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

rs901634398
Alleles:
reference
A
ancestral
alternate
G
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  31,826,772  (GRCh37) Explore rs901634398 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.9%
1.1%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 88.0%
12.0%
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 G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,128.7 generations 111  =  15  +  960.867
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_Papuan-5A + B_Papuan-15A Concordant SGDP 31,425,216 – 31,974,907 549,691.0 0.39567211 24 581.3894 825.6
S_Papuan-14B + S_Papuan-2A Concordant SGDP 31,565,428 – 31,900,053 334,624.5 0.11824245 14 256.2137 1,092.8
S_Papuan-5A + S_Papuan-14B Concordant SGDP 31,445,059 – 31,900,053 454,994.0 0.24706349 24 417.0479 1,150.9
S_Papuan-5A + S_Papuan-2A Concordant SGDP 31,132,895 – 33,855,187 2,722,292.0 2.01992367 41 2,923.6391 280.5
S_Papuan-6A + S_Papuan-2A Concordant SGDP 31,575,111 – 31,906,050 330,939.0 0.12940011 19 263.3708 1,442.8
S_Papuan-6A + B_Papuan-15A Concordant SGDP 31,132,895 – 31,900,053 767,158.0 0.37869973 35 672.1956 1,041.4
S_Papuan-6A + S_Papuan-5A Concordant SGDP 31,575,111 – 31,906,050 330,939.0 0.12940011 20 263.3708 1,518.8
S_Papuan-6A + S_Papuan-14B Concordant SGDP 31,132,895 – 32,040,037 907,142.5 0.59007468 40 908.4881 880.6
S_Papuan-3A + B_Papuan-15A Concordant SGDP 31,068,515 – 31,974,907 906,392.5 0.58198493 29 901.6563 643.3
S_Papuan-3A + S_Papuan-2A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 19 1,387.3858 273.9
S_Papuan-3A + S_Papuan-14B Concordant SGDP 30,816,453 – 31,900,053 1,083,599.5 1.12717293 32 1,422.8661 449.8
S_Papuan-14B + B_Papuan-15A Concordant SGDP 31,073,224 – 32,677,369 1,604,145.0 1.03566464 18 1,599.5213 225.1
S_Papuan-2A + B_Papuan-15A Concordant SGDP 31,425,216 – 31,974,907 549,691.0 0.39567211 26 581.3894 894.4
S_Papuan-3A + S_Papuan-6A Concordant SGDP 31,132,895 – 31,906,050 773,155.0 0.39064478 32 684.6302 934.8
S_Papuan-3A + S_Papuan-5A Concordant SGDP 31,359,539 – 32,695,551 1,336,011.5 0.93137531 16 1,387.3858 230.6
S_Papuan-6A + S_Finnish-2B Discordant SGDP 31,106,698 – 31,826,828 720,130.5 0.29288625 110 580.9716 3,786.8
S_Papuan-14B + S_Iraqi_Jew-1A Discordant SGDP 31,134,695 – 31,826,828 692,133.0 0.24711252 52 530.9139 1,958.9
S_Papuan-14B + B_French-3B Discordant SGDP 31,792,748 – 31,826,828 34,080.5 0.00267826 5 19.5012 5,127.9
S_Papuan-14B + S_Punjabi-1B Discordant SGDP 31,792,748 – 31,826,828 34,080.5 0.00267826 5 19.5012 5,127.9
S_Papuan-14B + S_English-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Korean-1A Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 5 17.3660 5,758.4
S_Papuan-14B + S_Eskimo_Naukan-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Quechua-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Yi-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-5A + S_Tubalar-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Karitiana-1B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 7 90.0720 1,554.3
S_Papuan-6A + S_Orcadian-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Bergamo-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Saami-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Iraqi_Jew-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-3A + S_Papuan-9A Discordant SGDP 31,079,206 – 31,826,828 747,622.5 0.31821021 91 614.4270 2,962.1
S_Papuan-6A + S_Jordanian-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Quechua-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + B_Dai-4B Discordant SGDP 31,575,111 – 31,868,351 293,240.5 0.01288349 17 152.0622 2,235.9
S_Papuan-6A + S_Tubalar-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Pima-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Altaian-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-5A + S_Finnish-1A Discordant SGDP 31,134,695 – 31,826,828 692,133.0 0.24711252 57 530.9139 2,147.2
S_Papuan-6A + S_Ulchi-1B Discordant SGDP 31,496,660 – 31,868,351 371,691.0 0.03014480 21 203.5275 2,063.6
S_Papuan-14B + S_Cambodian-2A Discordant SGDP 31,134,695 – 31,826,828 692,133.0 0.24711252 54 530.9139 2,034.2
S_Papuan-6A + S_Even-3B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Dai-2B Discordant SGDP 31,565,428 – 31,826,828 261,400.0 0.01024835 13 134.6707 1,930.6
S_Papuan-6A + S_Yakut-2B Discordant SGDP 31,687,839 – 31,868,351 180,512.0 0.00902271 9 94.8639 1,897.5
S_Papuan-14B + S_Papuan-13A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Aleut-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Kalash-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Naxi-3B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Luhya-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Miao-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 18 211.1397 1,705.0
S_Papuan-14B + S_French-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Han-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Jordanian-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Tu-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-2A + S_Papuan-4A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Uygur-1A Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 12 90.0720 2,664.5
