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 Mutation clock
Data source Estimated age of C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,767.8 generations 136  =  42  +  940.786
Pairwise results table Mutation 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 32 490.7150 1,304.2
S_Bougainville-2B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 10 318.4197 628.1
S_Bougainville-1B + S_Papuan-13B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 21 318.4197 1,319.0
S_Bougainville-2B + S_Bougainville-2A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 24 324.1838 1,480.6
S_Bougainville-2B + S_Papuan-11A Concordant SGDP 108,954,234 – 110,180,181 1,225,947.0 1.01345539 33 589.4546 1,119.7
S_Papuan-13B + S_Papuan-14A Concordant SGDP 107,942,939 – 110,020,181 2,077,242.5 1.63392273 42 998.0764 841.6
S_Papuan-14A + S_Papuan-12B Concordant SGDP 108,954,234 – 110,020,729 1,066,495.0 0.80262792 37 512.9176 1,442.7
B_Australian-3A + S_Papuan-7A Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 13 183.5891 1,416.2
B_Australian-3A + S_Papuan-12B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 3 15.1422 3,962.4
B_Australian-3A + S_Papuan-13B Concordant SGDP 109,586,062 – 109,615,525 29,463.0 0.01778213 3 15.1422 3,962.4
B_Australian-3A + S_Papuan-14A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 3 20.9063 2,869.9
B_Australian-3A + S_Papuan-11A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 12 197.6277 1,214.4
B_Australian-3A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,414 62,351.5 0.15000138 5 30.9287 3,233.2
B_Australian-3A + S_Bougainville-2B Concordant SGDP 109,586,062 – 109,966,456 380,394.0 0.38194789 19 183.5891 2,069.8
S_Papuan-11A + S_Papuan-13B Concordant SGDP 108,157,391 – 109,615,525 1,458,134.0 1.04071248 28 700.9043 799.0
B_Australian-4A + S_Bougainville-2A Concordant SGDP 109,554,071 – 109,627,534 73,463.0 0.10329138 7 36.2622 3,860.8
S_Papuan-11A + S_Papuan-7A Concordant SGDP 108,157,391 – 110,258,928 2,101,536.5 1.85890768 33 1,009.7375 653.6
B_Australian-4A + S_Bougainville-1B Concordant SGDP 109,586,062 – 109,648,746 62,684.0 0.15522514 2 31.0883 1,286.7
S_Papuan-13B + S_Papuan-12B Concordant SGDP 108,157,391 – 110,180,181 2,022,790.0 1.70246451 25 971.9392 514.4
B_Australian-4A + S_Papuan-11A Concordant SGDP 109,548,942 – 110,180,181 631,239.5 0.73458401 15 303.9950 986.9
S_Bougainville-2A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 25 318.4197 1,570.3
B_Australian-4A + S_Papuan-13B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 3 28.7291 2,088.5
S_Bougainville-2B + S_Bougainville-1B Concordant SGDP 108,954,234 – 109,648,746 694,512.0 0.48914636 18 334.3658 1,076.7
B_Australian-4A + S_Papuan-14A Concordant SGDP 109,557,756 – 109,649,341 91,584.5 0.21291243 4 44.9606 1,779.3
S_Bougainville-2B + S_Papuan-7A Concordant SGDP 108,954,234 – 110,613,184 1,658,949.5 1.95891925 38 797.2958 953.2
B_Australian-4A + S_Papuan-7A Concordant SGDP 109,548,942 – 110,613,184 1,064,242.0 1.68004787 22 511.8362 859.7
S_Bougainville-1B + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 23 324.1838 1,418.9
B_Australian-4A + S_Papuan-12B Concordant SGDP 109,557,756 – 109,615,525 57,769.0 0.06665607 3 28.7291 2,088.5
S_Bougainville-1B + S_Papuan-14A Concordant SGDP 108,607,294 – 109,648,746 1,041,452.0 0.92141399 30 500.8970 1,197.9
S_Bougainville-2A + S_Bougainville-1B Concordant SGDP 108,622,370 – 109,627,534 1,005,163.5 0.76173460 41 483.4785 1,696.0
S_Bougainville-1B + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 19 318.4197 1,193.4
S_Bougainville-2A + S_Papuan-11A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 30 324.1838 1,850.8
S_Papuan-11A + S_Papuan-14A Concordant SGDP 108,954,234 – 109,627,534 673,299.5 0.38319807 14 324.1838 863.7
S_Bougainville-2A + S_Papuan-13B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 42 770.1760 1,090.7
S_Papuan-11A + S_Papuan-12B Concordant SGDP 108,013,075 – 109,615,525 1,602,450.0 1.10164105 41 770.1760 1,064.7
S_Bougainville-2A + S_Papuan-14A Concordant SGDP 108,013,075 – 109,820,378 1,807,302.5 1.37348287 50 868.5052 1,151.4
S_Papuan-13B + S_Papuan-7A Concordant SGDP 107,935,881 – 109,615,525 1,679,644.0 1.19390305 28 807.2291 693.7
