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

rs367705534
Alleles:
reference
C
ancestral
alternate
T
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  31,806,325  (GRCh37) Explore rs367705534 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.7%
1.3%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 86.0%
14.0%
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 T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP379.9 generations 112  =  14  +  980.898
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_Papuan-14A + S_Papuan-9B Concordant SGDP 31,408,993 – 31,906,050 497,057.0 0.28818079 3 231.5446 259.1
S_Papuan-4B + S_Papuan-9B Concordant SGDP 31,444,582 – 31,906,050 461,467.5 0.25909792 3 208.2783 288.1
S_Papuan-4B + S_Papuan-12B Concordant SGDP 31,416,601 – 31,981,558 564,957.0 0.41226144 3 330.8092 181.4
S_Papuan-4B + S_Papuan-14A Concordant SGDP 31,444,582 – 31,981,558 536,975.5 0.39243411 3 314.9473 190.5
S_Papuan-4B + S_Papuan-9A Concordant SGDP 31,132,895 – 31,981,558 848,663.0 0.52398097 3 420.1848 142.8
S_Papuan-4A + S_Papuan-9B Concordant SGDP 31,444,582 – 31,906,050 461,467.5 0.25909792 3 208.2783 288.1
S_Papuan-4B + S_Papuan-4A Concordant SGDP 31,132,895 – 31,981,558 848,663.0 0.52398097 3 420.1848 142.8
S_Papuan-4A + S_Papuan-9A Concordant SGDP 31,077,511 – 31,989,209 911,698.0 0.59320754 3 475.5660 126.2
S_Papuan-10A + S_Papuan-12B Concordant SGDP 31,480,954 – 32,453,881 972,926.5 0.57426084 3 460.4087 130.3
S_Papuan-10A + S_Papuan-9A Concordant SGDP 31,480,954 – 31,989,209 508,255.0 0.31457836 3 252.6627 237.5
S_Papuan-14A + S_Papuan-12B Concordant SGDP 31,444,802 – 31,989,209 544,407.5 0.41225776 3 330.8062 181.4
S_Papuan-9A + S_Papuan-12B Concordant SGDP 31,444,802 – 31,989,209 544,407.5 0.41225776 3 330.8062 181.4
S_Papuan-10A + S_Papuan-4A Concordant SGDP 31,480,954 – 32,420,434 939,479.5 0.50793718 3 407.3497 147.3
S_Papuan-10A + S_Papuan-14A Concordant SGDP 31,480,954 – 31,989,209 508,255.0 0.31457836 3 252.6627 237.5
S_Papuan-9B + S_Palestinian-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Finnish-1B Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9B + S_Bulgarian-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Madiga-1A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Dusun-1A Discordant SGDP 31,727,319 – 31,868,351 141,032.0 0.00809458 3 7.4757 8,026.0
S_Papuan-9B + S_Burmese-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Uygur-1B Discordant SGDP 31,134,695 – 31,841,841 707,146.0 0.24835638 3 199.6851 300.5
S_Papuan-9B + S_Aleut-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Tubalar-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + B_Dai-4A Discordant SGDP 31,806,307 – 31,827,533 21,226.5 0.00154497 3 2.2360 26,833.9
S_Papuan-9A + S_Iraqi_Jew-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-9B + S_Orcadian-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-12B + S_Maori-1B Discordant SGDP 31,687,839 – 32,048,924 361,084.5 0.34027996 3 273.2240 219.6
S_Papuan-10A + S_Papuan-12A Discordant SGDP 31,134,695 – 32,370,637 1,235,942.0 0.69441234 3 556.5299 107.8
S_Papuan-9A + S_Basque-2B Discordant SGDP 31,727,319 – 31,841,841 114,522.0 0.00591590 3 5.7327 10,466.2
S_Papuan-10A + S_Georgian-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Bergamo-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-10A + S_Greek-2B Discordant SGDP 31,433,818 – 32,048,924 615,105.5 0.47953680 3 384.6294 156.0
S_Papuan-9A + S_Piapoco-2A Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
S_Papuan-4A + S_Bougainville-1A Discordant SGDP 31,565,428 – 31,983,119 417,690.5 0.26588415 3 213.7073 280.8
S_Papuan-9B + S_Even-3B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-4A + S_Mansi-2A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Tu-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-4A + S_Kalash-1B Discordant SGDP 31,806,307 – 32,043,090 236,783.5 0.32604496 3 261.8360 229.2
S_Papuan-9B + S_Uygur-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-4A + B_Papuan-15B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-9B + S_Kinh-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-4B + S_Tubalar-1B Discordant SGDP 31,583,614 – 32,452,204 868,590.0 0.49429173 3 396.4334 151.3
S_Papuan-9B + S_Irula-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-4B + S_Polish-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Kalash-2A Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
S_Papuan-14A + S_Papuan-3B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-9B + S_Atayal-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-14A + S_Papuan-5B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_French-2B Discordant SGDP 31,806,307 – 31,827,533 21,226.5 0.00154497 3 2.2360 26,833.9
S_Papuan-14A + S_Papuan-2B Discordant SGDP 31,575,111 – 31,868,351 293,240.5 0.01288349 3 11.3068 5,306.5
