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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs111495671
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  136,567,697  (GRCh37) Explore rs111495671 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 Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP7,978.7 generations 106  =  15  +  911.000
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_Ju_hoan_North-1A + S_Khomani_San-1A Concordant SGDP 135,729,071 – 136,801,475 1,072,404.5 0.29129866 171 748.7931 4,567.3
S_Ju_hoan_North-2B + S_Khomani_San-1A Concordant SGDP 136,411,978 – 136,801,475 389,497.5 0.12086568 33 284.6513 2,318.6
S_Ju_hoan_North-1A + B_Ju_hoan_North-4A Concordant SGDP 136,401,078 – 137,093,720 692,641.5 0.63258900 46 839.5391 1,095.8
S_Ju_hoan_North-2B + S_Ju_hoan_North-1A Concordant SGDP 136,406,898 – 137,034,384 627,485.5 0.40473764 31 625.9831 990.4
S_Ju_hoan_North-2B + B_Ju_hoan_North-4A Concordant SGDP 136,341,972 – 137,058,509 716,537.0 0.56883420 37 800.0051 925.0
S_Ju_hoan_North-3A + B_Ju_hoan_North-4A Concordant SGDP 135,439,018 – 136,644,413 1,205,395.0 0.34527206 100 855.8072 2,337.0
S_Ju_hoan_North-3A + S_Khomani_San-1A Concordant SGDP 136,080,221 – 136,644,413 564,192.5 0.06056790 110 320.2667 6,869.3
S_Ju_hoan_North-3A + S_Ju_hoan_North-2B Concordant SGDP 136,406,898 – 136,644,413 237,515.0 0.04190494 11 148.5312 1,481.2
S_Ju_hoan_North-3A + S_Ju_hoan_North-1A Concordant SGDP 136,399,121 – 136,644,413 245,292.0 0.04213799 17 152.4506 2,230.2
S_Mbuti-1A + S_Khomani_San-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 13 61.5101 4,226.9
S_Mbuti-1A + B_Ju_hoan_North-4A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 8 61.5101 2,601.2
S_Mbuti-1A + S_Ju_hoan_North-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 12 61.5101 3,901.8
S_Khomani_San-1A + B_Ju_hoan_North-4A Concordant SGDP 136,080,221 – 136,786,842 706,621.0 0.09231650 133 414.0313 6,424.6
S_Mbuti-1A + S_Ju_hoan_North-2B Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 10 61.5101 3,251.5
S_Mbuti-1A + S_Ju_hoan_North-3A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 9 61.5101 2,926.3
S_Mbuti-1A + S_Adygei-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Turkish-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Orcadian-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Lezgin-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mixe-3A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Tuscan-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Aleut-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Pima-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Tubalar-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Tlingit-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mongola-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mixtec-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mixtec-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + B_Crete-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Cambodian-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + B_Mixe-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Naxi-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Ju_hoan_North-1A + S_Czech-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Dai-3B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Druze-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Miao-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Norwegian-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_English-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Orcadian-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Estonian-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_North_Ossetian-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Finnish-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Spanish-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Finnish-3B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Yemenite_Jew-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Saami-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + B_French-3A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Basque-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Karitiana-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Greek-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Ju_hoan_North-2B + S_Kyrgyz-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Iranian-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Hezhen-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mozabite-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_BantuKenya-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Uygur-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Estonian-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Xibo-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Finnish-3A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Yi-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Saami-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mozabite-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_French-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Dai-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Georgian-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Xibo-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Icelandic-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Dai-1A Discordant SGDP 135,793,417 – 136,567,705 774,288.0 0.05643409 194 417.8055 9,286.6
S_Mbuti-1A + S_Samaritan-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Kinh-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Bergamo-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Dusun-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Jordanian-3A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Maori-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Norwegian-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Chukchi-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Orcadian-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Mansi-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Polish-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Brahmin-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Lezgin-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Balochi-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Adygei-1B Discordant SGDP 135,793,417 – 136,567,705 774,288.0 0.05643409 196 417.8055 9,382.4
S_Mbuti-1A + S_Brahui-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Spanish-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Makrani-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Tajik-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Burusho-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Yemenite_Jew-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Hazara-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Yemenite_Jew-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Sindhi-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + B_Dai-4A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Punjabi-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + B_Sardinian-3A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Punjabi-4A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Saharawi-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Bulgarian-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Piapoco-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Atayal-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_Pima-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_English-1A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Ju_hoan_North-1A + S_Mongola-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_English-1B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Ju_hoan_North-1A + S_Piapoco-2B Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
S_Mbuti-1A + S_English-2A Discordant SGDP 136,567,665 – 136,567,705 40.0 0.00000139 4 1.0203 78,407.4
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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