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

rs531528631
Alleles:
reference
C
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  31,612,461  (GRCh37) Explore rs531528631 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.3%
0.7%
AFR 95.5%
4.5%
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 G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP4,564.5 generations 102  =  5  +  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-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,603 – 31,975,519 418,915.5 0.25959952 29 409.7591 1,415.5
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 30,530,686 – 31,870,414 1,339,728.0 1.75823695 86 2,050.6590 838.8
S_Ju_hoan_North-2B + S_Ju_hoan_North-2A Concordant SGDP 31,556,603 – 31,870,414 313,810.5 0.04203703 26 185.2587 2,806.9
S_Ju_hoan_North-2A + B_Ju_hoan_North-4B Concordant SGDP 30,733,168 – 31,870,414 1,137,246.0 1.17646223 69 1,488.0479 927.4
S_Ju_hoan_North-2A + S_Ju_hoan_North-1B Concordant SGDP 31,068,515 – 33,707,610 2,639,095.5 1.74323778 106 2,662.3561 796.3
S_Ju_hoan_North-2B + S_Hezhen-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_She-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Mixtec-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Even-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Greek-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Abkhasian-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Tlingit-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Kalash-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Even-3B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Yakut-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Yakut-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Tubalar-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Mongola-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Ami-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Cambodian-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Mala-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Naxi-3A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Finnish-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Han-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Tuscan-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Yi-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + B_Dai-4B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Yi-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Aleut-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Tujia-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Daur-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Uygur-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Dai-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_She-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Korean-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Korean-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Hawaiian-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Burmese-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Makrani-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Thai-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Sindhi-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Kinh-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Saami-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Maori-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Iranian-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + B_Karitiana-3B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Orcadian-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Karitiana-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Yemenite_Jew-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Zapotec-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Papuan-3A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Mixe-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + B_Dinka-3A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Papuan-5A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Pima-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Papuan-12B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Quechua-3B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Papuan-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_BantuTswana-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Eskimo_Sireniki-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Even-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Irula-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Oroqen-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Kusunda-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Mozabite-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Hazara-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Naxi-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Kalash-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Tu-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Sindhi-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Korean-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Punjabi-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Papuan-9B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Abkhasian-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Relli-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Armenian-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Mala-3B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Czech-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Brahui-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Czech-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Sindhi-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Georgian-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Estonian-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Icelandic-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Saami-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Iranian-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Basque-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Sardinian-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Hungarian-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Jordanian-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_BedouinB-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Kyrgyz-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Kyrgyz-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Russian-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Russian-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Tajik-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Turkish-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Turkish-2B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Yemenite_Jew-1B Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + S_Yemenite_Jew-2A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2B + S_Khomani_San-1A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
S_Ju_hoan_North-2A + B_Sardinian-3A Discordant SGDP 31,612,415 – 31,612,474 59.0 0.00000174 4 1.0297 77,691.9
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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