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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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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

rs12257591
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 10   position  31,822,106  (GRCh37) Explore rs12257591 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.4%
1.6%
AFR 90.9%
9.1%
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 99.3%
0.7%
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 SGDP38,013.0 generations 136  =  36  +  1000.980
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_Saharawi-2A + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Saharawi-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Saharawi-2A + S_Esan-1B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 5 4.2134 23,733.8
S_Esan-1B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Saharawi-2A + S_Luhya-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 4 4.2134 18,987.0
S_Yoruba-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Esan-1B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Luhya-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 3 2.4994 24,005.8
S_Luhya-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 4 2.4994 32,007.8
S_Biaka-2A + S_Esan-2B Concordant SGDP 31,822,100 – 31,841,841 19,741.5 0.00198474 12 12.0637 19,894.4
S_Biaka-2A + S_Khomani_San-2B Concordant SGDP 31,693,149 – 31,822,112 128,963.0 0.00457854 49 66.5651 14,722.4
S_Biaka-2A + S_Esan-1B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Biaka-2A + S_Yoruba-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Biaka-2A + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Esan-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Luhya-2B + S_Yoruba-2B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 38 71.9932 10,556.5
S_Khomani_San-2B + S_Georgian-2B Concordant SGDP 31,822,025 – 31,822,112 87.0 0.00000145 3 1.0429 57,530.6
S_Luhya-2B + S_Esan-1B Concordant SGDP 31,688,920 – 31,827,533 138,613.5 0.00557346 39 71.9932 10,834.3
S_Esan-1B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Luhya-2B + S_Esan-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 4 2.4994 32,007.8
S_Esan-1B + S_Esan-2B Concordant SGDP 31,819,482 – 31,824,938 5,456.0 0.00074315 5 4.2134 23,733.8
S_Luhya-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Saharawi-2A + S_Biaka-2A Concordant SGDP 31,820,336 – 31,841,841 21,505.0 0.00222725 13 13.1042 19,841.0
S_Georgian-2B + B_Mbuti-4A Concordant SGDP 31,821,907 – 31,822,112 204.5 0.00000342 3 1.1009 54,501.1
S_Saharawi-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Yoruba-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Saharawi-2A + S_Yoruba-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 3 2.7199 22,059.4
S_Yoruba-2B + B_Mbuti-4A Concordant SGDP 31,822,100 – 32,051,343 229,243.0 0.33866899 51 381.9718 2,670.4
S_Saharawi-2A + S_Esan-2B Concordant SGDP 31,614,944 – 31,965,047 350,103.0 0.24796352 15 367.4203 816.5
S_Yoruba-2B + S_Esan-1B Concordant SGDP 31,536,157 – 31,874,064 337,906.5 0.12244606 14 261.1520 1,072.2
S_Esan-2B + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Yoruba-2B + S_Esan-2B Concordant SGDP 31,819,482 – 31,822,112 2,630.0 0.00057191 3 2.7199 22,059.4
S_Esan-2B + S_Khomani_San-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Khomani_San-2B + B_Mbuti-4A Concordant SGDP 31,485,956 – 31,824,938 338,982.0 0.02792865 167 186.0543 17,951.8
S_Biaka-2A + S_Luhya-2B Concordant SGDP 31,822,100 – 31,824,938 2,838.0 0.00017144 5 2.4994 40,009.7
S_Biaka-2A + S_Georgian-2B Concordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 3 1.0059 59,646.9
S_Esan-1B + S_North_Ossetian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Jordanian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Palestinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Punjabi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Czech-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Palestinian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Icelandic-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Georgian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_French-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Estonian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Chane-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Jordanian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Orcadian-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Brahmin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Spanish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Albanian-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + B_Sardinian-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Finnish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Zapotec-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Iraqi_Jew-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Quechua-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Even-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Orcadian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Aleut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + B_French-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Burmese-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Piapoco-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Abkhasian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Bulgarian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Atayal-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Biaka-2A + S_Polish-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_English-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Georgian-2B + S_Saharawi-2B Discordant SGDP 31,484,549 – 31,841,841 357,292.0 0.03021478 10 196.6720 1,016.9
S_Yoruba-2B + S_Saami-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Tubalar-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Georgian-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Yakut-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Greek-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Tu-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Iraqi_Jew-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Uygur-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Bergamo-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_She-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Tuscan-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Korean-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Kyrgyz-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Thai-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Chechen-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Maori-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Maori-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Pima-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Bougainville-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Mixtec-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Ulchi-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_BantuTswana-1B Discordant SGDP 31,536,157 – 32,453,323 917,166.0 0.54162157 22 874.5369 503.1
S_Yoruba-2B + S_Papuan-10B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Burmese-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-4A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Bougainville-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-14A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Mala-3A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-7A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Madiga-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-7B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Luhya-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-9B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Albanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-12A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Finnish-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Papuan-12B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Basque-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Chukchi-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Iraqi_Jew-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Mansi-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Samaritan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Bengali-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Bergamo-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Kapu-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Sardinian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Relli-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Jordanian-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Irula-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Lezgin-2B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Mala-3B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Turkish-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Pathan-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + B_Papuan-15B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Hazara-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Esan-1B + S_Karitiana-1B Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Kalash-1A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Saharawi-2A + S_Mende-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
S_Yoruba-2B + S_Kalash-2A Discordant SGDP 31,822,100 – 31,822,112 12.0 0.00000020 4 1.0059 79,529.2
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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