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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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

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 Mutation clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP2,674.7 generations 100  =  3  +  970.990
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_Mbuti-3B + S_Masai-2B Concordant SGDP 109,132,345 – 109,615,525 483,180.0 0.24193221 23 232.9264 1,974.9
S_Biaka-1B + S_Masai-2B Concordant SGDP 109,328,376 – 109,536,510 208,134.0 0.03536789 9 100.9043 1,783.9
S_Biaka-1B + S_Mbuti-3B Concordant SGDP 109,320,672 – 109,536,804 216,132.5 0.04051567 11 104.7436 2,100.4
S_Biaka-1B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Khomani_San-1B Discordant SGDP 109,533,585 – 109,534,671 1,086.0 0.00039543 2 1.5213 26,293.6
S_Biaka-1B + S_BantuTswana-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + B_Ju_hoan_North-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Masai-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Mende-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Gambian-1B Discordant SGDP 109,528,690 – 109,540,064 11,373.5 0.00970780 4 6.4593 12,385.3
S_Mbuti-3B + S_BantuKenya-2B Discordant SGDP 109,320,672 – 109,534,671 213,999.5 0.03960054 27 103.7198 5,206.3
S_Biaka-1B + S_Burmese-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Mbuti-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Mbuti-2A Discordant SGDP 109,448,898 – 109,540,064 91,165.5 0.02836375 18 44.7594 8,043.0
S_Biaka-1B + S_Biaka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Tlingit-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Piapoco-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Mansi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_BantuTswana-1B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 6 4.1097 29,199.4
S_Biaka-1B + S_Bengali-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Hazara-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Saharawi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Lezgin-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Ju_hoan_North-1B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 58 279.0969 4,156.3
S_Biaka-1B + S_Relli-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Mozabite-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Adygei-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Yadava-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Yoruba-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Irula-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 18 42.1710 8,536.7
S_Biaka-1B + S_Somali-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Brahmin-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Surui-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Kusunda-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Tubalar-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Brahui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Mbuti-3A Discordant SGDP 107,216,487 – 109,534,671 2,318,184.0 1.71510396 51 1,113.7283 915.8
S_Biaka-1B + S_Pathan-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Luhya-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Luhya-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Finnish-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Brahui-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Jordanian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Luo-2A Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 67 240.1914 5,578.9
S_Mbuti-3B + S_Yoruba-2B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 6 4.1097 29,199.4
S_Biaka-1B + S_Sindhi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Dinka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Punjabi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Russian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Punjabi-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_North_Ossetian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Luhya-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Ju_hoan_North-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Bulgarian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + B_Crete-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Estonian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + B_Mbuti-4A Discordant SGDP 109,132,345 – 109,534,671 402,326.0 0.06763272 59 194.1165 6,078.8
S_Biaka-1B + S_Finnish-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + B_Sardinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Finnish-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Esan-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_BantuKenya-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 66 240.1914 5,495.6
S_Biaka-1B + S_Mende-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 67 240.1914 5,578.9
S_Biaka-1B + S_French-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Saharawi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Georgian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Dinka-2A Discordant SGDP 109,451,934 – 109,534,671 82,737.0 0.01698171 28 40.7138 13,754.6
S_Biaka-1B + S_Georgian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Surui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Hungarian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Piapoco-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Hungarian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_BantuTswana-1A Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 6 4.1097 29,199.4
S_Biaka-1B + S_Icelandic-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Biaka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Iranian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Gambian-1B Discordant SGDP 109,533,585 – 109,536,804 3,219.0 0.00131056 4 2.5451 31,432.7
S_Biaka-1B + S_Masai-1A Discordant SGDP 108,954,234 – 109,534,671 580,437.0 0.17740386 47 279.6098 3,361.8
S_Mbuti-3B + S_Khonda_Dora-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Iranian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Burusho-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Iranian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Estonian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Druze-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Greek-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Palestinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Luo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_BedouinB-1A Discordant SGDP 109,413,972 – 109,534,671 120,699.5 0.02533628 22 58.9358 7,465.8
S_Mbuti-3B + S_Abkhasian-2B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 138 279.0969 9,889.0
S_Biaka-1B + S_BedouinB-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 15 42.1710 7,113.9
S_Biaka-1B + S_Bergamo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + B_Dinka-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Bergamo-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Mbuti-3B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Tuscan-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Masai-2B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
S_Biaka-1B + S_Orcadian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 2 1.0084 39,666.8
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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