HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs568034164
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  109,533,596  (GRCh37) Explore rs568034164 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.5%
0.5%
AFR 96.6%
3.4%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
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 Recombination clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP207.9 generations 100  =  3  +  970.333
Pairwise results table Recombination clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Mbuti-3B + S_Masai-2B Concordant SGDP 109,132,345 – 109,615,525 483,180.0 0.24193221 3 194.5458 308.4
S_Biaka-1B + S_Masai-2B Concordant SGDP 109,328,376 – 109,536,510 208,134.0 0.03536789 3 29.2943 2,048.2
S_Biaka-1B + S_Mbuti-3B Concordant SGDP 109,320,672 – 109,536,804 216,132.5 0.04051567 3 33.4125 1,795.7
S_Biaka-1B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Khomani_San-1B Discordant SGDP 109,533,585 – 109,534,671 1,086.0 0.00039543 3 1.3163 45,580.9
S_Biaka-1B + S_BantuTswana-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + B_Ju_hoan_North-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Masai-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Mende-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Gambian-1B Discordant SGDP 109,528,690 – 109,540,064 11,373.5 0.00970780 3 8.7662 6,844.4
S_Mbuti-3B + S_BantuKenya-2B Discordant SGDP 109,320,672 – 109,534,671 213,999.5 0.03960054 3 32.6804 1,836.0
S_Biaka-1B + S_Burmese-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Mbuti-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Mbuti-2A Discordant SGDP 109,448,898 – 109,540,064 91,165.5 0.02836375 3 23.6910 2,532.6
S_Biaka-1B + S_Biaka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Tlingit-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Piapoco-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Mansi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_BantuTswana-1B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 3 7.3493 8,164.0
S_Biaka-1B + S_Bengali-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Hazara-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Saharawi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Lezgin-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Ju_hoan_North-1B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 3 142.6120 420.7
S_Biaka-1B + S_Relli-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Mozabite-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Adygei-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Yadava-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Yoruba-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Irula-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 3 17.6580 3,397.9
S_Biaka-1B + S_Somali-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Brahmin-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Surui-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Kusunda-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Tubalar-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Brahui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Mbuti-3A Discordant SGDP 107,216,487 – 109,534,671 2,318,184.0 1.71510396 3 1,373.0832 43.7
S_Biaka-1B + S_Pathan-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Luhya-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Luhya-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Finnish-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Brahui-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Jordanian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Luo-2A Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 3 60.2916 995.2
S_Mbuti-3B + S_Yoruba-2B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 3 7.3493 8,164.0
S_Biaka-1B + S_Sindhi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Dinka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Punjabi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Russian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Punjabi-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_North_Ossetian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Luhya-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Ju_hoan_North-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Bulgarian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + B_Crete-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Estonian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + B_Mbuti-4A Discordant SGDP 109,132,345 – 109,534,671 402,326.0 0.06763272 3 55.1062 1,088.8
S_Biaka-1B + S_Finnish-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + B_Sardinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Finnish-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Esan-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_BantuKenya-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 3 60.2916 995.2
S_Biaka-1B + S_Mende-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 3 60.2916 995.2
S_Biaka-1B + S_French-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Saharawi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Georgian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Dinka-2A Discordant SGDP 109,451,934 – 109,534,671 82,737.0 0.01698171 3 14.5854 4,113.7
S_Biaka-1B + S_Georgian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Surui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Hungarian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Piapoco-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Hungarian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_BantuTswana-1A Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 3 7.3493 8,164.0
S_Biaka-1B + S_Icelandic-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Biaka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Iranian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Gambian-1B Discordant SGDP 109,533,585 – 109,536,804 3,219.0 0.00131056 3 2.0484 29,290.5
S_Biaka-1B + S_Masai-1A Discordant SGDP 108,954,234 – 109,534,671 580,437.0 0.17740386 3 142.9231 419.8
S_Mbuti-3B + S_Khonda_Dora-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Iranian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Burusho-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Iranian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Estonian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Druze-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Greek-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Palestinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Luo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_BedouinB-1A Discordant SGDP 109,413,972 – 109,534,671 120,699.5 0.02533628 3 21.2690 2,821.0
S_Mbuti-3B + S_Abkhasian-2B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 3 142.6120 420.7
S_Biaka-1B + S_BedouinB-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 3 17.6580 3,397.9
S_Biaka-1B + S_Bergamo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + B_Dinka-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Bergamo-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Mbuti-3B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Tuscan-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Masai-2B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
S_Biaka-1B + S_Orcadian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 3 1.0052 59,688.7
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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