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

rs545884536
Alleles:
reference
G
ancestral
alternate
A
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  109,597,042  (GRCh37) Explore rs545884536 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 98.1%
1.9%
EAS 98.9%
1.1%
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 Joint clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP437.8 generations 87  =  1  +  860.988
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_Altaian-1A + S_Burmese-2A Concordant SGDP 109,541,915 – 109,627,534 85,618.5 0.14311594 6 156.5896 766.3
S_Altaian-1A + S_Khonda_Dora-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
S_Altaian-1A + S_Mozabite-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Igorot-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 32 599.7824 1,067.1
S_Altaian-1A + S_Thai-1A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Zapotec-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 33 599.7824 1,100.4
S_Altaian-1A + S_Karitiana-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Altaian-1A + S_Bergamo-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Zapotec-2A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 51 584.0201 1,746.5
S_Altaian-1A + S_Mixtec-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Mixtec-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Altaian-1A + S_Mixtec-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Mixe-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 33 599.7824 1,100.4
S_Altaian-1A + S_Mixe-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Altaian-1A + S_Burusho-2A Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 4 22.8002 3,508.7
S_Altaian-1A + S_Saami-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Quechua-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Altaian-1A + B_Han-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Quechua-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Pima-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Quechua-1A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 42 584.0201 1,438.3
S_Altaian-1A + S_Burmese-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Altaian-1A + S_Mongola-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 7 96.5230 1,450.4
S_Altaian-1A + S_Dusun-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 599.7824 666.9
S_Altaian-1A + S_Yakut-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 599.7824 1,000.4
S_Altaian-1A + S_Itelman-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Altaian-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 17 599.7824 566.9
S_Altaian-1A + S_Relli-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 40 599.7824 1,333.8
S_Altaian-1A + S_Ulchi-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Hazara-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Ulchi-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Czech-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Ulchi-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Altaian-1A + S_Druze-2A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
S_Altaian-1A + S_Aleut-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Altaian-1A + S_Kyrgyz-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Even-3B Discordant SGDP 108,954,234 – 109,997,580 1,043,345.5 0.73733073 68 1,091.6704 1,245.8
S_Altaian-1A + B_Mixe-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Even-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Pima-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Even-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 599.7824 666.9
S_Altaian-1A + S_Mayan-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
S_Altaian-1A + S_Eskimo_Chaplin-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Korean-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 34 599.7824 1,133.7
S_Altaian-1A + S_Tlingit-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Ami-2B Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 52 584.0201 1,780.8
S_Altaian-1A + S_Cambodian-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 599.7824 1,000.4
S_Altaian-1A + S_Kinh-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Altaian-1A + S_Cambodian-2B Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 4 22.8002 3,508.7
S_Altaian-1A + S_Dusun-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Lahu-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 5 26.6308 3,755.0
S_Altaian-1A + S_Hawaiian-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Miao-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Eskimo_Naukan-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 33 599.7824 1,100.4
S_Altaian-1A + S_Han-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Eskimo_Sireniki-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Altaian-1A + S_Miao-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Altaian-1A + S_Mala-2A Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 4 22.8002 3,508.7
S_Altaian-1A + S_Tu-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Kusunda-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Daur-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Altaian-1A + S_Hazara-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Oroqen-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 31 599.7824 1,033.7
S_Altaian-1A + S_Armenian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Tujia-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Estonian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Hezhen-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 32 599.7824 1,067.1
S_Altaian-1A + S_Georgian-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 5 26.6308 3,755.0
S_Altaian-1A + S_Yi-1B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Masai-1B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Dai-2A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 37 584.0201 1,267.1
S_Altaian-1A + S_Kyrgyz-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 32 599.7824 1,067.1
S_Altaian-1A + S_Uygur-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Altaian-1A + B_Dai-4A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 42 584.0201 1,438.3
S_Altaian-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + B_Karitiana-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_She-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
S_Altaian-1A + S_Surui-1A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_She-1A Discordant SGDP 108,954,234 – 109,599,057 644,823.0 0.34405212 20 585.7567 682.9
S_Altaian-1A + S_Piapoco-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Dai-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Altaian-1A + S_Pima-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Altaian-1A + S_Japanese-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 599.7824 1,000.4
S_Altaian-1A + S_Mayan-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 599.7824 833.6
S_Altaian-1A + S_Korean-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Burmese-2A + S_Abkhasian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 4 1.0114 79,096.1
S_Altaian-1A + S_Korean-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 33 599.7824 1,100.4
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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