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 Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP511.9 generations 99  =  1  +  981.000
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_Sindhi-1A + S_Tuscan-2A Concordant SGDP 135,339,363 – 137,856,151 2,516,788.0 1.53149390 39 2,434.2534 320.4
S_Tuscan-2A + S_Daur-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Altaian-1A Discordant SGDP 135,760,098 – 136,781,557 1,021,459.5 0.09819052 69 569.8530 2,421.7
S_Sindhi-1A + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 53 575.9127 1,840.6
S_Tuscan-2A + S_Turkish-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Masai-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 84 552.7512 3,039.3
S_Tuscan-2A + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 21 232.8804 1,803.5
S_Tuscan-2A + S_Yadava-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 74 562.7585 2,629.9
S_Sindhi-1A + S_Naxi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 63 552.7512 2,279.5
S_Sindhi-1A + S_Uygur-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Hezhen-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Tujia-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 65 552.7512 2,351.9
S_Sindhi-1A + S_Yakut-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Altaian-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Thai-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Papuan-11A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 40 562.7585 1,421.6
S_Sindhi-1A + S_Japanese-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Albanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 552.7512 1,374.9
S_Sindhi-1A + S_Korean-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Iranian-1A Discordant SGDP 136,108,186 – 136,774,712 666,525.5 0.07291219 25 379.2620 1,318.3
S_Sindhi-1A + S_Burmese-1A Discordant SGDP 136,555,141 – 136,774,712 219,570.5 0.03093206 17 131.1395 2,592.7
S_Tuscan-2A + S_Jordanian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 44 987.4305 891.2
S_Sindhi-1A + S_Thai-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 69 562.7585 2,452.2
S_Sindhi-1A + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 84 552.7512 3,039.3
S_Sindhi-1A + B_Australian-3A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 58 575.9127 2,014.2
S_Sindhi-1A + S_Mandenka-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 67 575.9127 2,326.7
S_Sindhi-1A + B_Australian-4A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Tlingit-1B Discordant SGDP 135,597,516 – 136,774,712 1,177,196.0 0.25197117 53 767.6310 1,380.9
S_Sindhi-1A + S_Dusun-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Korean-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Dusun-1B Discordant SGDP 136,040,901 – 136,774,712 733,811.0 0.07604170 47 414.0626 2,270.2
S_Tuscan-2A + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 38 552.7512 1,374.9
S_Sindhi-1A + S_Bougainville-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 53 575.9127 1,840.6
S_Tuscan-2A + S_Bengali-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 37 575.9127 1,284.9
S_Tuscan-2A + S_Brahmin-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Papuan-10B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Saharawi-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 19 232.8804 1,631.7
S_Sindhi-1A + S_Papuan-7A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Greek-1A Discordant SGDP 135,760,098 – 136,648,600 888,502.5 0.08131169 30 492.5306 1,218.2
S_Sindhi-1A + S_Hawaiian-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 69 562.7585 2,452.2
S_Tuscan-2A + S_Samaritan-1B Discordant SGDP 135,352,905 – 136,774,712 1,421,807.0 0.37533515 85 983.7355 1,728.1
S_Sindhi-1A + S_Mansi-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 34 575.9127 1,180.7
S_Tuscan-2A + S_Palestinian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 48 562.7585 1,705.9
S_Sindhi-1A + S_Yadava-1A Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 22 222.8731 1,974.2
S_Tuscan-2A + S_Russian-2B Discordant SGDP 135,760,098 – 136,784,130 1,024,032.0 0.10025333 42 572.7380 1,466.6
S_Sindhi-1A + S_Irula-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 72 562.7585 2,558.8
S_Sindhi-1A + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 65 562.7585 2,310.0
S_Sindhi-1A + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 19 156.7428 2,424.4
