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 Joint clock
Data source Estimated age of A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP578.6 generations 97  =  1  +  961.000
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_Tubalar-2B + S_Han-1A Concordant SGDP 31,132,895 – 32,356,346 1,223,451.0 0.70946371 26 1,155.8274 449.9
S_Han-1A + S_Maori-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Han-1A + S_Burmese-1B Discordant SGDP 31,756,008 – 32,451,906 695,897.5 0.48434592 48 722.5075 1,328.7
S_Han-1A + S_Yi-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Pima-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Han-1A + S_Turkish-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Han-1A + S_Saami-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 6 45.7062 2,625.5
S_Han-1A + S_Makrani-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Korean-2B Discordant SGDP 31,031,900 – 31,756,030 724,129.5 0.39282274 72 662.8404 2,172.5
S_Tubalar-2B + S_Dai-2A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 5 38.0085 2,631.0
S_Tubalar-2B + S_Ulchi-1B Discordant SGDP 31,756,008 – 31,795,978 39,969.5 0.00119193 5 21.1389 4,730.6
S_Tubalar-2B + S_Ulchi-2B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 5 45.7062 2,187.9
S_Tubalar-2B + S_Tubalar-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Tubalar-2B + S_Yakut-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Papuan-2B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 10 90.0720 2,220.4
S_Han-1A + S_Madiga-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 7 30.9087 4,529.5
S_Tubalar-2B + S_Korean-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Czech-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Burmese-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_BedouinB-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Kinh-2A Discordant SGDP 31,756,008 – 32,353,201 597,193.0 0.43842554 37 638.3931 1,159.2
S_Han-1A + B_Dai-4A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 5 38.0085 2,631.0
S_Tubalar-2B + S_Bougainville-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 5 35.2000 2,840.9
S_Han-1A + S_Tu-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Papuan-3A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_She-2A Discordant SGDP 31,756,008 – 31,824,938 68,929.5 0.00256967 5 36.1419 2,766.9
S_Tubalar-2B + S_Papuan-8B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 12 147.3302 1,629.0
S_Han-1A + S_Kinh-1A Discordant SGDP 31,756,008 – 31,827,533 71,525.0 0.00334567 6 38.0085 3,157.2
S_Tubalar-2B + S_Papuan-9B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 15 157.3398 1,906.7
S_Han-1A + S_Papuan-4B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 8 90.0720 1,776.4
S_Tubalar-2B + S_Chukchi-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Han-1A + S_Mala-3B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Eskimo_Naukan-1B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Han-1A + S_Kusunda-1B Discordant SGDP 31,134,695 – 31,827,533 692,838.0 0.24731908 72 531.4175 2,709.7
S_Tubalar-2B + S_Kapu-2B Discordant SGDP 31,727,319 – 31,868,351 141,032.0 0.00809458 9 75.1710 2,394.5
S_Han-1A + S_Kalash-2B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 5 45.7062 2,187.9
S_Tubalar-2B + S_Brahui-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_Finnish-2A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 6 45.7062 2,625.5
S_Tubalar-2B + S_Pathan-2B Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 6 35.2000 3,409.1
S_Han-1A + S_Iraqi_Jew-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 10 157.3398 1,271.1
S_Tubalar-2B + S_Sindhi-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 6 35.2000 3,409.1
S_Han-1A + S_Sardinian-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Tubalar-2B + S_Luhya-1A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 6 35.2000 3,409.1
S_Han-1A + S_Yemenite_Jew-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Abkhasian-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 8 60.1740 2,659.0
S_Han-1A + B_Papuan-15A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Albanian-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Quechua-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Tubalar-2B + S_Bulgarian-1B Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_Uygur-1A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 7 45.7062 3,063.0
