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

rs959763281
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  109,575,913  (GRCh37) Explore rs959763281 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 100.0%
0.0%
OCN 96.0%
4.0%
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 SGDP334.2 generations 86  =  1  +  851.000
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_Maori-1A + S_Hawaiian-1A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 10 630.7422 317.1
S_Hawaiian-1A + S_Dusun-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Hawaiian-1A + S_Korean-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Hawaiian-1A + S_She-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
S_Hawaiian-1A + S_Dai-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Oroqen-2B Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 4 1.0966 72,951.2
S_Hawaiian-1A + S_Karitiana-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Hawaiian-1A + B_Karitiana-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Maori-1A + S_Hezhen-2A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 22 545.2926 806.9
S_Maori-1A + S_Even-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Maori-1A + S_Tlingit-1A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 4 1.0966 72,951.2
S_Maori-1A + S_Eskimo_Chaplin-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 599.7824 600.2
S_Maori-1A + S_Even-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Maori-1A + S_Eskimo_Sireniki-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 25 616.1245 811.5
S_Maori-1A + S_Aleut-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 16 599.7824 533.5
S_Hawaiian-1A + S_Hawaiian-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 66 1,221.0212 1,081.1
S_Hawaiian-1A + S_Saami-1A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 4 1.0966 72,951.2
S_Maori-1A + S_Uygur-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 7 96.5230 1,450.4
S_Hawaiian-1A + S_Chane-1B Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 25 540.4847 925.1
S_Maori-1A + S_Xibo-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Hawaiian-1A + S_Mayan-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 599.7824 633.6
S_Maori-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Hawaiian-1A + S_Hezhen-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Maori-1A + S_She-1A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 19 545.2926 696.9
S_Hawaiian-1A + S_Naxi-1B Discordant SGDP 109,573,916 – 109,583,351 9,435.0 0.01014696 4 13.6464 5,862.4
S_Maori-1A + S_Thai-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 599.7824 666.9
S_Hawaiian-1A + S_Japanese-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Maori-1A + S_Kinh-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 22 616.1245 714.1
S_Hawaiian-1A + S_Ami-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 599.7824 666.9
S_Maori-1A + S_Itelman-1B Discordant SGDP 108,954,234 – 110,044,774 1,090,539.5 0.82425140 44 1,183.8601 743.3
S_Hawaiian-1A + S_Dusun-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Maori-1A + S_Eskimo_Naukan-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 19 616.1245 616.8
S_Hawaiian-1A + S_Hazara-2B Discordant SGDP 108,954,234 – 110,031,035 1,076,801.0 0.80862409 51 1,164.7638 875.7
S_Maori-1A + S_Eskimo_Naukan-2B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 17 616.1245 551.8
S_Hawaiian-1A + S_Kyrgyz-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Maori-1A + S_Eskimo_Sireniki-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 17 599.7824 566.9
S_Hawaiian-1A + B_Mixe-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 52 1,221.0212 851.7
S_Maori-1A + S_Atayal-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 17 616.1245 551.8
S_Hawaiian-1A + S_Karitiana-1A Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 21 540.4847 777.1
S_Maori-1A + S_Piapoco-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Hawaiian-1A + S_Pima-1B Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 27 545.2926 990.3
S_Hawaiian-1A + S_Mixe-2A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 64 1,221.0212 1,048.3
S_Maori-1A + S_Tubalar-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 8 96.5230 1,657.6
S_Hawaiian-1A + S_Mixe-2B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 59 1,221.0212 966.4
S_Hawaiian-1A + S_Tujia-2B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 24 616.1245 779.1
S_Hawaiian-1A + S_Mixe-3A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 32 616.1245 1,038.8
S_Hawaiian-1A + S_Tujia-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 66 1,221.0212 1,081.1
S_Hawaiian-1A + S_Mixtec-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 66 1,221.0212 1,081.1
S_Hawaiian-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Mixtec-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Hawaiian-1A + S_She-2A Discordant SGDP 108,954,234 – 110,031,035 1,076,801.0 0.80862409 55 1,164.7638 944.4
S_Hawaiian-1A + S_Mixtec-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Hawaiian-1A + S_Dai-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 29 599.7824 967.0
S_Hawaiian-1A + S_Zapotec-2A Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 29 540.4847 1,073.1
S_Hawaiian-1A + S_Korean-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
S_Hawaiian-1A + S_Quechua-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 599.7824 733.6
S_Hawaiian-1A + S_Burmese-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 22 616.1245 714.1
S_Hawaiian-1A + S_Quechua-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Hawaiian-1A + S_Thai-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Quechua-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 61 1,221.0212 999.2
S_Hawaiian-1A + S_Dusun-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 599.7824 600.2
S_Hawaiian-1A + S_Mongola-1A Discordant SGDP 109,555,610 – 109,615,525 59,915.5 0.07148272 6 86.9456 1,380.2
S_Hawaiian-1A + S_Igorot-2B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 56 1,221.0212 917.3
S_Hawaiian-1A + S_Yakut-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Hawaiian-1A + S_Eskimo_Sireniki-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 25 616.1245 811.5
S_Hawaiian-1A + S_Ulchi-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Armenian-2A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 4 1.0966 72,951.2
S_Hawaiian-1A + S_Ulchi-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 599.7824 867.0
S_Hawaiian-1A + S_Kyrgyz-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 30 599.7824 1,000.4
S_Hawaiian-1A + S_Ulchi-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 599.7824 933.7
S_Hawaiian-1A + B_Han-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Even-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + B_Karitiana-3B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 616.1245 746.6
S_Hawaiian-1A + S_Eskimo_Chaplin-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 616.1245 746.6
S_Hawaiian-1A + B_Mixe-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 24 616.1245 779.1
S_Hawaiian-1A + S_Mansi-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 26 616.1245 844.0
S_Hawaiian-1A + S_Surui-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 63 1,221.0212 1,031.9
S_Hawaiian-1A + S_Cambodian-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Hawaiian-1A + S_Karitiana-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 599.7824 800.3
S_Hawaiian-1A + S_Cambodian-2A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 4 1.0966 72,951.2
S_Hawaiian-1A + S_Pima-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
S_Hawaiian-1A + S_Han-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 616.1245 746.6
S_Hawaiian-1A + S_Pima-2B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 38 1,099.6920 691.1
S_Hawaiian-1A + S_Miao-2A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 20 545.2926 733.6
S_Hawaiian-1A + S_Mayan-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Hawaiian-1A + S_Oroqen-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
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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