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

rs554692291
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  31,756,029  (GRCh37) Explore rs554692291 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 98.1%
1.9%
EAS 98.9%
1.1%
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 A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP48.9 generations 97  =  1  +  960.990
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_Tubalar-2B + S_Han-1A Concordant SGDP 31,132,895 – 32,356,346 1,223,451.0 0.70946371 3 568.5710 105.5
S_Han-1A + S_Maori-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Burmese-1B Discordant SGDP 31,756,008 – 32,451,906 695,897.5 0.48434592 3 388.4767 154.4
S_Han-1A + S_Yi-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Pima-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Turkish-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Saami-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Han-1A + S_Makrani-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Korean-2B Discordant SGDP 31,031,900 – 31,756,030 724,129.5 0.39282274 3 315.2582 190.3
S_Tubalar-2B + S_Dai-2A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 3 3.6765 16,319.7
S_Tubalar-2B + S_Ulchi-1B Discordant SGDP 31,756,008 – 31,795,978 39,969.5 0.00119193 3 1.9535 30,713.4
S_Tubalar-2B + S_Ulchi-2B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Tubalar-2B + S_Tubalar-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Tubalar-2B + S_Yakut-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Papuan-2B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 3 7.8602 7,633.4
S_Han-1A + S_Madiga-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Korean-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Czech-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Burmese-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_BedouinB-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Kinh-2A Discordant SGDP 31,756,008 – 32,353,201 597,193.0 0.43842554 3 351.7404 170.6
S_Han-1A + B_Dai-4A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 3 3.6765 16,319.7
S_Tubalar-2B + S_Bougainville-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Tu-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Papuan-3A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_She-2A Discordant SGDP 31,756,008 – 31,824,938 68,929.5 0.00256967 3 3.0557 19,635.2
S_Tubalar-2B + S_Papuan-8B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Han-1A + S_Kinh-1A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 3 3.6765 16,319.7
S_Tubalar-2B + S_Papuan-9B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Han-1A + S_Papuan-4B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 3 7.8602 7,633.4
S_Tubalar-2B + S_Chukchi-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Mala-3B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Eskimo_Naukan-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Kusunda-1B Discordant SGDP 31,134,695 – 31,827,533 692,838.0 0.24731908 3 198.8553 301.7
S_Tubalar-2B + S_Kapu-2B Discordant SGDP 31,727,319 – 31,868,351 141,032.0 0.00809458 3 7.4757 8,026.0
S_Han-1A + S_Kalash-2B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Tubalar-2B + S_Brahui-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_Finnish-2A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Tubalar-2B + S_Pathan-2B Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Iraqi_Jew-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Tubalar-2B + S_Sindhi-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Sardinian-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Luhya-1A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Yemenite_Jew-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Abkhasian-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 3 6.2493 9,601.0
S_Han-1A + B_Papuan-15A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Albanian-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Quechua-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Tubalar-2B + S_Bulgarian-1B Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_Uygur-1A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Tubalar-2B + S_Estonian-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Uygur-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Finnish-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 3 6.2493 9,601.0
S_Han-1A + S_Tu-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Tubalar-2B + S_Saami-2B Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_Thai-1B Discordant SGDP 31,756,008 – 32,403,755 647,746.5 0.46163056 3 370.3044 162.0
S_Tubalar-2B + S_Iranian-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Dusun-1A Discordant SGDP 31,092,468 – 32,451,906 1,359,438.0 0.78406091 3 628.2487 95.5
S_Tubalar-2B + S_Iraqi_Jew-2A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_Papuan-5B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Palestinian-3A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Han-1A + S_Papuan-14B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Palestinian-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Itelman-1A Discordant SGDP 31,548,099 – 32,451,906 903,806.5 0.49759921 3 399.0794 150.3
S_Tubalar-2B + S_Bergamo-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Brahmin-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Sardinian-1B Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 3 2.8367 21,151.2
S_Han-1A + S_Madiga-2A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Jordanian-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Kusunda-2B Discordant SGDP 31,756,008 – 32,289,718 533,710.0 0.43397829 3 348.1826 172.3
S_Tubalar-2B + S_Jordanian-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Pathan-1A Discordant SGDP 31,697,077 – 32,403,755 706,678.0 0.46364421 3 371.9154 161.3
S_Tubalar-2B + S_Orcadian-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Punjabi-4B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Russian-2A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_English-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Tubalar-2B + S_Adygei-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Han-1A + S_Finnish-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 3 6.2493 9,601.0
S_Tubalar-2B + B_French-3B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
S_Han-1A + S_French-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Tubalar-2B + S_Chane-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 3 1.7652 33,990.3
S_Han-1A + S_Palestinian-1B Discordant SGDP 31,697,077 – 32,451,906 754,829.0 0.48635957 3 390.0877 153.8
S_Tubalar-2B + S_Karitiana-1A Discordant SGDP 31,134,695 – 31,756,030 621,334.5 0.24397384 3 196.1791 305.8
S_Han-1A + S_Bergamo-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Mixe-2A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Polish-1A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Han-1A + S_Altaian-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 3 4.5064 13,314.5
S_Han-1A + S_Yemenite_Jew-2B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 3 7.8602 7,633.4
S_Han-1A + S_Even-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Yemenite_Jew-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Yakut-2A Discordant SGDP 31,697,077 – 32,451,906 754,829.0 0.48635957 3 390.0877 153.8
S_Han-1A + B_French-3A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Cambodian-2B Discordant SGDP 31,756,008 – 32,451,906 695,897.5 0.48434592 3 388.4767 154.4
S_Han-1A + S_Piapoco-2A Discordant SGDP 31,700,429 – 31,756,030 55,601.0 0.00186764 3 2.4941 24,056.7
S_Han-1A + S_Naxi-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 3 1.0003 59,979.1
S_Han-1A + S_Mayan-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 3 2.6113 22,977.4
S_Han-1A + S_Miao-1A Discordant SGDP 31,756,008 – 32,540,301 784,292.5 0.65031800 3 521.2544 115.1
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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