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

rs781662414
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  136,644,986  (GRCh37) Explore rs781662414 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 100.0%
0.0%
OCN 100.0%
0.0%
SAS 98.7%
1.3%
WEA 99.3%
0.7%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Mutation clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP796.4 generations 99  =  1  +  981.000
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_Sindhi-1A + S_Tuscan-2A Concordant SGDP 135,339,363 – 137,856,151 2,516,788.0 1.53149390 37 1,209.0582 612.0
S_Tuscan-2A + S_Daur-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Altaian-1A Discordant SGDP 135,760,098 – 136,781,557 1,021,459.5 0.09819052 67 491.3006 2,727.5
S_Sindhi-1A + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 51 493.3566 2,067.5
S_Tuscan-2A + S_Turkish-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Masai-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 82 481.9379 3,402.9
S_Tuscan-2A + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 19 185.7822 2,045.4
S_Tuscan-2A + S_Yadava-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 72 488.0147 2,950.7
S_Sindhi-1A + S_Naxi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 61 481.9379 2,531.4
S_Sindhi-1A + S_Uygur-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Hezhen-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Tujia-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 63 481.9379 2,614.4
S_Sindhi-1A + S_Yakut-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Altaian-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Thai-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Papuan-11A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 38 488.0147 1,557.3
S_Sindhi-1A + S_Japanese-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Albanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 36 481.9379 1,494.0
S_Sindhi-1A + S_Korean-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Iranian-1A Discordant SGDP 136,108,186 – 136,774,712 666,525.5 0.07291219 23 320.9322 1,433.3
S_Sindhi-1A + S_Burmese-1A Discordant SGDP 136,555,141 – 136,774,712 219,570.5 0.03093206 15 106.3938 2,819.7
S_Tuscan-2A + S_Jordanian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 42 683.2046 1,229.5
S_Sindhi-1A + S_Thai-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 67 488.0147 2,745.8
S_Sindhi-1A + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 82 481.9379 3,402.9
S_Sindhi-1A + B_Australian-3A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 56 493.3566 2,270.2
S_Sindhi-1A + S_Mandenka-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 65 493.3566 2,635.0
S_Sindhi-1A + B_Australian-4A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Tlingit-1B Discordant SGDP 135,597,516 – 136,774,712 1,177,196.0 0.25197117 51 566.0541 1,801.9
S_Sindhi-1A + S_Dusun-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Korean-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Dusun-1B Discordant SGDP 136,040,901 – 136,774,712 733,811.0 0.07604170 45 353.2293 2,547.9
S_Tuscan-2A + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 36 481.9379 1,494.0
S_Sindhi-1A + S_Bougainville-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 51 493.3566 2,067.5
S_Tuscan-2A + S_Bengali-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 35 493.3566 1,418.9
S_Tuscan-2A + S_Brahmin-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Papuan-10B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Saharawi-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 17 185.7822 1,830.1
S_Sindhi-1A + S_Papuan-7A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Greek-1A Discordant SGDP 135,760,098 – 136,648,600 888,502.5 0.08131169 28 427.4812 1,310.0
S_Sindhi-1A + S_Hawaiian-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 67 488.0147 2,745.8
S_Tuscan-2A + S_Samaritan-1B Discordant SGDP 135,352,905 – 136,774,712 1,421,807.0 0.37533515 83 683.4674 2,428.8
S_Sindhi-1A + S_Mansi-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 32 493.3566 1,297.2
S_Tuscan-2A + S_Palestinian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 46 488.0147 1,885.2
S_Sindhi-1A + S_Yadava-1A Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 20 179.7054 2,225.9
S_Tuscan-2A + S_Russian-2B Discordant SGDP 135,760,098 – 136,784,130 1,024,032.0 0.10025333 40 492.5354 1,624.2
S_Sindhi-1A + S_Irula-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 70 488.0147 2,868.8
S_Sindhi-1A + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 63 488.0147 2,581.9
