267586 3 267.1407 224.6
S_Khomani_San-1B + S_Khomani_San-2A Concordant SGDP 30,998,177 – 31,824,938 826,760.5 0.47080762 3 377.6461 158.9
S_Ju_hoan_North-3A + S_Ju_hoan_North-1A Concordant SGDP 31,444,035 – 31,870,414 426,379.0 0.16908465 3 136.2677 440.3
S_Ju_hoan_North-3A + S_Ju_hoan_North-3B Concordant SGDP 31,408,348 – 31,870,414 462,066.0 0.19978861 3 160.8309 373.1
S_Khomani_San-1B + S_Zapotec-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Khomani_San-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Papuan-5B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Jordanian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Tajik-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Papuan-3B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Pathan-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Yakut-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Yakut-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Aleut-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Even-3B Discordant SGDP 31,616,924 – 31,625,779 8,855.0 0.00025727 3 1.2058 49,759.0
S_Ju_hoan_North-3A + S_Altaian-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Tubalar-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Mongola-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Cambodian-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Daur-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_She-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Yi-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Relli-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Tujia-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Abkhasian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Dai-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Quechua-3B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Uygur-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Yemenite_Jew-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Thai-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Yi-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Kinh-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Greek-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + B_Australian-3A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Even-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Hawaiian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Hezhen-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Kalash-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Korean-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Czech-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Papuan-12A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Georgian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Mala-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Bergamo-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Sindhi-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Jordanian-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Finnish-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Orcadian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Mala-3A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Mixtec-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Sindhi-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Brahui-2A Discordant SGDP 31,616,924 – 31,636,829 19,905.5 0.00063210 3 1.5057 39,849.2
S_Ju_hoan_North-3B + S_Saami-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Brahui-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Icelandic-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Sindhi-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Tuscan-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_French-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Kyrgyz-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Iranian-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Russian-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Sardinian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Turkish-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Tuscan-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + B_French-3B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Orcadian-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Karitiana-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Russian-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Maori-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Abkhasian-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Estonian-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Spanish-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-1A + S_Hungarian-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Yemenite_Jew-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Yakut-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + S_Yemenite_Jew-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Even-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3A + B_Dai-4A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Oroqen-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Mongola-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Uygur-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Tlingit-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Tu-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Naxi-3A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Ami-2A Discordant SGDP 31,616,924 – 31,625,779 8,855.0 0.00025727 3 1.2058 49,759.0
S_Ju_hoan_North-3B + S_Han-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Papuan-9A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Naxi-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Papuan-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Korean-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Irula-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Korean-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Madiga-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Burmese-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Kalash-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Thai-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Abkhasian-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Dusun-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Czech-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Kusunda-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Sardinian-1B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Balochi-1A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Khomani_San-1B + S_Kyrgyz-2A Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
S_Ju_hoan_North-3B + S_Hazara-2B Discordant SGDP 31,616,924 – 31,616,953 29.5 0.00000086 3 1.0007 59,958.5
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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