S_Papuan-6A + S_Atayal-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Uygur-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 16 211.1397 1,515.6
S_Papuan-6A + S_Finnish-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Yi-2B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 15 147.3302 2,036.2
S_Papuan-6A + S_Basque-2B Discordant SGDP 31,459,257 – 31,868,351 409,094.5 0.13559097 26 305.8381 1,700.2
S_Papuan-6A + S_Uygur-2A Discordant SGDP 31,826,747 – 31,868,351 41,604.0 0.00343850 5 23.7207 4,215.7
S_Papuan-6A + S_Palestinian-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_She-2A Discordant SGDP 31,744,517 – 31,868,351 123,834.0 0.00751774 9 66.4545 2,708.6
S_Papuan-6A + S_Bergamo-2B Discordant SGDP 31,575,111 – 31,868,351 293,240.5 0.01288349 17 152.0622 2,235.9
S_Papuan-6A + S_Tu-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Jordanian-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Korean-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Yemenite_Jew-2A Discordant SGDP 31,826,747 – 32,420,230 593,483.0 0.46585087 90 658.5525 2,733.3
S_Papuan-6A + S_Burmese-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 21 211.1397 1,989.2
S_Papuan-6A + S_Chane-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Thai-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Piapoco-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Kinh-2A Discordant SGDP 31,687,839 – 31,868,351 180,512.0 0.00902271 8 94.8639 1,686.6
S_Papuan-6A + S_Mayan-1B Discordant SGDP 31,697,077 – 32,420,230 723,153.5 0.47098767 92 724.9038 2,538.3
S_Papuan-6A + S_Dusun-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-5A + S_Papuan-14A Discordant SGDP 31,826,747 – 31,974,668 147,920.5 0.24396228 10 267.1717 748.6
S_Papuan-6A + S_Maori-1B Discordant SGDP 31,041,075 – 31,868,351 827,276.0 0.37217585 95 695.8332 2,730.5
S_Papuan-5A + S_Sardinian-1B Discordant SGDP 31,134,695 – 31,826,828 692,133.0 0.24711252 80 530.9139 3,013.7
S_Papuan-6A + S_Hawaiian-1A Discordant SGDP 31,826,747 – 31,868,351 41,604.0 0.00343850 4 23.7207 3,372.6
S_Papuan-14B + S_Ulchi-2A Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 5 17.3660 5,758.4
S_Papuan-6A + S_Itelman-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Dai-3B Discordant SGDP 31,484,549 – 31,826,828 342,279.0 0.02897093 16 188.4707 1,697.9
S_Papuan-6A + S_Bengali-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Dai-2A Discordant SGDP 31,484,549 – 31,826,828 342,279.0 0.02897093 14 188.4707 1,485.6
S_Papuan-6A + S_Bengali-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Korean-2A Discordant SGDP 31,565,428 – 32,448,679 883,250.5 0.48747853 65 814.9431 1,595.2
S_Papuan-6A + S_Relli-2A Discordant SGDP 31,687,839 – 31,868,351 180,512.0 0.00902271 8 94.8639 1,686.6
S_Papuan-14B + S_Kinh-1B Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 5 17.3660 5,758.4
S_Papuan-6A + S_Yadava-2A Discordant SGDP 31,687,839 – 31,868,351 180,512.0 0.00902271 11 94.8639 2,319.1
S_Papuan-14B + S_Chukchi-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Mala-3B Discordant SGDP 31,459,257 – 31,868,351 409,094.5 0.13559097 30 305.8381 1,961.8
S_Papuan-14B + S_Mala-3A Discordant SGDP 31,565,428 – 31,826,828 261,400.0 0.01024835 9 134.6707 1,336.6
S_Papuan-6A + S_Brahmin-1A Discordant SGDP 31,826,747 – 31,868,351 41,604.0 0.00343850 4 23.7207 3,372.6
S_Papuan-14B + S_Punjabi-4B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Madiga-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Albanian-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Madiga-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Czech-2A Discordant SGDP 31,565,428 – 31,826,828 261,400.0 0.01024835 14 134.6707 2,079.1
S_Papuan-6A + S_Kusunda-1A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_Estonian-2B Discordant SGDP 31,484,549 – 31,826,828 342,279.0 0.02897093 11 188.4707 1,167.3
S_Papuan-6A + S_Kusunda-2B Discordant SGDP 31,687,839 – 31,868,351 180,512.0 0.00902271 10 94.8639 2,108.3
S_Papuan-14B + S_Iraqi_Jew-2B Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 5 17.3660 5,758.4
S_Papuan-6A + S_Pathan-1B Discordant SGDP 31,687,839 – 31,826,828 138,989.0 0.00560017 10 72.1949 2,770.3
S_Papuan-14B + S_Palestinian-3A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-6A + S_Pathan-2B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-14B + S_North_Ossetian-1A Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 5 17.3660 5,758.4
S_Papuan-6A + S_Sindhi-2A Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
S_Papuan-2A + S_Bougainville-1A Discordant SGDP 31,792,748 – 31,826,828 34,080.5 0.00267826 4 19.5012 4,102.3
S_Papuan-6A + S_Abkhasian-1B Discordant SGDP 31,583,614 – 31,826,828 243,214.0 0.00864802 16 124.6611 2,567.0
S_Papuan-2A + S_Polish-1B Discordant SGDP 31,795,978 – 31,826,828 30,850.5 0.00194718 4 17.3660 4,606.7
S_Papuan-6A + S_Bulgarian-1B Discordant SGDP 31,826,747 – 31,826,828 81.0 0.00001597 4 1.0517 76,070.8
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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