S_Sindhi-1A + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 17 129.7773 2,619.9
S_Sindhi-1A + S_Mala-3B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Tajik-1B Discordant SGDP 135,340,792 – 136,645,005 1,304,212.5 0.37223633 118 627.0220 3,763.8
S_Sindhi-1A + S_Madiga-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 60 488.0147 2,458.9
S_Tuscan-2A + S_Mozabite-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Brahui-2A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 67 694.6233 1,929.1
S_Tuscan-2A + S_Tlingit-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Luhya-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Tu-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Burusho-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Xibo-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Sindhi-1B Discordant SGDP 135,340,792 – 137,629,297 2,288,504.5 1.32475411 117 1,099.4822 2,128.3
S_Tuscan-2A + S_Ami-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Armenian-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Kinh-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Finnish-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 70 488.0147 2,868.8
S_Tuscan-2A + S_Papuan-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 69 488.0147 2,827.8
S_Tuscan-2A + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 29 428.1460 1,354.7
S_Sindhi-1A + S_French-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 58 488.0147 2,377.0
S_Tuscan-2A + S_Yadava-1A Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 28 179.7054 3,116.2
S_Sindhi-1A + S_Greek-1A Discordant SGDP 135,760,098 – 136,648,600 888,502.5 0.08131169 33 427.4812 1,543.9
S_Tuscan-2A + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 51 488.0147 2,090.1
S_Sindhi-1A + S_Hungarian-1B Discordant SGDP 135,597,516 – 136,648,600 1,051,084.5 0.23985311 50 505.5206 1,978.2
S_Tuscan-2A + S_Balochi-1B Discordant SGDP 135,340,792 – 136,649,985 1,309,193.0 0.37402263 53 629.4126 1,684.1
S_Sindhi-1A + S_Iranian-2A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 66 694.6233 1,900.3
S_Tuscan-2A + S_Atayal-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Iraqi_Jew-2B Discordant SGDP 135,340,792 – 136,774,712 1,433,919.5 0.38519553 95 689.2814 2,756.5
S_Tuscan-2A + S_Basque-2A Discordant SGDP 135,760,098 – 136,784,130 1,024,032.0 0.10025333 65 492.5354 2,639.4
S_Sindhi-1A + S_Iraqi_Jew-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 62 488.0147 2,540.9
S_Tuscan-2A + S_Georgian-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Iraqi_Jew-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 60 481.9379 2,489.9
S_Tuscan-2A + S_Hungarian-1B Discordant SGDP 135,597,516 – 136,648,600 1,051,084.5 0.23985311 45 505.5206 1,780.3
S_Sindhi-1A + S_Samaritan-1B Discordant SGDP 135,352,905 – 136,785,841 1,432,936.0 0.38510046 96 688.8093 2,787.4
S_Tuscan-2A + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 44 488.0147 1,803.2
S_Sindhi-1A + S_Palestinian-2A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 60 571.3960 2,100.1
S_Tuscan-2A + S_Druze-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 37 488.0147 1,516.3
S_Sindhi-1A + S_Palestinian-3A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 62 694.6233 1,785.1
S_Tuscan-2A + S_Druze-1B Discordant SGDP 135,340,792 – 136,774,712 1,433,919.5 0.38519553 85 689.2814 2,466.3
S_Sindhi-1A + S_Sardinian-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Tuscan-2A + S_Tuscan-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Sardinian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 74 488.0147 3,032.7
S_Tuscan-2A + S_Russian-1B Discordant SGDP 135,597,516 – 136,784,130 1,186,614.0 0.25879475 59 570.5747 2,068.1
S_Sindhi-1A + S_Jordanian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 43 683.2046 1,258.8
S_Tuscan-2A + S_Abkhasian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 34 488.0147 1,393.4
S_Sindhi-1A + S_Kyrgyz-1A Discordant SGDP 136,494,791 – 136,774,712 279,920.5 0.03837478 20 135.3618 2,955.0
S_Tuscan-2A + B_Crete-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 2 1.0214 39,163.5
S_Sindhi-1A + S_Russian-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 27 185.7822 2,906.6
S_Tuscan-2A + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 51 488.0147 2,090.1
S_Sindhi-1A + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,648,600 258,851.5 0.04675468 16 125.2487 2,554.9
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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