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 Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP706.3 generations 87  =  1  +  860.988
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_Altaian-1A + S_Burmese-2A Concordant SGDP 109,541,915 – 109,627,534 85,618.5 0.14311594 4 42.0969 1,900.4
S_Altaian-1A + S_Khonda_Dora-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
S_Altaian-1A + S_Mozabite-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Igorot-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 318.4197 1,884.3
S_Altaian-1A + S_Thai-1A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Zapotec-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 31 318.4197 1,947.1
S_Altaian-1A + S_Karitiana-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Altaian-1A + S_Bergamo-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Zapotec-2A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 49 309.5531 3,165.9
S_Altaian-1A + S_Mixtec-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Mixtec-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Altaian-1A + S_Mixtec-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Mixe-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 31 318.4197 1,947.1
S_Altaian-1A + S_Mixe-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Altaian-1A + S_Burusho-2A Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 2 13.4301 2,978.4
S_Altaian-1A + S_Saami-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Quechua-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Altaian-1A + B_Han-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Quechua-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Pima-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Quechua-1A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 40 309.5531 2,584.4
S_Altaian-1A + S_Burmese-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Altaian-1A + S_Mongola-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 5 35.4234 2,823.0
S_Altaian-1A + S_Dusun-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 318.4197 1,130.6
S_Altaian-1A + S_Yakut-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 318.4197 1,758.7
S_Altaian-1A + S_Itelman-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Altaian-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 15 318.4197 942.2
S_Altaian-1A + S_Relli-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 38 318.4197 2,386.8
S_Altaian-1A + S_Ulchi-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Hazara-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Ulchi-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Czech-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Ulchi-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Altaian-1A + S_Druze-2A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
S_Altaian-1A + S_Aleut-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Altaian-1A + S_Kyrgyz-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Even-3B Discordant SGDP 108,954,234 – 109,997,580 1,043,345.5 0.73733073 66 501.8058 2,630.5
S_Altaian-1A + B_Mixe-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Even-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Pima-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Even-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 318.4197 1,130.6
S_Altaian-1A + S_Mayan-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
S_Altaian-1A + S_Eskimo_Chaplin-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Korean-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 32 318.4197 2,009.9
S_Altaian-1A + S_Tlingit-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Ami-2B Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 50 309.5531 3,230.5
S_Altaian-1A + S_Cambodian-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 318.4197 1,758.7
S_Altaian-1A + S_Kinh-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Altaian-1A + S_Cambodian-2B Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 2 13.4301 2,978.4
S_Altaian-1A + S_Dusun-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Lahu-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 15.0107 3,997.1
S_Altaian-1A + S_Hawaiian-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Miao-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Eskimo_Naukan-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 31 318.4197 1,947.1
S_Altaian-1A + S_Han-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Eskimo_Sireniki-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Altaian-1A + S_Miao-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Altaian-1A + S_Mala-2A Discordant SGDP 109,589,629 – 109,615,525 25,896.0 0.01171270 2 13.4301 2,978.4
S_Altaian-1A + S_Tu-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Kusunda-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Daur-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Altaian-1A + S_Hazara-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Oroqen-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 318.4197 1,821.5
S_Altaian-1A + S_Armenian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Tujia-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Estonian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Hezhen-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 318.4197 1,884.3
S_Altaian-1A + S_Georgian-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 15.0107 3,997.1
S_Altaian-1A + S_Yi-1B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Masai-1B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Dai-2A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 35 309.5531 2,261.3
S_Altaian-1A + S_Kyrgyz-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 318.4197 1,884.3
S_Altaian-1A + S_Uygur-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Altaian-1A + B_Dai-4A Discordant SGDP 108,954,234 – 109,597,053 642,819.0 0.34308372 40 309.5531 2,584.4
S_Altaian-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + B_Karitiana-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_She-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
S_Altaian-1A + S_Surui-1A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_She-1A Discordant SGDP 108,954,234 – 109,599,057 644,823.0 0.34405212 18 310.5150 1,159.4
S_Altaian-1A + S_Piapoco-2B Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Dai-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Altaian-1A + S_Pima-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Altaian-1A + S_Japanese-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 318.4197 1,758.7
S_Altaian-1A + S_Mayan-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 318.4197 1,444.6
S_Altaian-1A + S_Korean-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Burmese-2A + S_Abkhasian-2A Discordant SGDP 109,597,034 – 109,597,053 19.0 0.00000289 2 1.0091 39,638.5
S_Altaian-1A + S_Korean-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 31 318.4197 1,947.1
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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