S_Sindhi-1A + S_Mala-3B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Tajik-1B Discordant SGDP 135,340,792 – 136,645,005 1,304,212.5 0.37223633 120 924.8111 2,595.1
S_Sindhi-1A + S_Madiga-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 62 562.7585 2,203.4
S_Tuscan-2A + S_Mozabite-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Brahui-2A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 69 1,010.5920 1,365.5
S_Tuscan-2A + S_Tlingit-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Luhya-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Tu-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Burusho-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Xibo-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Sindhi-1B Discordant SGDP 135,340,792 – 137,629,297 2,288,504.5 1.32475411 119 2,159.2855 1,102.2
S_Tuscan-2A + S_Ami-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Armenian-2B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Kinh-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Finnish-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 72 562.7585 2,558.8
S_Tuscan-2A + S_Papuan-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 71 562.7585 2,523.3
S_Tuscan-2A + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 31 493.9515 1,255.2
S_Sindhi-1A + S_French-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 60 562.7585 2,132.4
S_Tuscan-2A + S_Yadava-1A Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 30 222.8731 2,692.1
S_Sindhi-1A + S_Greek-1A Discordant SGDP 135,760,098 – 136,648,600 888,502.5 0.08131169 35 492.5306 1,421.2
S_Tuscan-2A + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 53 562.7585 1,883.6
S_Sindhi-1A + S_Hungarian-1B Discordant SGDP 135,597,516 – 136,648,600 1,051,084.5 0.23985311 52 697.4030 1,491.2
S_Tuscan-2A + S_Balochi-1B Discordant SGDP 135,340,792 – 136,649,985 1,309,193.0 0.37402263 55 928.6307 1,184.5
S_Sindhi-1A + S_Iranian-2A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 68 1,010.5920 1,345.7
S_Tuscan-2A + S_Atayal-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Iraqi_Jew-2B Discordant SGDP 135,340,792 – 136,774,712 1,433,919.5 0.38519553 97 997.4378 1,945.0
S_Tuscan-2A + S_Basque-2A Discordant SGDP 135,760,098 – 136,784,130 1,024,032.0 0.10025333 67 572.7380 2,339.6
S_Sindhi-1A + S_Iraqi_Jew-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 64 562.7585 2,274.5
S_Tuscan-2A + S_Georgian-1B Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Iraqi_Jew-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 62 552.7512 2,243.3
S_Tuscan-2A + S_Hungarian-1B Discordant SGDP 135,597,516 – 136,648,600 1,051,084.5 0.23985311 47 697.4030 1,347.9
S_Sindhi-1A + S_Samaritan-1B Discordant SGDP 135,352,905 – 136,785,841 1,432,936.0 0.38510046 98 996.8897 1,966.1
S_Tuscan-2A + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 46 562.7585 1,634.8
S_Sindhi-1A + S_Palestinian-2A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 62 780.7852 1,588.1
S_Tuscan-2A + S_Druze-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 39 562.7585 1,386.0
S_Sindhi-1A + S_Palestinian-3A Discordant SGDP 135,340,792 – 136,785,841 1,445,048.5 0.39496084 64 1,010.5920 1,266.6
S_Tuscan-2A + S_Druze-1B Discordant SGDP 135,340,792 – 136,774,712 1,433,919.5 0.38519553 87 997.4378 1,744.5
S_Sindhi-1A + S_Sardinian-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Tuscan-2A + S_Tuscan-1A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Sardinian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 76 562.7585 2,701.0
S_Tuscan-2A + S_Russian-1B Discordant SGDP 135,597,516 – 136,784,130 1,186,614.0 0.25879475 61 777.6105 1,568.9
S_Sindhi-1A + S_Jordanian-1B Discordant SGDP 135,340,792 – 136,762,052 1,421,259.5 0.38028236 45 987.4305 911.5
S_Tuscan-2A + S_Abkhasian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 36 562.7585 1,279.4
S_Sindhi-1A + S_Kyrgyz-1A Discordant SGDP 136,494,791 – 136,774,712 279,920.5 0.03837478 22 166.0617 2,649.6
S_Tuscan-2A + B_Crete-2A Discordant SGDP 136,644,960 – 136,645,005 44.5 0.00000881 4 1.0284 77,790.1
S_Sindhi-1A + S_Russian-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 29 232.8804 2,490.5
S_Tuscan-2A + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 53 562.7585 1,883.6
S_Sindhi-1A + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,648,600 258,851.5 0.04675468 18 162.6525 2,213.3
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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