S_Papuan-9B + S_Bergamo-2A Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-14A + S_Sardinian-1A Discordant SGDP 31,806,307 – 32,451,906 645,599.0 0.48254522 3 387.0362 155.0
S_Papuan-9B + S_Karitiana-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Ulchi-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-12B + S_Papuan-7B Discordant SGDP 31,583,614 – 32,420,230 836,616.0 0.47448293 3 380.5863 157.7
S_Papuan-9A + S_Ulchi-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Estonian-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Yakut-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Iraqi_Jew-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Even-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Palestinian-3A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-9A + S_Naxi-3B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Jordanian-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Han-1A Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 3 7.8602 7,633.4
S_Papuan-9A + S_Chane-1B Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
S_Papuan-9A + S_Yi-1B Discordant SGDP 31,575,111 – 31,868,351 293,240.5 0.01288349 3 11.3068 5,306.5
S_Papuan-9B + S_Quechua-1B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Korean-2A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Altaian-1B Discordant SGDP 31,134,695 – 31,841,841 707,146.0 0.24835638 3 199.6851 300.5
S_Papuan-9A + S_Ami-2A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Even-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Thai-1A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Miao-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Kinh-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Uygur-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Maori-1B Discordant SGDP 31,134,695 – 31,989,209 854,514.0 0.52025224 3 417.2018 143.8
S_Papuan-9B + S_Yi-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Chukchi-1A Discordant SGDP 31,806,307 – 31,827,533 21,226.5 0.00154497 3 2.2360 26,833.9
S_Papuan-9B + S_She-2A Discordant SGDP 31,806,307 – 31,824,938 18,631.0 0.00076896 3 1.6152 37,147.7
S_Papuan-9A + S_Itelman-1A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-9B + S_Thai-1A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Bengali-2A Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9B + B_Australian-3A Discordant SGDP 31,565,428 – 31,841,841 276,413.0 0.01149221 3 10.1938 5,885.9
S_Papuan-9A + S_Bengali-2B Discordant SGDP 31,806,307 – 31,824,938 18,631.0 0.00076896 3 1.6152 37,147.7
S_Papuan-9B + S_Papuan-14B Discordant SGDP 31,806,307 – 31,824,938 18,631.0 0.00076896 3 1.6152 37,147.7
S_Papuan-9A + S_Kapu-1B Discordant SGDP 31,687,839 – 31,841,841 154,002.0 0.00684403 3 6.4752 9,266.1
S_Papuan-9B + S_Mala-2A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Papuan-9A + S_Relli-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Pathan-1B Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9A + S_Yadava-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9B + S_Albanian-1B Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9A + S_Irula-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Luhya-1B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Mala-3B Discordant SGDP 31,687,839 – 31,841,841 154,002.0 0.00684403 3 6.4752 9,266.1
S_Papuan-9B + S_Finnish-2B Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Brahmin-1A Discordant SGDP 31,575,111 – 31,841,841 266,730.5 0.01070481 3 9.5638 6,273.6
S_Papuan-9B + S_Saami-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Madiga-2B Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9B + S_Druze-1B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Papuan-9A + S_Kusunda-2B Discordant SGDP 31,727,319 – 31,827,533 100,214.0 0.00487860 3 4.9029 12,237.7
S_Papuan-9B + S_Palestinian-1B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9A + S_Pathan-2B Discordant SGDP 31,806,307 – 31,824,938 18,631.0 0.00076896 3 1.6152 37,147.7
S_Papuan-9B + S_Jordanian-2B Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
S_Papuan-9A + S_Kalash-2B Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + B_French-3A Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
S_Papuan-9A + S_Sindhi-2A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-9B + S_Pima-2A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-9A + S_Abkhasian-1A Discordant SGDP 31,806,307 – 31,841,841 35,534.5 0.00258227 3 3.0658 19,570.6
S_Papuan-12B + S_Papuan-1B Discordant SGDP 31,583,614 – 32,420,230 836,616.0 0.47448293 3 380.5863 157.7
S_Papuan-9A + S_Czech-2A Discordant SGDP 31,806,307 – 31,806,326 19.5 0.00000004 3 1.0000 59,998.1
S_Papuan-12B + S_Finnish-1B Discordant SGDP 31,806,307 – 31,868,351 62,044.5 0.00476095 3 4.8088 12,477.2
S_Papuan-9A + S_English-2A Discordant SGDP 31,806,307 – 31,820,336 14,029.5 0.00035502 3 1.2840 46,728.4
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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