S_Tubalar-2B + S_Estonian-2A Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 6 35.2000 3,409.1
S_Han-1A + S_Uygur-2B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Finnish-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 8 60.1740 2,659.0
S_Han-1A + S_Tu-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 7 45.7062 3,063.0
S_Tubalar-2B + S_Saami-2B Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_Thai-1B Discordant SGDP 31,756,008 – 32,403,755 647,746.5 0.46163056 31 681.2228 910.1
S_Tubalar-2B + S_Iranian-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Dusun-1A Discordant SGDP 31,092,468 – 32,451,906 1,359,438.0 0.78406091 61 1,280.7790 952.5
S_Tubalar-2B + S_Iraqi_Jew-2A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_Papuan-5B Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Palestinian-3A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 11 170.5729 1,289.8
S_Han-1A + S_Papuan-14B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Palestinian-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Itelman-1A Discordant SGDP 31,548,099 – 32,451,906 903,806.5 0.49759921 41 832.9065 984.5
S_Tubalar-2B + S_Bergamo-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Brahmin-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Sardinian-1B Discordant SGDP 31,688,606 – 31,756,030 67,423.5 0.00229590 6 35.2000 3,409.1
S_Han-1A + S_Madiga-2A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Tubalar-2B + S_Jordanian-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Kusunda-2B Discordant SGDP 31,756,008 – 32,289,718 533,710.0 0.43397829 31 604.3634 1,025.9
S_Tubalar-2B + S_Jordanian-1A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Pathan-1A Discordant SGDP 31,697,077 – 32,403,755 706,678.0 0.46364421 35 711.1208 984.4
S_Tubalar-2B + S_Orcadian-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Punjabi-4B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Russian-2A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_English-2B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Tubalar-2B + S_Adygei-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 7 45.7062 3,063.0
S_Han-1A + S_Finnish-1B Discordant SGDP 31,756,008 – 31,868,351 112,343.0 0.00656165 7 60.1740 2,326.6
S_Tubalar-2B + B_French-3B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 12 138.2450 1,736.0
S_Han-1A + S_French-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Tubalar-2B + S_Chane-1A Discordant SGDP 31,744,517 – 31,756,030 11,512.5 0.00095652 4 7.2912 10,972.1
S_Han-1A + S_Palestinian-1B Discordant SGDP 31,697,077 – 32,451,906 754,829.0 0.48635957 42 752.4056 1,116.4
S_Tubalar-2B + S_Karitiana-1A Discordant SGDP 31,134,695 – 31,756,030 621,334.5 0.24397384 75 494.4196 3,033.9
S_Han-1A + S_Bergamo-2A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Mixe-2A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 6 30.9087 3,882.4
S_Han-1A + S_Polish-1A Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 6 45.7062 2,625.5
S_Han-1A + S_Altaian-1B Discordant SGDP 31,756,008 – 31,841,841 85,833.0 0.00438297 7 45.7062 3,063.0
S_Han-1A + S_Yemenite_Jew-2B Discordant SGDP 31,697,077 – 31,868,351 171,274.5 0.00857530 12 90.0720 2,664.5
S_Han-1A + S_Even-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Yemenite_Jew-1B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Yakut-2A Discordant SGDP 31,697,077 – 32,451,906 754,829.0 0.48635957 41 752.4056 1,089.8
S_Han-1A + B_French-3A Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Cambodian-2B Discordant SGDP 31,756,008 – 32,451,906 695,897.5 0.48434592 53 722.5075 1,467.1
S_Han-1A + S_Piapoco-2A Discordant SGDP 31,700,429 – 31,756,030 55,601.0 0.00186764 5 29.1826 3,426.7
S_Han-1A + S_Naxi-3B Discordant SGDP 31,756,008 – 31,756,030 21.5 0.00000044 4 1.0107 79,155.6
S_Han-1A + S_Mayan-1A Discordant SGDP 31,697,077 – 31,756,030 58,953.0 0.00201408 5 30.9087 3,235.3
S_Han-1A + S_Miao-1A Discordant SGDP 31,756,008 – 32,540,301 784,292.5 0.65031800 49 897.7148 1,091.7
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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