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

rs533161787
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  136,655,768  (GRCh37) Explore rs533161787 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 97.9%
2.1%
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 Mutation clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP970.0 generations 93  =  1  +  921.000
Pairwise results table Mutation clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Dai-3B + S_Daur-2B Concordant SGDP 136,555,597 – 136,825,844 270,247.0 0.15563943 7 130.7186 1,071.0
S_Daur-2B + S_Basque-2B Discordant SGDP 136,557,025 – 136,776,467 219,442.0 0.02883100 13 106.3322 2,445.2
S_Daur-2B + S_Armenian-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 21 185.7822 2,260.7
S_Daur-2B + S_Balochi-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Brahmin-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 37 481.9379 1,535.5
S_Daur-2B + S_Tajik-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 28 185.7822 3,014.3
S_Daur-2B + S_Tuscan-1B Discordant SGDP 135,782,261 – 136,762,052 979,790.5 0.07868380 55 471.2994 2,334.0
S_Daur-2B + S_Masai-1B Discordant SGDP 135,909,353 – 136,762,052 852,698.5 0.07621271 62 410.2953 3,022.2
S_Daur-2B + S_Yakut-2B Discordant SGDP 135,782,261 – 136,822,338 1,040,077.0 0.16396375 40 500.2370 1,599.2
S_Daur-2B + S_Altaian-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 23 185.7822 2,476.0
S_Daur-2B + S_Mongola-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_BantuHerero-1A Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 60 473.3238 2,535.3
S_Daur-2B + S_Mozabite-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 45 479.4006 1,877.3
S_Dai-3B + S_Thai-2B Discordant SGDP 136,655,758 – 137,311,903 656,144.5 0.73542195 96 315.9494 6,076.9
S_Daur-2B + S_Hungarian-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 46 479.4006 1,919.1
S_Daur-2B + S_Iraqi_Jew-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 28 185.7822 3,014.3
S_Daur-2B + S_Tlingit-2A Discordant SGDP 136,654,786 – 136,655,774 988.0 0.00031418 2 1.4742 27,132.6
S_Daur-2B + S_Palestinian-3B Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 62 473.3238 2,619.8
S_Daur-2B + S_Tlingit-1B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 46 479.4006 1,919.1
S_Daur-2B + S_Russian-2B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 46 479.4006 1,919.1
S_Daur-2B + S_Lahu-1B Discordant SGDP 136,654,786 – 136,655,774 988.0 0.00031418 2 1.4742 27,132.6
S_Daur-2B + S_Mandenka-1B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 60 479.4006 2,503.1
S_Daur-2B + S_Tu-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Brahui-2A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 46 479.4006 1,919.1
S_Daur-2B + S_Tujia-2A Discordant SGDP 135,782,261 – 136,822,338 1,040,077.0 0.16396375 46 500.2370 1,839.1
S_Daur-2B + S_Sindhi-1B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 48 479.4006 2,002.5
S_Daur-2B + S_Hezhen-1B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Finnish-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 30 185.7822 3,229.6
S_Daur-2B + S_Xibo-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Georgian-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 20 185.7822 2,153.1
S_Daur-2B + S_Yi-2B Discordant SGDP 136,654,786 – 136,655,774 988.0 0.00031418 2 1.4742 27,132.6
S_Daur-2B + S_Iranian-2A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 44 479.4006 1,835.6
S_Daur-2B + S_Uygur-2A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Samaritan-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Naxi-1B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 43 478.2189 1,798.3
S_Daur-2B + S_Palestinian-2A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 51 479.4006 2,127.7
S_Daur-2B + S_Japanese-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Sardinian-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 23 185.7822 2,476.0
S_Daur-2B + S_Korean-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Russian-1B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 53 479.4006 2,211.1
S_Daur-2B + S_Korean-1A Discordant SGDP 135,909,353 – 136,776,467 867,114.0 0.08243101 33 417.2147 1,581.9
S_Daur-2B + S_Chechen-1B Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 28 179.7054 3,116.2
S_Daur-2B + S_Burmese-2A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + B_Crete-2A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Burmese-1B Discordant SGDP 136,080,619 – 136,776,467 695,848.0 0.07473184 30 335.0070 1,791.0
