HumanGenomeDating
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

rs375787151
Alleles:
reference
T
ancestral
alternate
C
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  109,599,447  (GRCh37) Explore rs375787151 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.2%
1.8%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 80.0%
20.0%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP922.1 generations 136  =  42  +  940.810
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_Bougainville-1B + S_Papuan-7A Concordant SGDP 108,607,294 – 109,627,534 1,020,239.5 0.81546570 34 1,143.0875 594.9
S_Bougainville-2B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 12 599.7824 400.1
S_Bougainville-1B + S_Papuan-13B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 23 599.7824 766.9
S_Bougainville-2B + S_Bougainville-2A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 26 630.7422 824.4
S_Bougainville-2B + S_Papuan-11A Concordant SGDP 108,954,234 – 110,180,181 1,225,947.0 1.01345539 35 1,400.2189 499.9
S_Papuan-13B + S_Papuan-14A Concordant SGDP 107,942,939 – 110,020,181 2,077,242.5 1.63392273 44 2,305.2146 381.7
S_Papuan-14A + S_Papuan-12B Concordant SGDP 108,954,234 – 110,020,729 1,066,495.0 0.80262792 39 1,155.0199 675.3
B_Australian-3A + S_Papuan-7A Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 15 489.1474 613.3
B_Australian-3A + S_Papuan-12B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 5 29.3679 3,405.1
B_Australian-3A + S_Papuan-13B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 5 29.3679 3,405.1
B_Australian-3A + S_Papuan-14A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 5 60.3278 1,657.6
B_Australian-3A + S_Papuan-11A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 14 519.1556 539.3
B_Australian-3A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,414 62,351.5 0.15000138 7 150.9298 927.6
B_Australian-3A + S_Bougainville-2B Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 21 489.1474 858.6
S_Papuan-11A + S_Papuan-13B Concordant SGDP 108,157,391 – 109,615,525 1,458,134.0 1.04071248 30 1,533.4743 391.3
B_Australian-4A + S_Bougainville-2A Concordant SGDP 109,554,071 – 109,627,534 73,463.0 0.10329138 9 118.8953 1,513.9
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,391 – 110,258,928 2,101,536.5 1.85890768 35 2,496.8637 280.4
B_Australian-4A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,746 62,684.0 0.15522514 4 155.2684 515.2
S_Papuan-13B + S_Papuan-12B Concordant SGDP 108,157,391 – 110,180,181 2,022,790.0 1.70246451 27 2,333.9108 231.4
B_Australian-4A + S_Papuan-11A Concordant SGDP 109,548,942 – 110,180,181 631,239.5 0.73458401 17 891.6622 381.3
S_Bougainville-2A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 27 599.7824 900.3
B_Australian-4A + S_Papuan-13B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 5 82.0540 1,218.7
S_Bougainville-2B + S_Bougainville-1B Concordant SGDP 108,954,234 – 109,648,746 694,512.0 0.48914636 20 725.6829 551.2
B_Australian-4A + S_Papuan-14A Concordant SGDP 109,557,756 – 109,649,341 91,584.5 0.21291243 6 215.2905 557.4
S_Bougainville-2B + S_Papuan-7A Concordant SGDP 108,954,234 – 110,613,184 1,658,949.5 1.95891925 40 2,364.4312 338.3
B_Australian-4A + S_Papuan-7A Concordant SGDP 109,548,942 – 110,613,184 1,064,242.0 1.68004787 24 1,855.8745 258.6
S_Bougainville-1B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 25 630.7422 792.7
B_Australian-4A + S_Papuan-12B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 5 82.0540 1,218.7
S_Bougainville-1B + S_Papuan-14A Concordant SGDP 108,607,294 – 109,648,746 1,041,452.0 0.92141399 32 1,238.0282 517.0
S_Bougainville-2A + S_Bougainville-1B Concordant SGDP 108,622,370 – 109,627,534 1,005,163.5 0.76173460 43 1,092.8662 786.9
S_Bougainville-1B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 599.7824 700.3
S_Bougainville-2A + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 32 630.7422 1,014.7
S_Papuan-11A + S_Papuan-14A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 16 630.7422 507.3
S_Bougainville-2A + S_Papuan-13B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 44 1,651.4888 532.9
S_Papuan-11A + S_Papuan-12B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 43 1,651.4888 520.7
S_Bougainville-2A + S_Papuan-14A Concordant SGDP 108,013,075 – 109,820,378 1,807,302.5 1.37348287 52 1,967.2915 528.6
S_Papuan-13B + S_Papuan-7A Concordant SGDP 107,935,881 – 109,615,525 1,679,644.0 1.19390305 30 1,762.3516 340.5
S_Bougainville-2A + S_Papuan-7A Concordant SGDP 107,782,171 – 109,627,534 1,845,363.0 1.44708092 57 2,044.4390 557.6
S_Papuan-14A + S_Papuan-7A Concordant SGDP 107,942,939 – 109,627,534 1,684,595.0 1.21490924 33 1,781.5330 370.5
S_Papuan-7A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 16 599.7824 533.5
B_Australian-3A + B_Australian-4A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 15 519.1556 577.9
B_Australian-3A + S_Bougainville-2A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 9 60.3278 2,983.7
B_Australian-3A + S_Korean-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
S_Papuan-7A + S_Papuan-3B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 45 586.4513 1,534.7
S_Papuan-12B + S_Papuan-5B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Khonda_Dora-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 44 616.1245 1,428.3
S_Papuan-14A + S_Papuan-9B Discordant SGDP 109,586,336 – 109,883,892 297,555.5 0.30574079 18 388.4193 926.8
B_Australian-3A + S_Surui-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Igorot-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + B_Karitiana-3A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Chane-1B Discordant SGDP 109,593,803 – 109,615,525 21,722.5 0.00910502 5 18.7108 5,344.5
B_Australian-3A + S_Iranian-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Saami-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Armenian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Dusun-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Karitiana-2A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Dusun-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Pima-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Hawaiian-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Mayan-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Sindhi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-4A + S_Naxi-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,615,525 396,691.5 0.23492736 17 379.3538 896.3
