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

rs540289005
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 10   position  31,705,165  (GRCh37) Explore rs540289005 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.4%
1.6%
AFR 89.8%
10.2%
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 Mutation clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP9,652.6 generations 123  =  28  +  951.000
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_Ju_hoan_North-2B + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 68 129.2898 10,519.0
S_Khomani_San-2A + S_Khomani_San-1B Concordant SGDP 30,998,177 – 31,824,938 826,760.5 0.47080762 50 397.8450 2,513.5
S_Ju_hoan_North-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,603 – 31,870,414 313,810.5 0.04203703 18 151.6290 2,374.2
S_Ju_hoan_North-1B + S_Ju_hoan_North-3B Concordant SGDP 31,557,667 – 31,951,947 394,280.0 0.25042696 58 190.2544 6,097.1
S_Ju_hoan_North-1B + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 54 129.2898 8,353.3
S_Ju_hoan_North-1A + S_Ju_hoan_North-3B Concordant SGDP 31,480,954 – 31,910,782 429,827.5 0.25894213 9 207.3172 868.2
S_Ju_hoan_North-1A + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 34 137.4035 4,948.9
S_Ju_hoan_North-2A + S_Ju_hoan_North-1A Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 48 168.2236 5,706.7
S_Ju_hoan_North-2A + S_Ju_hoan_North-1B Concordant SGDP 31,068,515 – 33,707,610 2,639,095.5 1.74323778 135 1,267.7658 2,129.7
S_Ju_hoan_North-2A + S_Ju_hoan_North-3A Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 31 137.4035 4,512.3
S_Ju_hoan_North-2A + S_Ju_hoan_North-3B Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 46 168.2236 5,468.9
S_Ju_hoan_North-3B + S_Khomani_San-1B Concordant SGDP 31,480,954 – 31,910,782 429,827.5 0.25894213 13 207.3172 1,254.1
S_Ju_hoan_North-3B + S_Khomani_San-2A Concordant SGDP 31,480,954 – 31,824,938 343,983.5 0.04086920 36 166.1121 4,334.4
S_Ju_hoan_North-3B + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 31 137.4035 4,512.3
S_Ju_hoan_North-2B + S_Khomani_San-1B Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 48 136.6708 7,024.2
S_Ju_hoan_North-2A + B_Ju_hoan_North-4B Concordant SGDP 31,054,926 – 31,870,414 815,488.0 0.38557722 31 392.4342 1,579.9
S_Ju_hoan_North-1A + S_Ju_hoan_North-3A Concordant SGDP 31,444,035 – 31,870,414 426,379.0 0.16908465 18 205.6619 1,750.4
S_Ju_hoan_North-2A + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,795,978 238,310.5 0.01002565 41 115.3890 7,106.4
S_Ju_hoan_North-1A + S_Ju_hoan_North-1B Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 50 168.2236 5,944.5
S_Ju_hoan_North-2B + S_Ju_hoan_North-3A Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 47 136.6708 6,877.8
S_Ju_hoan_North-1A + S_Khomani_San-1B Concordant SGDP 31,107,575 – 32,162,772 1,055,197.0 0.71285433 66 507.4946 2,601.0
S_Ju_hoan_North-2B + S_Ju_hoan_North-3B Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 43 136.6708 6,292.5
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 31,068,515 – 31,870,414 801,899.0 0.36691039 34 385.9115 1,762.1
S_Ju_hoan_North-2B + S_Ju_hoan_North-1A Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 46 136.6708 6,731.5
S_Khomani_San-2A + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 57 129.2898 8,817.4
S_Khomani_San-1B + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 36 137.4035 5,240.0
S_Ju_hoan_North-3A + S_Ju_hoan_North-3B Concordant SGDP 31,408,348 – 31,870,414 462,066.0 0.19978861 28 222.7917 2,513.6
S_Ju_hoan_North-3A + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 35 137.4035 5,094.5
S_Khomani_San-2A + S_Relli-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Yemenite_Jew-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_BedouinB-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Basque-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Bulgarian-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Kalash-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Madiga-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Tu-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Naxi-3B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Aleut-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Even-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Tubalar-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Pima-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Yadava-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Oroqen-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Mala-3A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_She-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Pathan-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Burmese-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Abkhasian-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Thai-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Saami-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Dusun-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Druze-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Chukchi-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Tuscan-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Orcadian-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Turkish-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + B_Australian-4A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + B_French-3A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Papuan-4B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-1B + S_Papuan-5B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Papuan-7A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Tubalar-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Papuan-12A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Even-3B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Brahmin-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Yakut-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Georgian-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Cambodian-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Icelandic-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Han-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Kyrgyz-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Daur-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Russian-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_She-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Spanish-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Korean-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3A + S_Turkish-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Ami-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Mozabite-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + B_Australian-3B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Maori-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Bougainville-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Papuan-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Kapu-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Papuan-7A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Irula-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Mansi-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Mala-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Khonda_Dora-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Brahmin-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Brahui-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Makrani-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Kalash-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Balochi-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Burusho-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Sindhi-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Finnish-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Armenian-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Iranian-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_English-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + S_Chechen-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Saami-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-3B + B_Sardinian-3B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Iranian-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-2A + S_Lezgin-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Druze-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1A + S_Papuan-4A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Sardinian-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1A + S_Papuan-9B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Jordanian-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1A + S_Sardinian-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Tajik-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1A + S_Polish-1A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Yemenite_Jew-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1B + S_Papuan-14A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + B_Dai-4B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Ju_hoan_North-1B + S_Papuan-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + B_Papuan-15A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Mixe-2A Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-1B + S_Papuan-3B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Mongola-1B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-1B + S_French-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
S_Khomani_San-2A + S_Mongola-2B Discordant SGDP 31,705,159 – 31,705,229 69.5 0.00000016 2 1.0334 38,708.7
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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