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

rs372420380
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 2   position  136,585,828  (GRCh37) Explore rs372420380 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 98.9%
1.1%
OCN 98.0%
2.0%
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 T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP117.2 generations 94  =  1  +  931.000
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_Ami-1B + S_Hawaiian-1B Concordant SGDP 135,757,046 – 136,825,844 1,068,798.0 0.25986017 3 208.8881 287.2
S_Ami-1B + S_Palestinian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Druze-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Georgian-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
S_Hawaiian-1B + S_Jordanian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Hawaiian-1B + B_Australian-3B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 3 76.7879 781.4
S_Ami-1B + S_Tajik-1B Discordant SGDP 135,760,098 – 136,585,834 825,736.5 0.06906363 3 56.2509 1,066.6
S_Ami-1B + S_Lahu-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Tlingit-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Tlingit-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Yakut-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 3 76.7879 781.4
S_Ami-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Quechua-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 3 76.7879 781.4
S_Ami-1B + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Tuscan-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 3 37.2521 1,610.6
S_Ami-1B + S_Tu-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Tujia-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Daur-2B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 3 68.9217 870.6
S_Hawaiian-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Hezhen-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Hawaiian-1B + S_Turkish-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Naxi-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Hungarian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_She-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + S_Iraqi_Jew-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + S_Japanese-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Palestinian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
S_Ami-1B + S_Korean-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + S_Sardinian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Korean-1A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 3 210.3892 285.2
S_Ami-1B + S_Kyrgyz-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Burmese-1A Discordant SGDP 136,555,141 – 136,785,841 230,699.5 0.04069738 3 33.5579 1,788.0
S_Ami-1B + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 3 27.9656 2,145.5
S_Ami-1B + S_Thai-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Kinh-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Hawaiian-1B + S_Thai-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + B_Australian-4B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Hawaiian-1B + S_Papuan-10B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Dusun-1B Discordant SGDP 135,942,298 – 136,785,841 843,542.5 0.08827139 3 71.6171 837.8
S_Hawaiian-1B + S_Iranian-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Bougainville-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Russian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Mozabite-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Bougainville-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Papuan-11A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Iranian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Papuan-6A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Iraqi_Jew-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Papuan-7B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Samaritan-1B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
S_Ami-1B + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 3 66.8055 898.1
S_Ami-1B + S_Druze-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Mansi-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Palestinian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Bengali-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Sardinian-1B Discordant SGDP 136,500,227 – 136,774,712 274,484.5 0.03728607 3 30.8289 1,946.2
S_Ami-1B + S_Yadava-1B Discordant SGDP 135,954,725 – 136,762,052 807,326.5 0.07313183 3 59.5055 1,008.3
S_Ami-1B + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Yadava-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + S_Jordanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Irula-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Russian-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 3 83.5561 718.1
S_Ami-1B + S_Abkhasian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Mala-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Ami-1B + S_Saharawi-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Brahmin-2A Discordant SGDP 135,782,261 – 136,762,052 979,790.5 0.07868380 3 63.9470 938.3
S_Ami-1B + B_Crete-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Brahui-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Hawaiian-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Balochi-1B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 3 66.8055 898.1
S_Hawaiian-1B + S_Tujia-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Luo-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 3 71.8133 835.5
S_Hawaiian-1B + B_Australian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Ami-1B + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Hawaiian-1B + S_Papuan-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Albanian-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Madiga-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 3 76.7879 781.4
S_Ami-1B + S_Armenian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 3 64.8977 924.5
S_Ami-1B + S_Atayal-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Masai-1B Discordant SGDP 136,391,342 – 136,762,052 370,710.0 0.05242810 3 42.9425 1,397.2
S_Ami-1B + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 3 75.7438 792.1
S_Hawaiian-1B + S_Russian-2A Discordant SGDP 135,597,516 – 136,774,712 1,177,196.0 0.25197117 3 202.5769 296.2
S_Ami-1B + S_French-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Hawaiian-1B + S_Lezgin-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 3 1.0096 59,430.4
S_Ami-1B + S_Basque-2B Discordant SGDP 136,557,025 – 136,785,841 228,815.5 0.03729117 3 30.8329 1,946.0
S_Hawaiian-1B + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 3 76.7879 781.4
S_Ami-1B + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 3 48.0982 1,247.4
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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