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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

rs112108654
Alleles:
reference
T
ancestral
alternate
G
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 10   position  31,672,979  (GRCh37) Explore rs112108654 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.4%
1.6%
AFR 89.8%
10.2%
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 G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP10,220.4 generations 123  =  25  +  981.000
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_Ju_hoan_North-2B + S_Ju_hoan_North-1B Concordant SGDP 31,556,603 – 31,870,414 313,810.5 0.04203703 3 34.6296 1,732.6
S_Ju_hoan_North-2B + B_Ju_hoan_North-4B Concordant SGDP 31,556,603 – 31,873,306 316,702.5 0.10924376 3 88.3950 678.8
S_Khomani_San-2A + S_Khomani_San-1B Concordant SGDP 30,998,177 – 31,824,938 826,760.5 0.47080762 3 377.6461 158.9
S_Ju_hoan_North-2A + S_Khomani_San-1B Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 3 106.5296 563.2
S_Ju_hoan_North-1B + B_Ju_hoan_North-4B Concordant SGDP 31,068,515 – 31,870,414 801,899.0 0.36691039 3 294.5283 203.7
S_Ju_hoan_North-1B + S_Khomani_San-1B Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 3 106.5296 563.2
S_Ju_hoan_North-3B + S_Khomani_San-2A Concordant SGDP 31,480,954 – 31,824,938 343,983.5 0.04086920 3 33.6954 1,780.7
S_Ju_hoan_North-1A + S_Khomani_San-2A Concordant SGDP 31,107,575 – 31,824,938 717,363.0 0.29153703 3 234.2296 256.2
S_Ju_hoan_North-3B + S_Ju_hoan_North-1B Concordant SGDP 31,557,667 – 31,951,947 394,280.0 0.25042696 3 201.3416 298.0
S_Ju_hoan_North-3B + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 3 11.5734 5,184.3
S_Ju_hoan_North-3A + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 3 11.5734 5,184.3
S_Ju_hoan_North-3A + S_Ju_hoan_North-1B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 3 11.5734 5,184.3
S_Ju_hoan_North-3A + S_Ju_hoan_North-2B Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 3 11.3226 5,299.2
S_Ju_hoan_North-2B + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 3 10.1227 5,927.3
S_Ju_hoan_North-3B + S_Khomani_San-1B Concordant SGDP 31,480,954 – 31,910,782 429,827.5 0.25894213 3 208.1537 288.2
S_Ju_hoan_North-2B + S_Khomani_San-1B Concordant SGDP 31,557,667 – 31,840,315 282,647.5 0.01290321 3 11.3226 5,299.2
S_Ju_hoan_North-2A + S_Ju_hoan_North-1A Concordant SGDP 31,557,667 – 31,906,050 348,382.5 0.13191199 3 106.5296 563.2
S_Ju_hoan_North-1A + S_Khomani_San-1B Concordant SGDP 31,107,575 – 32,162,772 1,055,197.0 0.71285433 3 571.2835 105.0
S_Ju_hoan_North-2A + S_Ju_hoan_North-1B Concordant SGDP 31,068,515 – 33,707,610 2,639,095.5 1.74323778 3 1,395.5902 43.0
S_Ju_hoan_North-1B + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 3 10.1227 5,927.3
S_Ju_hoan_North-2A + S_Khomani_San-2A Concordant SGDP 31,557,667 – 31,795,978 238,310.5 0.01002565 3 9.0205 6,651.5
S_Khomani_San-2A + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,824,938 267,270.5 0.01140339 3 10.1227 5,927.3
S_Khomani_San-1B + B_Ju_hoan_North-4B Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 3 11.5734 5,184.3
S_Ju_hoan_North-3A + S_Ju_hoan_North-3B Concordant SGDP 31,408,348 – 31,870,414 462,066.0 0.19978861 3 160.8309 373.1
S_Ju_hoan_North-3A + S_Ju_hoan_North-2A Concordant SGDP 31,557,667 – 31,841,841 284,174.0 0.01321669 3 11.5734 5,184.3
S_Khomani_San-2A + S_Kapu-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Papuan-9A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Orcadian-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Icelandic-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Czech-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Sindhi-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Madiga-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Tu-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Mansi-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-14B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Maori-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + B_Dai-4B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Irula-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Uygur-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Mala-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Korean-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Pathan-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Ami-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Armenian-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + B_Australian-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Saami-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Maori-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Iranian-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_BedouinB-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Tuscan-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Khonda_Dora-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Yemenite_Jew-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Brahmin-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Pima-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Georgian-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-4A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Iranian-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-12A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Kyrgyz-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Sardinian-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Lezgin-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Han-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3A + S_Spanish-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Oroqen-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Mozabite-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_She-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + B_Australian-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Burmese-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + B_Australian-4A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Thai-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Papuan-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Dusun-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Burusho-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Bougainville-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Hungarian-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Chukchi-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Icelandic-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Relli-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Russian-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Mala-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + S_Turkish-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Brahmin-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-3B + B_Sardinian-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Makrani-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-2A + S_Hazara-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Kalash-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-2A + S_Kyrgyz-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Abkhasian-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-2B + S_Jordanian-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Bulgarian-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-2B + S_Chechen-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Estonian-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1A + S_Papuan-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Saami-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1A + S_Kalash-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Icelandic-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1A + S_Polish-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Druze-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1B + S_Tubalar-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Sardinian-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1B + S_Papuan-3A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Jordanian-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1B + S_Papuan-7A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Yemenite_Jew-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Ju_hoan_North-1B + S_Papuan-7B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Yemenite_Jew-1A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Mixe-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + B_French-3A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Mongola-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Tu-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Tubalar-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-5B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Yakut-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-4B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Even-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-9B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Even-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Papuan-2A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Yakut-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + S_Finnish-1B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Aleut-2B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-1B + B_Papuan-15A Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
S_Khomani_San-2A + S_Naxi-3B Discordant SGDP 31,672,973 – 31,673,025 52.0 0.00000014 3 1.0001 59,993.3
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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