S_Bougainville-2A + S_Papuan-7A Concordant SGDP 107,782,171 – 109,627,534 1,845,363.0 1.44708092 55 886.7742 1,240.5
S_Papuan-14A + S_Papuan-7A Concordant SGDP 107,942,939 – 109,627,534 1,684,595.0 1.21490924 31 809.6056 765.8
S_Papuan-7A + S_Papuan-12B Concordant SGDP 108,954,234 – 109,615,525 661,291.0 0.35170335 14 318.4197 879.3
B_Australian-3A + B_Australian-4A Concordant SGDP 109,586,062 – 109,995,703 409,641.0 0.40190984 13 197.6277 1,315.6
B_Australian-3A + S_Bougainville-2A Concordant SGDP 109,586,062 – 109,627,534 41,471.5 0.04927684 7 20.9063 6,696.5
B_Australian-3A + S_Korean-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
S_Papuan-7A + S_Papuan-3B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 43 310.7222 2,767.7
S_Papuan-12B + S_Papuan-5B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Khonda_Dora-1A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 42 323.9289 2,593.2
S_Papuan-14A + S_Papuan-9B Discordant SGDP 109,586,336 – 109,883,892 297,555.5 0.30574079 16 143.8266 2,224.9
B_Australian-3A + S_Surui-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Igorot-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + B_Karitiana-3A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Chane-1B Discordant SGDP 109,593,803 – 109,615,525 21,722.5 0.00910502 3 11.4268 5,250.8
B_Australian-3A + S_Iranian-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Saami-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Armenian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Dusun-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Karitiana-2A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Dusun-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Pima-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Hawaiian-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Mayan-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Sindhi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-4A + S_Naxi-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
S_Papuan-7A + S_Lahu-1A Discordant SGDP 109,218,834 – 109,615,525 396,691.5 0.23492736 15 191.4119 1,567.3
B_Australian-4A + S_Naxi-1A Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 2 19.9871 2,001.3
S_Papuan-12B + S_Papuan-10A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 58 310.7222 3,733.2
B_Australian-4A + S_Japanese-3A Discordant SGDP 109,328,376 – 109,615,525 287,149.5 0.20894417 23 138.8318 3,313.4
S_Papuan-12B + S_Papuan-7B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 62 310.7222 3,990.7
B_Australian-4A + S_Mandenka-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Japanese-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
S_Bougainville-2A + S_Irula-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Korean-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 20.5199 5,848.0
S_Bougainville-2B + S_Kapu-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Dusun-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
S_Papuan-11A + S_Papuan-10A Discordant SGDP 108,954,234 – 110,096,282 1,142,047.5 0.83979795 83 549.1828 3,022.7
B_Australian-3A + S_Maori-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 5 15.0107 6,661.9
S_Papuan-14A + S_Burmese-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Igorot-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
S_Papuan-14A + S_Papuan-3A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 78 762.4785 2,046.0
B_Australian-3A + S_Eskimo_Sireniki-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
S_Papuan-14A + S_Papuan-4B Discordant SGDP 108,954,234 – 109,883,892 929,657.5 0.64291901 43 447.2356 1,922.9
B_Australian-3A + S_Brahmin-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Hazara-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Hazara-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Mozabite-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Sindhi-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 48 310.7222 3,089.6
B_Australian-3A + S_Zapotec-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Saami-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Mixe-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Basque-2B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 47 310.7222 3,025.2
