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 Joint clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP863.2 generations 97  =  3  +  941.000
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_Palestinian-2B + S_Palestinian-3B Concordant SGDP 136,290,439 – 137,420,154 1,129,715.5 0.92267696 22 1,281.4050 343.4
S_French-1A + S_Palestinian-3B Concordant SGDP 135,757,046 – 136,781,557 1,024,511.5 0.13914428 21 604.0809 695.3
S_French-1A + S_Palestinian-2B Concordant SGDP 136,290,439 – 136,781,557 491,118.5 0.07384053 11 295.8093 743.7
S_Palestinian-3B + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 66 552.7512 2,388.1
S_Palestinian-3B + S_Papuan-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 41 493.9515 1,660.1
S_Palestinian-3B + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 71 552.7512 2,569.0
S_Palestinian-3B + S_Dusun-1B Discordant SGDP 136,040,901 – 136,762,052 721,151.0 0.07112854 48 404.0553 2,375.9
S_Palestinian-3B + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Palestinian-3B + S_Jordanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 46 552.7512 1,664.4
S_French-1A + S_Hazara-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_French-1A + S_English-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_French-1A + S_Brahui-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_French-1A + S_Makrani-2A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_French-1A + S_Balochi-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_French-1A + S_Makrani-1A Discordant SGDP 135,760,098 – 137,306,640 1,546,542.5 0.81377161 80 1,394.3577 1,147.5
S_French-1A + S_Irula-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Luo-2B Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 17 156.7428 2,169.2
S_French-1A + S_Greek-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Basque-2B Discordant SGDP 136,557,025 – 136,762,052 205,026.5 0.02261269 15 117.5029 2,553.1
S_French-1A + S_Bergamo-2B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Palestinian-2A Discordant SGDP 135,760,098 – 137,851,404 2,091,306.5 1.21104218 163 1,973.6609 1,651.8
S_French-1A + S_Lezgin-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 19 156.7428 2,424.4
S_French-1A + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 36 562.7585 1,279.4
S_French-1A + S_Yadava-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_French-1A + S_Spanish-1A Discordant SGDP 136,615,626 – 137,851,404 1,235,778.0 1.13840801 141 1,504.8998 1,873.9
S_Palestinian-3B + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 33 552.7512 1,194.0
S_French-1A + S_Spanish-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Papuan-11A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 53 552.7512 1,917.7
S_French-1A + S_Tajik-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Bengali-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 66 552.7512 2,388.1
S_Palestinian-2B + S_Mozabite-1B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Madiga-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + S_Yakut-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Finnish-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 69 552.7512 2,496.6
S_Palestinian-2B + S_Tujia-2B Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 44 488.3165 1,802.1
S_Palestinian-2B + S_Korean-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Druze-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + B_Australian-4A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Tuscan-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Ami-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Russian-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 75 552.7512 2,713.7
S_Palestinian-3B + S_Thai-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Tajik-1B Discordant SGDP 135,760,098 – 136,619,279 859,181.0 0.07377702 73 472.4285 3,090.4
S_Palestinian-3B + B_Australian-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 55 552.7512 1,990.0
S_Palestinian-2B + S_Mansi-2B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 31 288.7149 2,147.4
S_French-1A + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 75 552.7512 2,713.7
S_Palestinian-3B + S_Thai-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + S_Brahmin-2A Discordant SGDP 136,290,439 – 136,762,052 471,613.0 0.06416660 31 278.7075 2,224.6
S_Palestinian-3B + S_Kinh-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + S_Brahui-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + B_Australian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 55 552.7512 1,990.0
S_Palestinian-2B + S_Sindhi-1B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 24 288.7149 1,662.5
S_Palestinian-3B + S_Bougainville-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + S_Armenian-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Bougainville-1B Discordant SGDP 135,760,098 – 136,755,811 995,713.5 0.08759616 51 549.0194 1,857.9
S_Palestinian-2B + S_Saharawi-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 29 562.7585 1,030.6
S_Palestinian-3B + S_Papuan-10A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 44 552.7512 1,592.0
S_Palestinian-2B + S_Georgian-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Papuan-7A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-2B + S_Georgian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Hawaiian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 70 552.7512 2,532.8
S_Palestinian-2B + S_Iranian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Yadava-1B Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 22 222.8731 1,974.2
S_Palestinian-2B + S_Iranian-2A Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 29 288.7149 2,008.9
S_Palestinian-3B + S_Mala-3B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-2B + S_Samaritan-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Palestinian-2B + S_Palestinian-3A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 21 232.8804 1,803.5
S_Palestinian-3B + S_Albanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 552.7512 1,338.8
S_Palestinian-2B + S_Sardinian-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Finnish-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 70 552.7512 2,532.8
S_Palestinian-2B + S_Sardinian-2B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Greek-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 64 552.7512 2,315.7
S_Palestinian-2B + S_Abkhasian-2B Discordant SGDP 136,290,439 – 136,774,712 484,273.0 0.06907976 29 288.7149 2,008.9
S_Palestinian-3B + S_Masai-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 50 552.7512 1,809.1
S_Palestinian-2B + B_Crete-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 27 232.8804 2,318.8
S_Palestinian-3B + S_Iraqi_Jew-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 65 552.7512 2,351.9
S_Palestinian-3B + S_Altaian-1B Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Druze-1B Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 67 537.1480 2,494.7
S_Palestinian-3B + S_Tlingit-2A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 58 552.7512 2,098.6
S_Palestinian-3B + S_Tlingit-1A Discordant SGDP 136,615,626 – 136,615,634 8.0 0.00000006 4 1.0039 79,689.8
S_Palestinian-3B + S_Jordanian-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 53 552.7512 1,917.7
S_Palestinian-3B + S_Daur-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Russian-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Hezhen-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 71 552.7512 2,569.0
S_Palestinian-3B + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 20 158.4384 2,524.6
S_Palestinian-3B + S_Naxi-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Lezgin-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 46 552.7512 1,664.4
S_Palestinian-3B + S_Japanese-2A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Turkish-1A Discordant SGDP 136,615,626 – 136,619,279 3,652.5 0.00114285 4 3.6675 21,813.3
S_Palestinian-3B + S_Korean-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 63 552.7512 2,279.5
S_Palestinian-3B + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 66 552.7512 2,388.1
S_Palestinian-3B + S_Burmese-1A Discordant SGDP 136,555,141 – 136,762,052 206,910.5 0.02601890 19 121.1322 3,137.1
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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