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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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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 Recombination clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP213.9 generations 136  =  42  +  940.762
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_Bougainville-1B + S_Papuan-7A Concordant SGDP 108,607,294 – 109,627,534 1,020,239.5 0.81546570 3 653.3726 91.8
S_Bougainville-2B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 3 282.3627 212.5
S_Bougainville-1B + S_Papuan-13B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 3 282.3627 212.5
S_Bougainville-2B + S_Bougainville-2A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 3 307.5585 195.1
S_Bougainville-2B + S_Papuan-11A Concordant SGDP 108,954,234 – 110,180,181 1,225,947.0 1.01345539 3 811.7643 73.9
S_Papuan-13B + S_Papuan-14A Concordant SGDP 107,942,939 – 110,020,181 2,077,242.5 1.63392273 3 1,308.1382 45.9
S_Papuan-14A + S_Papuan-12B Concordant SGDP 108,954,234 – 110,020,729 1,066,495.0 0.80262792 3 643.1023 93.3
B_Australian-3A + S_Papuan-7A Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 3 306.5583 195.7
B_Australian-3A + S_Papuan-12B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 3 15.2257 3,940.7
B_Australian-3A + S_Papuan-13B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 3 15.2257 3,940.7
B_Australian-3A + S_Papuan-14A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 3 40.4215 1,484.4
B_Australian-3A + S_Papuan-11A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 3 322.5279 186.0
B_Australian-3A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,414 62,351.5 0.15000138 3 121.0011 495.9
B_Australian-3A + S_Bougainville-2B Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 3 306.5583 195.7
S_Papuan-11A + S_Papuan-13B Concordant SGDP 108,157,391 – 109,615,525 1,458,134.0 1.04071248 3 833.5700 72.0
B_Australian-4A + S_Bougainville-2A Concordant SGDP 109,554,071 – 109,627,534 73,463.0 0.10329138 3 83.6331 717.4
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,391 – 110,258,928 2,101,536.5 1.85890768 3 1,488.1261 40.3
B_Australian-4A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,746 62,684.0 0.15522514 3 125.1801 479.3
S_Papuan-13B + S_Papuan-12B Concordant SGDP 108,157,391 – 110,180,181 2,022,790.0 1.70246451 3 1,362.9716 44.0
B_Australian-4A + S_Papuan-11A Concordant SGDP 109,548,942 – 110,180,181 631,239.5 0.73458401 3 588.6672 101.9
S_Bougainville-2A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 3 282.3627 212.5
B_Australian-4A + S_Papuan-13B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 3 54.3249 1,104.5
S_Bougainville-2B + S_Bougainville-1B Concordant SGDP 108,954,234 – 109,648,746 694,512.0 0.48914636 3 392.3171 152.9
B_Australian-4A + S_Papuan-14A Concordant SGDP 109,557,756 – 109,649,341 91,584.5 0.21291243 3 171.3299 350.2
S_Bougainville-2B + S_Papuan-7A Concordant SGDP 108,954,234 – 110,613,184 1,658,949.5 1.95891925 3 1,568.1354 38.3
B_Australian-4A + S_Papuan-7A Concordant SGDP 109,548,942 – 110,613,184 1,064,242.0 1.68004787 3 1,345.0383 44.6
S_Bougainville-1B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 3 307.5585 195.1
B_Australian-4A + S_Papuan-12B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 3 54.3249 1,104.5
S_Bougainville-1B + S_Papuan-14A Concordant SGDP 108,607,294 – 109,648,746 1,041,452.0 0.92141399 3 738.1312 81.3
S_Bougainville-2A + S_Bougainville-1B Concordant SGDP 108,622,370 – 109,627,534 1,005,163.5 0.76173460 3 610.3877 98.3
S_Bougainville-1B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 3 282.3627 212.5
S_Bougainville-2A + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 3 307.5585 195.1
S_Papuan-11A + S_Papuan-14A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 3 307.5585 195.1
S_Bougainville-2A + S_Papuan-13B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 3 882.3128 68.0
S_Papuan-11A + S_Papuan-12B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 3 882.3128 68.0
S_Bougainville-2A + S_Papuan-14A Concordant SGDP 108,013,075 – 109,820,378 1,807,302.5 1.37348287 3 1,099.7863 54.6
S_Papuan-13B + S_Papuan-7A Concordant SGDP 107,935,881 – 109,615,525 1,679,644.0 1.19390305 3 956.1224 62.8
S_Bougainville-2A + S_Papuan-7A Concordant SGDP 107,782,171 – 109,627,534 1,845,363.0 1.44708092 3 1,158.6647 51.8
S_Papuan-14A + S_Papuan-7A Concordant SGDP 107,942,939 – 109,627,534 1,684,595.0 1.21490924 3 972.9274 61.7
S_Papuan-7A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 3 282.3627 212.5
B_Australian-3A + B_Australian-4A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 3 322.5279 186.0
B_Australian-3A + S_Bougainville-2A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 3 40.4215 1,484.4
B_Australian-3A + S_Korean-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-7A + S_Papuan-3B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
S_Papuan-12B + S_Papuan-5B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Khonda_Dora-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
S_Papuan-14A + S_Papuan-9B Discordant SGDP 109,586,336 – 109,883,892 297,555.5 0.30574079 3 245.5926 244.3
B_Australian-3A + S_Surui-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Igorot-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + B_Karitiana-3A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Chane-1B Discordant SGDP 109,593,803 – 109,615,525 21,722.5 0.00910502 3 8.2840 7,242.9
B_Australian-3A + S_Iranian-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Saami-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Armenian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Dusun-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Karitiana-2A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Dusun-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Pima-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Hawaiian-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Mayan-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Sindhi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-4A + S_Naxi-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,615,525 396,691.5 0.23492736 3 188.9419 317.6
