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

rs535456766
Alleles:
reference
T
ancestral
alternate
C
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  136,531,531  (GRCh37) Explore rs535456766 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.6%
1.4%
AFR 90.9%
9.1%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP7,862.2 generations 115  =  22  +  930.989
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 + B_Ju_hoan_North-4A Concordant SGDP 136,401,078 – 137,093,720 692,641.5 0.63258900 49 839.5391 1,167.3
S_Ju_hoan_North-2B + S_Khomani_San-2B Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 12 49.3533 4,862.9
S_Ju_hoan_North-2B + S_Khomani_San-1A Concordant SGDP 136,411,978 – 136,801,475 389,497.5 0.12086568 35 284.6513 2,459.1
S_Ju_hoan_North-2B + S_Ju_hoan_North-1A Concordant SGDP 136,406,898 – 137,034,384 627,485.5 0.40473764 32 625.9831 1,022.4
S_Ju_hoan_North-2B + B_Ju_hoan_North-4A Concordant SGDP 136,341,972 – 137,058,509 716,537.0 0.56883420 41 800.0051 1,025.0
S_Ju_hoan_North-1A + S_Khomani_San-1A Concordant SGDP 135,729,071 – 136,801,475 1,072,404.5 0.29129866 173 748.7931 4,620.8
S_Khomani_San-2A + S_Khomani_San-1A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 14 49.3533 5,673.4
S_Ju_hoan_North-3A + S_Ju_hoan_North-1A Concordant SGDP 136,399,121 – 136,644,413 245,292.0 0.04213799 18 152.4506 2,361.4
S_Ju_hoan_North-3A + B_Ju_hoan_North-4A Concordant SGDP 135,439,018 – 136,644,413 1,205,395.0 0.34527206 103 855.8072 2,407.1
S_Mbuti-1A + S_Khomani_San-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 14 61.5101 4,552.1
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_Mbuti-1A + S_Khomani_San-2A Concordant SGDP 136,491,330 – 136,559,711 68,381.0 0.01247340 11 43.8016 5,022.6
S_Mbuti-1A + B_Ju_hoan_North-4A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 9 61.5101 2,926.3
S_Mbuti-1A + S_Ju_hoan_North-1A Concordant SGDP 136,489,176 – 136,588,252 99,076.0 0.01619202 13 61.5101 4,226.9
S_Ju_hoan_North-1A + S_Khomani_San-2A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 15 49.3533 6,078.6
S_Ju_hoan_North-3A + S_Khomani_San-2A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 14 49.3533 5,673.4
S_Ju_hoan_North-1A + S_Khomani_San-2B Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 13 49.3533 5,268.1
S_Ju_hoan_North-3A + S_Khomani_San-1A Concordant SGDP 136,080,221 – 136,644,413 564,192.5 0.06056790 113 320.2667 7,056.6
S_Khomani_San-2A + B_Ju_hoan_North-4A Concordant SGDP 136,482,918 – 136,559,711 76,792.5 0.01436618 13 49.3533 5,268.1
S_Khomani_San-1A + B_Ju_hoan_North-4A Concordant SGDP 136,080,221 – 136,786,842 706,621.0 0.09231650 134 414.0313 6,472.9
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_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_Bergamo-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Samaritan-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Icelandic-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Greek-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Yemenite_Jew-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_North_Ossetian-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Orcadian-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Finnish-3A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + B_Sardinian-3A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Eskimo_Naukan-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Punjabi-3A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Ju_hoan_North-1A + S_Czech-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Saharawi-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Tuscan-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_BantuKenya-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Norwegian-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Saami-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Lezgin-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Basque-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Adygei-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Spanish-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Turkish-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mozabite-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + B_French-3B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mixe-3A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Karitiana-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mixtec-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Mixe-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mongola-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Hungarian-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Tlingit-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Eskimo_Chaplin-1A Discordant SGDP 136,531,527 – 136,762,052 230,524.5 0.02921296 37 135.0221 5,480.6
S_Mbuti-1A + S_Aleut-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + B_Karitiana-3B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Dai-3B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Finnish-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Uygur-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Finnish-3B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Xibo-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Saami-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Yi-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_French-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Xibo-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Georgian-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Dai-1A Discordant SGDP 135,793,417 – 136,531,556 738,138.5 0.04865630 167 394.2315 8,472.2
S_Mbuti-1A + S_Icelandic-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Thai-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Iranian-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Kinh-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Druze-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Maori-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Bergamo-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Chukchi-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Jordanian-3B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mozabite-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Orcadian-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Mansi-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Polish-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Brahmin-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Lezgin-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Balochi-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Adygei-1B Discordant SGDP 135,793,417 – 136,531,556 738,138.5 0.04865630 171 394.2315 8,675.1
S_Mbuti-1A + S_Brahui-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Spanish-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Brahui-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Tajik-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Makrani-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Yemenite_Jew-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Pathan-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + B_Crete-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Burusho-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + B_Mixe-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Hazara-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Surui-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Sindhi-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Ju_hoan_North-1A + S_Mongola-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Punjabi-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Ju_hoan_North-1A + S_Kyrgyz-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Punjabi-4A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Itelman-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Bulgarian-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Bulgarian-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Atayal-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2A + S_Spanish-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_English-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Eskimo_Sireniki-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_English-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Oroqen-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Estonian-2A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Tajik-2B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Estonian-1A Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Khomani_San-2B + S_Chane-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
S_Mbuti-1A + S_Estonian-1B Discordant SGDP 136,531,527 – 136,531,556 28.5 0.00000236 4 1.0156 78,773.7
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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