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

rs572392201
Alleles:
reference
T
ancestral
alternate
A
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  136,535,140  (GRCh37) Explore rs572392201 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.6%
1.4%
AFR 90.9%
9.1%
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 A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP8,437.6 generations 116  =  23  +  930.989
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 + B_Ju_hoan_North-4A Concordant SGDP 136,341,972 – 137,058,509 716,537.0 0.56883420 39 344.9378 2,261.3
S_Ju_hoan_North-2B + S_Khomani_San-2A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 12 37.8604 6,339.1
S_Ju_hoan_North-2B + S_Ju_hoan_North-3A Concordant SGDP 136,406,898 – 136,644,413 237,515.0 0.04190494 9 115.0072 1,565.1
S_Ju_hoan_North-2B + S_Ju_hoan_North-1A Concordant SGDP 136,406,898 – 137,034,384 627,485.5 0.40473764 30 302.1930 1,985.5
S_Khomani_San-2A + B_Ju_hoan_North-4A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 11 37.8604 5,810.8
S_Khomani_San-2B + S_Khomani_San-1A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 10 37.8604 5,282.6
S_Ju_hoan_North-3A + S_Ju_hoan_North-1A Concordant SGDP 136,399,121 – 136,644,413 245,292.0 0.04213799 16 118.7402 2,695.0
S_Ju_hoan_North-1A + S_Khomani_San-2A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 13 37.8604 6,867.3
S_Mbuti-1A + S_Khomani_San-2B Concordant SGDP 136,491,330 – 136,559,711 68,381.0 0.01247340 7 33.8229 4,139.2
S_Mbuti-1A + S_Khomani_San-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 12 48.5565 4,942.7
S_Mbuti-1A + S_Khomani_San-2A Concordant SGDP 136,491,330 – 136,559,711 68,381.0 0.01247340 9 33.8229 5,321.8
S_Mbuti-1A + B_Ju_hoan_North-4A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 7 48.5565 2,883.2
S_Mbuti-1A + S_Ju_hoan_North-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 11 48.5565 4,530.8
S_Ju_hoan_North-2B + S_Khomani_San-1A Concordant SGDP 136,411,978 – 136,801,475 389,497.5 0.12086568 33 187.9588 3,511.4
S_Ju_hoan_North-3A + B_Ju_hoan_North-4A Concordant SGDP 135,439,018 – 136,644,413 1,205,395.0 0.34527206 101 579.5896 3,485.2
S_Ju_hoan_North-1A + B_Ju_hoan_North-4A Concordant SGDP 136,401,078 – 137,093,720 692,641.5 0.63258900 47 333.4679 2,818.9
S_Ju_hoan_North-3A + S_Khomani_San-2B Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 10 37.8604 5,282.6
S_Ju_hoan_North-1A + S_Khomani_San-1A Concordant SGDP 135,729,071 – 136,801,475 1,072,404.5 0.29129866 171 515.7542 6,631.1
S_Ju_hoan_North-3A + S_Khomani_San-1A Concordant SGDP 136,080,221 – 136,644,413 564,192.5 0.06056790 111 271.8124 8,167.4
S_Khomani_San-2B + S_Khomani_San-2A Concordant SGDP 135,755,745 – 136,781,557 1,025,812.0 0.16248506 19 493.3898 770.2
S_Khomani_San-1A + B_Ju_hoan_North-4A Concordant SGDP 136,080,221 – 136,786,842 706,621.0 0.09231650 132 340.1781 7,760.6
S_Mbuti-1A + S_Ju_hoan_North-3A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 7 48.5565 2,883.2
S_Mbuti-1A + S_Ju_hoan_North-2B Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 8 48.5565 3,295.1
S_Mbuti-1A + S_Bergamo-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Samaritan-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Icelandic-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Georgian-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Yemenite_Jew-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Lezgin-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Orcadian-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Finnish-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Eskimo_Chaplin-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Spanish-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2A + S_Bulgarian-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Ju_hoan_North-2B + S_Kyrgyz-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + B_Mixe-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Tuscan-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_BantuKenya-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Norwegian-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Saami-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Polish-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_French-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Adygei-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Spanish-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Tajik-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mozabite-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + B_Crete-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mixe-3B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Karitiana-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mixtec-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2A + S_Mixe-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mixtec-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2A + S_Tajik-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mongola-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Itelman-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Tubalar-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + B_Karitiana-3B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Tlingit-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Estonian-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Aleut-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Finnish-3A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Uygur-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Saami-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Xibo-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_French-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Yi-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Basque-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Xibo-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Greek-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Dai-1A Discordant SGDP 135,793,417 – 136,535,149 741,731.5 0.04896259 170 357.0311 9,523.0
S_Mbuti-1A + S_Iranian-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Thai-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Druze-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Kinh-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Bergamo-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Maori-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Jordanian-3B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Chukchi-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Norwegian-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mozabite-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Orcadian-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Mansi-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Lezgin-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Brahmin-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_North_Ossetian-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Balochi-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Adygei-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Brahui-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Spanish-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Brahui-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Turkish-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Makrani-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Yemenite_Jew-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Pathan-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + B_French-3A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Burusho-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Saharawi-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Hazara-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Ju_hoan_North-2B + S_Mongola-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Sindhi-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Ju_hoan_North-1A + S_Czech-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Punjabi-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2A + S_Punjabi-3A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Punjabi-4B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2A + S_Hungarian-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Bulgarian-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Eskimo_Sireniki-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_Atayal-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Oroqen-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_English-1A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Eskimo_Naukan-2A Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_English-1B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + B_Sardinian-3B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Mbuti-1A + S_English-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
S_Khomani_San-2B + S_Chane-1A Discordant SGDP 136,535,063 – 136,735,800 200,737.0 0.02769701 26 97.3538 5,341.3
S_Mbuti-1A + S_Estonian-2B Discordant SGDP 136,535,063 – 136,535,149 86.0 0.00000751 2 1.0413 38,414.3
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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