B_Australian-4A + S_Naxi-1A Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 3 22.2524 2,696.3
S_Papuan-12B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-4A + S_Japanese-3A Discordant SGDP 109,328,376 – 109,615,525 287,149.5 0.20894417 3 168.1553 356.8
S_Papuan-12B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-4A + S_Mandenka-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Japanese-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
S_Bougainville-2A + S_Irula-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Korean-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Bougainville-2B + S_Kapu-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Dusun-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-11A + S_Papuan-10A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 3 672.8384 89.2
B_Australian-3A + S_Maori-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
S_Papuan-14A + S_Burmese-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Igorot-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
S_Papuan-14A + S_Papuan-3A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 3 876.6793 68.4
B_Australian-3A + S_Eskimo_Sireniki-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-14A + S_Papuan-4B Discordant SGDP 108,954,234 – 109,883,892 929,657.5 0.64291901 3 515.3352 116.4
B_Australian-3A + S_Brahmin-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Hazara-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Hazara-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Mozabite-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Sindhi-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-3A + S_Zapotec-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Saami-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Mixe-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Basque-2B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-3A + S_Mixe-3B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + B_Han-3B Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 3 22.2524 2,696.3
B_Australian-3A + S_Mixtec-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + B_Mixe-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Mixtec-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Surui-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Zapotec-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Karitiana-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Quechua-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Karitiana-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Quechua-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Pima-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Mongola-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Mayan-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Mongola-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-4A + S_Naxi-3A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
B_Australian-3A + S_Yakut-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-4A + S_Japanese-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Ulchi-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-4A + S_Madiga-2A Discordant SGDP 109,586,365 – 109,627,003 40,637.5 0.02772475 3 23.1798 2,588.5
B_Australian-3A + S_Even-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-4A + S_Surui-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Eskimo_Chaplin-1B Discordant SGDP 109,586,336 – 109,609,883 23,547.0 0.01192801 3 10.5424 5,691.3
S_Bougainville-2A + S_Somali-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Mansi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
S_Bougainville-2B + S_Iranian-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
B_Australian-3A + S_Cambodian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
S_Papuan-13B + S_Papuan-8A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-3A + S_Miao-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-14A + S_Kinh-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
B_Australian-3A + S_Tu-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
S_Papuan-14A + S_Papuan-8A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 3 876.6793 68.4
B_Australian-3A + S_Oroqen-1A Discordant SGDP 109,587,446 – 109,615,525 28,079.0 0.01302444 3 11.4195 5,254.1
S_Papuan-14A + S_Papuan-14B Discordant SGDP 108,954,234 – 109,912,835 958,601.0 0.65578019 3 525.6242 114.2
B_Australian-3A + S_Oroqen-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
S_Papuan-14A + S_Madiga-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 3 293.1956 204.6
B_Australian-3A + S_Hezhen-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
B_Australian-3A + S_Yi-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 3 1.0561 56,810.2
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 3 516.5375 116.2
B_Australian-3A + S_Tujia-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-12B + S_Papuan-6B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-3A + S_Naxi-1B Discordant SGDP 109,599,440 – 109,615,525 16,085.5 0.00711214 3 6.6897 8,969.0
S_Papuan-12B + S_Papuan-4A Discordant SGDP 107,782,611 – 109,599,489 1,816,877.5 1.38293439 3 1,107.3475 54.2
B_Australian-3A + S_She-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 23.4530 2,558.3
S_Papuan-12B + S_Papuan-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 3 276.7291 216.8
B_Australian-3A + S_Dai-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 3 12.6201 4,754.3
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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