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

rs533440641
Alleles:
reference
G
ancestral
alternate
C
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  109,522,980  (GRCh37) Explore rs533440641 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 97.7%
2.3%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP303.8 generations 93  =  1  +  920.989
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_Khomani_San-2A + S_Khomani_San-1B Concordant SGDP 109,522,747 – 109,530,357 7,610.0 0.00348510 3 3.7881 15,839.2
S_Khomani_San-1B + S_Samaritan-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Hungarian-1A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Finnish-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Albanian-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Mende-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + B_Mandenka-3A Discordant SGDP 109,522,977 – 109,530,357 7,380.5 0.00340293 3 3.7223 16,118.9
S_Khomani_San-1B + S_Lezgin-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-2A + S_Luo-2B Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-2A + S_Pathan-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-2A + S_Khonda_Dora-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-2A + S_BantuKenya-2B Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-2A + S_Mbuti-1B Discordant SGDP 109,471,639 – 109,524,125 52,486.0 0.01044617 3 9.3569 6,412.4
S_Khomani_San-2A + S_Mbuti-2B Discordant SGDP 109,471,639 – 109,522,998 51,359.0 0.01003928 3 9.0314 6,643.5
S_Khomani_San-1B + S_Luo-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Ju_hoan_North-3A Discordant SGDP 108,954,234 – 109,522,998 568,764.0 0.17244605 3 138.9568 431.8
S_Khomani_San-2A + S_Luhya-1A Discordant SGDP 109,471,639 – 109,540,064 68,424.5 0.02253832 3 19.0307 3,152.8
S_Khomani_San-1B + S_Tajik-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-2A + S_Abkhasian-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Saharawi-2A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-2A + B_Dinka-3A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Piapoco-1B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-2A + S_Saharawi-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_BantuKenya-1A Discordant SGDP 109,487,963 – 109,522,998 35,035.0 0.00939475 3 8.5158 7,045.7
S_Khomani_San-2A + S_Khomani_San-1A Discordant SGDP 109,471,639 – 109,611,374 139,734.5 0.18726817 3 150.8145 397.8
S_Khomani_San-1B + S_Greek-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-2A + S_BantuHerero-2B Discordant SGDP 108,980,153 – 109,540,064 559,911.0 0.09415087 3 76.3207 786.2
S_Khomani_San-1B + S_Iranian-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Mozabite-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_BedouinB-1A Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-1B + S_Mongola-2A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Jordanian-3A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Tubalar-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Russian-1A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_BantuTswana-2B Discordant SGDP 109,522,977 – 109,536,510 13,533.0 0.00568871 3 5.5510 10,808.9
S_Khomani_San-1B + S_Adygei-2B Discordant SGDP 109,521,900 – 109,522,998 1,098.0 0.00039087 3 1.3127 45,707.3
S_Khomani_San-1B + S_Tlingit-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Yemenite_Jew-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Naxi-2B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + B_Yoruba-3B Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-1B + S_Naxi-3B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Mandenka-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Biaka-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Surui-1A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Naxi-1B Discordant SGDP 109,521,900 – 109,522,998 1,098.0 0.00039087 3 1.3127 45,707.3
S_Khomani_San-2A + S_Mbuti-3A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Japanese-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Saharawi-1A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Mbuti-2A Discordant SGDP 109,522,977 – 109,534,671 11,694.5 0.00496550 3 4.9724 12,066.6
S_Khomani_San-1B + S_Estonian-1B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Japanese-3B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Finnish-3A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + B_Australian-4A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Hungarian-2A Discordant SGDP 109,521,900 – 109,522,998 1,098.0 0.00039087 3 1.3127 45,707.3
S_Khomani_San-1B + S_Gambian-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Icelandic-1B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Gambian-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Masai-1A Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-1B + S_Mansi-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Palestinian-3A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Bengali-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Bergamo-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Relli-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Tuscan-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Yadava-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Jordanian-2A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Mala-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Orcadian-1B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Mala-3A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Abkhasian-2B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Somali-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Ju_hoan_North-2B Discordant SGDP 108,954,234 – 109,522,998 568,764.0 0.17244605 3 138.9568 431.8
S_Khomani_San-1B + S_Madiga-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Tajik-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Brahmin-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Ju_hoan_North-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Madiga-2B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + B_Crete-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Kusunda-1A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + B_Papuan-15A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Brahui-2A Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Esan-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Luhya-2B Discordant SGDP 109,451,350 – 109,522,998 71,648.0 0.01263291 3 11.1063 5,402.3
S_Khomani_San-1B + S_Esan-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Brahui-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Mandenka-2B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Luo-2A Discordant SGDP 109,522,977 – 109,524,125 1,148.5 0.00041459 3 1.3317 45,056.1
S_Khomani_San-1B + S_Dinka-1B Discordant SGDP 108,954,234 – 109,522,998 568,764.0 0.17244605 3 138.9568 431.8
S_Khomani_San-1B + S_Hazara-1B Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Surui-2B Discordant SGDP 109,520,160 – 109,522,998 2,838.0 0.00100100 3 1.8008 33,318.5
S_Khomani_San-1B + S_Punjabi-4A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Piapoco-2A Discordant SGDP 109,522,977 – 109,522,998 21.5 0.00000769 3 1.0062 59,632.9
S_Khomani_San-1B + S_Punjabi-1A Discordant SGDP 109,328,376 – 109,522,998 194,622.5 0.02968687 3 24.7495 2,424.3
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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