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 Joint clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP2,101.1 generations 100  =  3  +  970.990
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_Mbuti-3B + S_Masai-2B Concordant SGDP 109,132,345 – 109,615,525 483,180.0 0.24193221 25 426.4722 1,172.4
S_Biaka-1B + S_Masai-2B Concordant SGDP 109,328,376 – 109,536,510 208,134.0 0.03536789 11 129.1986 1,702.8
S_Biaka-1B + S_Mbuti-3B Concordant SGDP 109,320,672 – 109,536,804 216,132.5 0.04051567 13 137.1561 1,895.6
S_Biaka-1B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Khomani_San-1B Discordant SGDP 109,533,585 – 109,534,671 1,086.0 0.00039543 4 1.8376 43,534.6
S_Biaka-1B + S_BantuTswana-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + B_Ju_hoan_North-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Masai-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Mende-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Gambian-1B Discordant SGDP 109,528,690 – 109,540,064 11,373.5 0.00970780 6 14.2255 8,435.5
S_Mbuti-3B + S_BantuKenya-2B Discordant SGDP 109,320,672 – 109,534,671 213,999.5 0.03960054 29 135.4002 4,283.6
S_Biaka-1B + S_Burmese-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Mbuti-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Mbuti-2A Discordant SGDP 109,448,898 – 109,540,064 91,165.5 0.02836375 20 67.4504 5,930.3
S_Biaka-1B + S_Biaka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Tlingit-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Piapoco-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Mansi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_BantuTswana-1B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 8 10.4590 15,297.8
S_Biaka-1B + S_Bengali-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Hazara-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Saharawi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Lezgin-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Ju_hoan_North-1B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 60 420.7088 2,852.3
S_Biaka-1B + S_Relli-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Mozabite-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Adygei-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Yadava-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Yoruba-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Irula-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 20 58.8290 6,799.4
S_Biaka-1B + S_Somali-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Brahmin-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Surui-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Kusunda-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Tubalar-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Brahui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Mbuti-3A Discordant SGDP 107,216,487 – 109,534,671 2,318,184.0 1.71510396 53 2,485.8115 426.4
S_Biaka-1B + S_Pathan-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Luhya-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Luhya-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Finnish-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Brahui-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Jordanian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Luo-2A Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 69 299.4831 4,607.9
S_Mbuti-3B + S_Yoruba-2B Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 8 10.4590 15,297.8
S_Biaka-1B + S_Sindhi-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Dinka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Punjabi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Russian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Punjabi-4B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_North_Ossetian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Luhya-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Ju_hoan_North-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Bulgarian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + B_Crete-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Estonian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + B_Mbuti-4A Discordant SGDP 109,132,345 – 109,534,671 402,326.0 0.06763272 61 248.2227 4,914.9
S_Biaka-1B + S_Finnish-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + B_Sardinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Finnish-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Esan-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_BantuKenya-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 68 299.4831 4,541.2
S_Biaka-1B + S_Mende-1B Discordant SGDP 109,036,356 – 109,534,671 498,315.5 0.07411454 69 299.4831 4,607.9
S_Biaka-1B + S_French-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Saharawi-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Georgian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Dinka-2A Discordant SGDP 109,451,934 – 109,534,671 82,737.0 0.01698171 30 54.2991 11,049.9
S_Biaka-1B + S_Georgian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Surui-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Hungarian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Piapoco-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Hungarian-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_BantuTswana-1A Discordant SGDP 109,533,585 – 109,540,064 6,478.5 0.00793666 8 10.4590 15,297.8
S_Biaka-1B + S_Icelandic-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Biaka-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Iranian-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Gambian-1B Discordant SGDP 109,533,585 – 109,536,804 3,219.0 0.00131056 6 3.5936 33,393.0
S_Biaka-1B + S_Masai-1A Discordant SGDP 108,954,234 – 109,534,671 580,437.0 0.17740386 49 421.5328 2,324.8
S_Mbuti-3B + S_Khonda_Dora-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Iranian-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Burusho-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Iranian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Estonian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Druze-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Greek-1A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Palestinian-3B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Luo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_BedouinB-1A Discordant SGDP 109,413,972 – 109,534,671 120,699.5 0.02533628 24 79.2048 6,060.2
S_Mbuti-3B + S_Abkhasian-2B Discordant SGDP 108,954,234 – 109,533,603 579,368.5 0.17701495 140 420.7088 6,655.4
S_Biaka-1B + S_BedouinB-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + B_Yoruba-3B Discordant SGDP 109,448,898 – 109,534,671 85,773.0 0.02082251 17 58.8290 5,779.5
S_Biaka-1B + S_Bergamo-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + B_Dinka-3A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Bergamo-2A Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Mbuti-3B + S_Mende-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Tuscan-1B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Masai-2B + S_Mandenka-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
S_Biaka-1B + S_Orcadian-2B Discordant SGDP 109,533,585 – 109,533,603 17.5 0.00000652 4 1.0136 78,925.4
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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