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

rs372508878
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  136,564,601  (GRCh37) Explore rs372508878 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.9%
1.1%
AFR 93.2%
6.8%
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 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 SGDP10,507.9 generations 107  =  8  +  990.970
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_Mandenka-2A + S_Khomani_San-1B Concordant SGDP 136,494,791 – 136,602,042 107,250.5 0.01678074 3 14.4246 4,159.6
S_Mandenka-2B + S_Khomani_San-1A Concordant SGDP 136,556,012 – 136,565,535 9,523.0 0.00304087 3 3.4327 17,479.0
S_Ju_hoan_North-1B + S_Khomani_San-1B Concordant SGDP 135,436,058 – 136,772,749 1,336,691.0 0.36529398 3 293.2352 204.6
S_Ju_hoan_North-1B + S_Mandenka-2A Concordant SGDP 136,494,791 – 136,602,042 107,250.5 0.01678074 3 14.4246 4,159.6
S_BantuTswana-2B + S_Khomani_San-1A Concordant SGDP 136,555,141 – 136,566,474 11,333.0 0.00454331 3 4.6346 12,946.0
S_Mandenka-2B + S_Khomani_San-1B Concordant SGDP 136,556,012 – 136,565,535 9,523.0 0.00304087 3 3.4327 17,479.0
S_BantuTswana-2B + S_Mandenka-2B Concordant SGDP 136,556,012 – 136,646,325 90,312.5 0.01676442 3 14.4115 4,163.3
S_BantuTswana-2B + S_Ju_hoan_North-1B Concordant SGDP 136,555,141 – 136,632,444 77,302.5 0.01599323 3 13.7946 4,349.5
S_Khomani_San-1B + S_Saami-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Greek-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Punjabi-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Estonian-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2A + S_Dusun-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Dai-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Saharawi-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + B_Ju_hoan_North-4A Discordant SGDP 135,437,187 – 136,572,640 1,135,453.0 0.33627945 3 270.0236 222.2
S_Khomani_San-1A + S_Ju_hoan_North-2B Discordant SGDP 136,411,978 – 136,787,291 375,313.0 0.07797775 3 63.3822 946.6
S_Khomani_San-1A + S_Turkish-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2A + S_Dinka-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2A + S_Yoruba-1B Discordant SGDP 136,556,012 – 136,564,602 8,590.0 0.00300843 3 3.4067 17,612.1
S_Mandenka-2A + S_Czech-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Norwegian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Tlingit-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Turkish-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Miao-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Uygur-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2A + S_Naxi-1A Discordant SGDP 135,760,098 – 136,564,602 804,504.5 0.06697593 3 54.5807 1,099.3
S_Khomani_San-1A + S_Spanish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Dai-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Yemenite_Jew-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Kinh-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Piapoco-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Kusunda-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Cambodian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Burusho-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Xibo-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Luhya-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Kinh-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Bulgarian-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Atayal-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Lezgin-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Finnish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Mandenka-2B + S_Mende-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Basque-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mozabite-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Druze-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mixe-3A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_North_Ossetian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mongola-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + B_Crete-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mongola-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Pima-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Tubalar-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Adygei-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Naxi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Adygei-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Miao-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Tajik-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Hezhen-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Turkish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Thai-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + B_Sardinian-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Chukchi-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Karitiana-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mozabite-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Mixtec-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Mansi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Aleut-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Brahmin-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Dai-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Hazara-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Daur-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Punjabi-4B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Yi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Czech-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Xibo-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_English-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Sindhi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_English-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Bulgarian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_BantuKenya-1A Discordant SGDP 136,556,012 – 136,564,602 8,590.0 0.00300843 3 3.4067 17,612.1
S_Khomani_San-1B + S_English-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Estonian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Estonian-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Finnish-3A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Finnish-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Saami-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_French-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_French-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Georgian-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Basque-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Icelandic-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Icelandic-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Kyrgyz-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Iranian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Ju_hoan_North-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Samaritan-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Ju_hoan_North-1A Discordant SGDP 136,559,711 – 136,572,640 12,929.0 0.00056393 3 1.4511 41,346.7
S_Khomani_San-1A + S_Tuscan-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Yemenite_Jew-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Jordanian-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + B_French-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Norwegian-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Piapoco-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Orcadian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1B + S_Pima-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
S_Khomani_San-1A + S_Orcadian-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 3 1.0003 59,979.1
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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