B_Australian-3A + S_Mixe-3B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + B_Han-3B Discordant SGDP 109,587,446 – 109,627,003 39,556.5 0.02656556 4 19.9871 4,002.6
B_Australian-3A + S_Mixtec-1A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + B_Mixe-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 5 15.0107 6,661.9
B_Australian-3A + S_Mixtec-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Surui-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
B_Australian-3A + S_Zapotec-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Karitiana-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Quechua-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 6 20.5199 5,848.0
B_Australian-3A + S_Karitiana-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Quechua-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Pima-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
B_Australian-3A + S_Mongola-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
B_Australian-3A + S_Mayan-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-3A + S_Mongola-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-4A + S_Naxi-3A Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 2 15.0107 2,664.8
B_Australian-3A + S_Yakut-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
B_Australian-4A + S_Japanese-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 2 20.5199 1,949.3
B_Australian-3A + S_Ulchi-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-4A + S_Madiga-2A Discordant SGDP 109,586,365 – 109,627,003 40,637.5 0.02772475 2 20.5060 1,950.6
B_Australian-3A + S_Even-2A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
B_Australian-4A + S_Surui-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Eskimo_Chaplin-1B Discordant SGDP 109,586,336 – 109,609,883 23,547.0 0.01192801 4 12.3026 6,502.7
S_Bougainville-2A + S_Somali-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Mansi-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
S_Bougainville-2B + S_Iranian-1A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
B_Australian-3A + S_Cambodian-2B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 5 15.0107 6,661.9
S_Papuan-13B + S_Papuan-8A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 57 310.7222 3,668.9
B_Australian-3A + S_Miao-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
S_Papuan-14A + S_Kinh-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 35 323.9289 2,161.0
B_Australian-3A + S_Tu-2A Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
S_Papuan-14A + S_Papuan-8A Discordant SGDP 108,013,075 – 109,599,489 1,586,413.5 1.09459909 68 762.4785 1,783.7
B_Australian-3A + S_Oroqen-1A Discordant SGDP 109,587,446 – 109,615,525 28,079.0 0.01302444 4 14.4779 5,525.7
S_Papuan-14A + S_Papuan-14B Discordant SGDP 108,954,234 – 109,912,835 958,601.0 0.65578019 78 461.1285 3,383.0
B_Australian-3A + S_Oroqen-2B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
S_Papuan-14A + S_Madiga-2A Discordant SGDP 108,954,234 – 109,627,003 672,768.5 0.36524447 69 323.9289 4,260.2
B_Australian-3A + S_Hezhen-1A Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 4 20.5199 3,898.7
S_Papuan-7A + S_Lahu-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 3 20.5199 2,924.0
B_Australian-3A + S_Yi-1B Discordant SGDP 109,599,440 – 109,599,489 49.0 0.00007018 2 1.0235 39,080.8
S_Papuan-7A + S_Papuan-6A Discordant SGDP 108,954,234 – 109,884,467 930,232.5 0.64442192 23 447.5116 1,027.9
B_Australian-3A + S_Tujia-1B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 7 20.5199 6,822.6
S_Papuan-12B + S_Papuan-6B Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 58 310.7222 3,733.2
B_Australian-3A + S_Naxi-1B Discordant SGDP 109,599,440 – 109,615,525 16,085.5 0.00711214 4 8.7210 9,173.2
S_Papuan-12B + S_Papuan-4A Discordant SGDP 107,782,611 – 109,599,489 1,816,877.5 1.38293439 137 873.1012 3,138.2
B_Australian-3A + S_She-2B Discordant SGDP 109,586,336 – 109,627,003 40,666.5 0.02806625 5 20.5199 4,873.3
S_Papuan-12B + S_Papuan-2A Discordant SGDP 108,954,234 – 109,599,489 645,254.5 0.34466140 54 310.7222 3,475.8
B_Australian-3A + S_Dai-1B Discordant SGDP 109,586,336 – 109,615,525 29,189.0 0.01452513 4 15.0107 5,329.5
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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