S_Dai-3B + S_Quechua-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Ami-1B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 46 478.2189 1,923.8
S_Daur-2B + S_Madiga-2B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 39 478.2189 1,631.1
S_Daur-2B + S_Ami-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Makrani-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 47 479.4006 1,960.8
S_Daur-2B + S_Thai-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Sindhi-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 59 479.4006 2,461.4
S_Daur-2B + S_Thai-2A Discordant SGDP 135,993,765 – 136,762,052 768,286.5 0.07200356 35 369.7775 1,893.0
S_Daur-2B + S_Albanian-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Kinh-2A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Saharawi-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 20 185.7822 2,153.1
S_Daur-2B + S_Kinh-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_French-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 52 479.4006 2,169.4
S_Daur-2B + B_Australian-3B Discordant SGDP 135,778,044 – 136,776,467 998,423.5 0.08599847 60 480.2433 2,498.7
S_Daur-2B + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 22 185.7822 2,368.4
S_Daur-2B + B_Australian-4A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Greek-1A Discordant SGDP 135,778,044 – 136,655,774 877,730.0 0.07673410 52 422.3104 2,462.6
S_Daur-2B + S_Dusun-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Iranian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 40 488.0147 1,639.3
S_Daur-2B + S_Bougainville-2A Discordant SGDP 136,654,786 – 136,655,774 988.0 0.00031418 2 1.4742 27,132.6
S_Daur-2B + S_Iraqi_Jew-2A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 50 479.4006 2,085.9
S_Daur-2B + S_Bougainville-1A Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 42 473.3238 1,774.7
S_Daur-2B + S_Iraqi_Jew-1A Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 54 478.2189 2,258.4
S_Daur-2B + S_Papuan-1B Discordant SGDP 136,654,786 – 136,655,774 988.0 0.00031418 2 1.4742 27,132.6
S_Daur-2B + S_Druze-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Papuan-10A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 34 479.4006 1,418.4
S_Daur-2B + S_Druze-1B Discordant SGDP 135,770,859 – 136,774,712 1,003,853.0 0.08580250 36 482.8494 1,491.1
S_Daur-2B + S_Papuan-11B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Palestinian-3A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 50 479.4006 2,085.9
S_Daur-2B + S_Papuan-7B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 47 479.4006 1,960.8
S_Daur-2B + S_Sardinian-1B Discordant SGDP 136,500,227 – 136,774,712 274,484.5 0.03728607 8 132.7526 1,205.2
S_Daur-2B + S_Papuan-9B Discordant SGDP 135,778,044 – 136,655,774 877,730.0 0.07673410 43 422.3104 2,036.4
S_Daur-2B + S_Tuscan-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Hawaiian-1A Discordant SGDP 135,782,261 – 136,655,774 873,512.5 0.07563774 44 420.2860 2,093.8
S_Daur-2B + S_Jordanian-1A Discordant SGDP 135,993,765 – 136,774,712 780,946.5 0.07691672 41 375.8543 2,181.7
S_Daur-2B + S_Mansi-2B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 48 479.4006 2,002.5
S_Daur-2B + S_Russian-2A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 30 185.7822 3,229.6
S_Daur-2B + S_Bengali-2B Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Abkhasian-2B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 46 479.4006 1,919.1
S_Daur-2B + S_Yadava-1A Discordant SGDP 136,389,749 – 136,762,052 372,303.0 0.05395958 25 179.7054 2,782.3
S_Daur-2B + S_Lezgin-1B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 45 479.4006 1,877.3
S_Daur-2B + S_Yadava-1B Discordant SGDP 135,993,765 – 136,762,052 768,286.5 0.07200356 41 369.7775 2,217.5
S_Daur-2B + S_Turkish-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Irula-2A Discordant SGDP 135,597,516 – 136,655,774 1,058,258.0 0.24401194 81 508.9638 3,182.9
S_Daur-2B + S_Mandenka-1A Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 57 479.4006 2,378.0
S_Daur-2B + S_Khonda_Dora-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Karitiana-1A Discordant SGDP 136,655,758 – 136,655,774 15.5 0.00000118 2 1.0074 39,704.6
S_Daur-2B + S_Mala-3A Discordant SGDP 135,778,044 – 136,762,052 984,008.0 0.07978017 38 473.3238 1,605.7
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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