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 Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP533.0 generations 86  =  1  +  851.000
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_Maori-1A + S_Hawaiian-1A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 8 324.1838 493.5
S_Hawaiian-1A + S_Dusun-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Hawaiian-1A + S_Korean-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Hawaiian-1A + S_She-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
S_Hawaiian-1A + S_Dai-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Oroqen-2B Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 2 1.0530 37,985.3
S_Hawaiian-1A + S_Karitiana-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Hawaiian-1A + B_Karitiana-3A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Maori-1A + S_Hezhen-2A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 20 302.9759 1,320.2
S_Maori-1A + S_Even-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Maori-1A + S_Tlingit-1A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 2 1.0530 37,985.3
S_Maori-1A + S_Eskimo_Chaplin-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 16 318.4197 1,005.0
S_Maori-1A + S_Even-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Maori-1A + S_Eskimo_Sireniki-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 323.9289 1,420.1
S_Maori-1A + S_Aleut-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 14 318.4197 879.3
S_Hawaiian-1A + S_Hawaiian-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 64 549.1828 2,330.7
S_Hawaiian-1A + S_Saami-1A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 2 1.0530 37,985.3
S_Maori-1A + S_Uygur-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 5 35.4234 2,823.0
S_Hawaiian-1A + S_Chane-1B Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 23 302.2202 1,522.1
S_Maori-1A + S_Xibo-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Hawaiian-1A + S_Mayan-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 17 318.4197 1,067.8
S_Maori-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Hawaiian-1A + S_Hezhen-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Maori-1A + S_She-1A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 17 302.9759 1,122.2
S_Hawaiian-1A + S_Naxi-1B Discordant SGDP 109,573,916 – 109,583,351 9,435.0 0.01014696 2 5.5288 7,234.8
S_Maori-1A + S_Thai-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 318.4197 1,130.6
S_Hawaiian-1A + S_Japanese-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Maori-1A + S_Kinh-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 20 323.9289 1,234.8
S_Hawaiian-1A + S_Ami-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 18 318.4197 1,130.6
S_Maori-1A + S_Itelman-1B Discordant SGDP 108,954,234 – 110,044,774 1,090,539.5 0.82425140 42 524.4590 1,601.7
S_Hawaiian-1A + S_Dusun-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Maori-1A + S_Eskimo_Naukan-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 17 323.9289 1,049.6
S_Hawaiian-1A + S_Hazara-2B Discordant SGDP 108,954,234 – 110,031,035 1,076,801.0 0.80862409 49 517.8645 1,892.4
S_Maori-1A + S_Eskimo_Naukan-2B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 15 323.9289 926.1
S_Hawaiian-1A + S_Kyrgyz-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Maori-1A + S_Eskimo_Sireniki-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 15 318.4197 942.2
S_Hawaiian-1A + B_Mixe-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 50 549.1828 1,820.9
S_Maori-1A + S_Atayal-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 15 323.9289 926.1
S_Hawaiian-1A + S_Karitiana-1A Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 19 302.2202 1,257.4
S_Maori-1A + S_Piapoco-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Hawaiian-1A + S_Pima-1B Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 25 302.9759 1,650.3
S_Hawaiian-1A + S_Mixe-2A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 62 549.1828 2,257.9
S_Maori-1A + S_Tubalar-1B Discordant SGDP 109,543,810 – 109,615,525 71,715.5 0.07637451 6 35.4234 3,387.6
S_Hawaiian-1A + S_Mixe-2B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 57 549.1828 2,075.8
S_Hawaiian-1A + S_Tujia-2B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 22 323.9289 1,358.3
S_Hawaiian-1A + S_Mixe-3A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 30 323.9289 1,852.3
S_Hawaiian-1A + S_Tujia-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 64 549.1828 2,330.7
S_Hawaiian-1A + S_Mixtec-1A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 64 549.1828 2,330.7
S_Hawaiian-1A + S_Xibo-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Mixtec-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Hawaiian-1A + S_She-2A Discordant SGDP 108,954,234 – 110,031,035 1,076,801.0 0.80862409 53 517.8645 2,046.9
S_Hawaiian-1A + S_Mixtec-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Hawaiian-1A + S_Dai-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 318.4197 1,695.9
S_Hawaiian-1A + S_Zapotec-2A Discordant SGDP 108,954,234 – 109,581,776 627,542.0 0.29783063 27 302.2202 1,786.8
S_Hawaiian-1A + S_Korean-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
S_Hawaiian-1A + S_Quechua-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 20 318.4197 1,256.2
S_Hawaiian-1A + S_Burmese-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 20 323.9289 1,234.8
S_Hawaiian-1A + S_Quechua-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Hawaiian-1A + S_Thai-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Quechua-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 59 549.1828 2,148.6
S_Hawaiian-1A + S_Dusun-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 16 318.4197 1,005.0
S_Hawaiian-1A + S_Mongola-1A Discordant SGDP 109,555,610 – 109,615,525 59,915.5 0.07148272 4 29.7594 2,688.2
S_Hawaiian-1A + S_Igorot-2B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 54 549.1828 1,966.6
S_Hawaiian-1A + S_Yakut-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Hawaiian-1A + S_Eskimo_Sireniki-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 23 323.9289 1,420.1
S_Hawaiian-1A + S_Ulchi-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Armenian-2A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 2 1.0530 37,985.3
S_Hawaiian-1A + S_Ulchi-2B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 24 318.4197 1,507.4
S_Hawaiian-1A + S_Kyrgyz-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 28 318.4197 1,758.7
S_Hawaiian-1A + S_Ulchi-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 26 318.4197 1,633.1
S_Hawaiian-1A + B_Han-3B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Even-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + B_Karitiana-3B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 21 323.9289 1,296.6
S_Hawaiian-1A + S_Eskimo_Chaplin-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 21 323.9289 1,296.6
S_Hawaiian-1A + B_Mixe-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 22 323.9289 1,358.3
S_Hawaiian-1A + S_Mansi-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 24 323.9289 1,481.8
S_Hawaiian-1A + S_Surui-1B Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 61 549.1828 2,221.5
S_Hawaiian-1A + S_Cambodian-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Hawaiian-1A + S_Karitiana-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 22 318.4197 1,381.8
S_Hawaiian-1A + S_Cambodian-2A Discordant SGDP 109,575,893 – 109,576,003 110.5 0.00005448 2 1.0530 37,985.3
S_Hawaiian-1A + S_Pima-1A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
S_Hawaiian-1A + S_Han-1B Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 21 323.9289 1,296.6
S_Hawaiian-1A + S_Pima-2B Discordant SGDP 108,954,234 – 110,002,153 1,047,918.5 0.74461388 36 504.0009 1,428.6
S_Hawaiian-1A + S_Miao-2A Discordant SGDP 108,954,234 – 109,583,351 629,116.5 0.30289591 18 302.9759 1,188.2
S_Hawaiian-1A + S_Mayan-2A Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Hawaiian-1A + S_Oroqen-1B Discordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
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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