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

rs778455691
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 2   position  136,615,633  (GRCh37) Explore rs778455691 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
AFR 100.0%
0.0%
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 98.0%
2.0%
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 SGDP51.4 generations 97  =  3  +  940.333
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_Palestinian-2B + S_Palestinian-3B Concordant SGDP 136,290,439 – 137,420,154 1,129,715.5 0.92267696 3 739.1416 81.2
S_French-1A + S_Palestinian-3B Concordant SGDP 135,757,046 – 136,781,557 1,024,511.5 0.13914428 3 112.3154 534.2
S_French-1A + S_Palestinian-2B Concordant SGDP 136,290,439 – 136,781,557 491,118.5 0.07384053 3 60.0724 998.8
S_Palestinian-3B + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Papuan-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 3 66.8055 898.1
S_Palestinian-3B + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Dusun-1B Discordant SGDP 136,040,901 – 136,762,052 721,151.0 0.07112854 3 57.9028 1,036.2
S_Palestinian-3B + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Jordanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_French-1A + S_Hazara-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_French-1A + S_English-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_French-1A + S_Brahui-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_French-1A + S_Makrani-2A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_French-1A + S_Balochi-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_French-1A + S_Makrani-1A Discordant SGDP 135,760,098 – 137,306,640 1,546,542.5 0.81377161 3 652.0173 92.0
S_French-1A + S_Irula-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Luo-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_French-1A + S_Greek-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Basque-2B Discordant SGDP 136,557,025 – 136,762,052 205,026.5 0.02261269 3 19.0902 3,143.0
S_French-1A + S_Bergamo-2B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Palestinian-2A Discordant SGDP 135,760,098 – 137,851,404 2,091,306.5 1.21104218 3 969.8337 61.9
S_French-1A + S_Lezgin-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_French-1A + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_French-1A + S_Yadava-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_French-1A + S_Spanish-1A Discordant SGDP 136,615,626 – 137,851,404 1,235,778.0 1.13840801 3 911.7264 65.8
S_Palestinian-3B + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_French-1A + S_Spanish-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Papuan-11A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_French-1A + S_Tajik-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Bengali-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Mozabite-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Madiga-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + S_Yakut-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Finnish-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Tujia-2B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 3 64.8977 924.5
S_Palestinian-2B + S_Korean-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Druze-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + B_Australian-4A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Tuscan-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Ami-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Russian-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Thai-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Tajik-1B Discordant SGDP 135,760,098 – 136,619,279 859,181.0 0.07377702 3 60.0216 999.6
S_Palestinian-3B + B_Australian-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Mansi-2B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 3 56.2638 1,066.4
S_French-1A + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Thai-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + S_Brahmin-2A Discordant SGDP 136,290,439 – 136,762,052 471,613.0 0.06416660 3 52.3333 1,146.5
S_Palestinian-3B + S_Kinh-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + S_Brahui-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + B_Australian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Sindhi-1B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 3 56.2638 1,066.4
S_Palestinian-3B + S_Bougainville-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + S_Armenian-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Bougainville-1B Discordant SGDP 135,760,098 – 136,755,811 995,713.5 0.08759616 3 71.0769 844.2
S_Palestinian-2B + S_Saharawi-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Palestinian-3B + S_Papuan-10A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Georgian-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Papuan-7A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-2B + S_Georgian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Hawaiian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Iranian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Yadava-1B Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 3 44.1677 1,358.5
S_Palestinian-2B + S_Iranian-2A Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 3 56.2638 1,066.4
S_Palestinian-3B + S_Mala-3B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-2B + S_Samaritan-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Palestinian-3A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
S_Palestinian-3B + S_Albanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Sardinian-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Finnish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Sardinian-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Greek-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + S_Abkhasian-2B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 3 56.2638 1,066.4
S_Palestinian-3B + S_Masai-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-2B + B_Crete-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
S_Palestinian-3B + S_Iraqi_Jew-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Altaian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Druze-1B Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 3 64.8241 925.6
S_Palestinian-3B + S_Tlingit-2A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Tlingit-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 3 1.0001 59,996.9
S_Palestinian-3B + S_Jordanian-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Daur-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Russian-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Hezhen-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 3 37.2521 1,610.6
S_Palestinian-3B + S_Naxi-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Japanese-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Turkish-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 3 1.9143 31,343.4
S_Palestinian-3B + S_Korean-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Palestinian-3B + S_Burmese-1A Discordant SGDP 136,555,141 – 136,762,052 206,910.5 0.02601890 3 21.8151 2,750.4
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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