B_Australian-4A + S_Naxi-1A Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 4 41.2396 1,939.9
S_Papuan-12B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 60 586.4513 2,046.2
B_Australian-4A + S_Japanese-3A Discordant SGDP 109,328,376 – 109,615,525 287,149.5 0.20894417 25 305.9871 1,634.1
S_Papuan-12B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 64 586.4513 2,182.6
B_Australian-4A + S_Mandenka-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Japanese-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
S_Bougainville-2A + S_Irula-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Korean-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 8 42.9729 3,723.3
S_Bougainville-2B + S_Kapu-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Dusun-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
S_Papuan-11A + S_Papuan-10A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 85 1,221.0212 1,392.3
B_Australian-3A + S_Maori-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 7 26.6308 5,257.1
S_Papuan-14A + S_Burmese-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Igorot-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
S_Papuan-14A + S_Papuan-3A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 80 1,638.1578 976.7
B_Australian-3A + S_Eskimo_Sireniki-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
S_Papuan-14A + S_Papuan-4B Discordant SGDP 108,954,234 – 109,883,892 929,657.5 0.64291901 45 961.5708 936.0
B_Australian-3A + S_Brahmin-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Hazara-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Hazara-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Mozabite-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Sindhi-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 50 586.4513 1,705.2
B_Australian-3A + S_Zapotec-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Saami-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Mixe-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Basque-2B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 49 586.4513 1,671.1
B_Australian-3A + S_Mixe-3B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + B_Han-3B Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 6 41.2396 2,909.8
B_Australian-3A + S_Mixtec-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + B_Mixe-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 7 26.6308 5,257.1
B_Australian-3A + S_Mixtec-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Surui-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
B_Australian-3A + S_Zapotec-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Karitiana-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Quechua-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 8 42.9729 3,723.3
B_Australian-3A + S_Karitiana-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Quechua-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Pima-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
B_Australian-3A + S_Mongola-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
B_Australian-3A + S_Mayan-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-3A + S_Mongola-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-4A + S_Naxi-3A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 26.6308 3,004.0
B_Australian-3A + S_Yakut-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
B_Australian-4A + S_Japanese-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 42.9729 1,861.6
B_Australian-3A + S_Ulchi-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-4A + S_Madiga-2A Discordant SGDP 109,586,365 – 109,627,003 40,637.5 0.02772475 4 42.6858 1,874.2
B_Australian-3A + S_Even-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
B_Australian-4A + S_Surui-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Eskimo_Chaplin-1B Discordant SGDP 109,586,336 – 109,609,883 23,547.0 0.01192801 6 21.8450 5,493.3
S_Bougainville-2A + S_Somali-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Mansi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
S_Bougainville-2B + S_Iranian-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
B_Australian-3A + S_Cambodian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 7 26.6308 5,257.1
S_Papuan-13B + S_Papuan-8A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 59 586.4513 2,012.1
B_Australian-3A + S_Miao-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
S_Papuan-14A + S_Kinh-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 37 616.1245 1,201.1
B_Australian-3A + S_Tu-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
S_Papuan-14A + S_Papuan-8A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 70 1,638.1578 854.6
B_Australian-3A + S_Oroqen-1A Discordant SGDP 109,587,446 – 109,615,525 28,079.0 0.01302444 6 24.8975 4,819.8
S_Papuan-14A + S_Papuan-14B Discordant SGDP 108,954,234 – 109,912,835 958,601.0 0.65578019 80 985.7526 1,623.1
B_Australian-3A + S_Oroqen-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
S_Papuan-14A + S_Madiga-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 71 616.1245 2,304.7
B_Australian-3A + S_Hezhen-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 42.9729 2,792.5
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 42.9729 2,327.0
B_Australian-3A + S_Yi-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 4 1.0797 74,096.9
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 25 963.0491 519.2
B_Australian-3A + S_Tujia-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 9 42.9729 4,188.7
S_Papuan-12B + S_Papuan-6B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 60 586.4513 2,046.2
B_Australian-3A + S_Naxi-1B Discordant SGDP 109,599,440 – 109,615,525 16,085.5 0.00711214 6 14.4108 8,327.1
S_Papuan-12B + S_Papuan-4A Discordant SGDP 107,782,611 – 109,599,489 1,816,877.5 1.38293439 139 1,979.4487 1,404.4
B_Australian-3A + S_She-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 42.9729 3,257.9
S_Papuan-12B + S_Papuan-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 56 586.4513 1,909.8
B_Australian-3A + S_Dai-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 6 26.6308 4,506.1
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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