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

rs372420380
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 2   position  136,585,828  (GRCh37) Explore rs372420380 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 99.6%
0.4%
AFR 100.0%
0.0%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 98.9%
1.1%
OCN 98.0%
2.0%
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 T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP1,007.2 generations 94  =  1  +  931.000
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_Ami-1B + S_Hawaiian-1B Concordant SGDP 135,757,046 – 136,825,844 1,068,798.0 0.25986017 22 514.0230 856.0
S_Ami-1B + S_Palestinian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 67 481.9379 2,780.4
S_Ami-1B + S_Druze-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 50 488.0147 2,049.1
S_Ami-1B + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 57 488.0147 2,336.0
S_Ami-1B + S_Georgian-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 22 185.7822 2,368.4
S_Hawaiian-1B + S_Jordanian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 70 488.0147 2,868.8
S_Hawaiian-1B + B_Australian-3B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 57 488.8574 2,332.0
S_Ami-1B + S_Tajik-1B Discordant SGDP 135,760,098 – 136,585,834 825,736.5 0.06906363 63 397.3535 3,171.0
S_Ami-1B + S_Lahu-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Tlingit-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Tlingit-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Yakut-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 37 488.8574 1,513.7
S_Ami-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 52 488.0147 2,131.1
S_Ami-1B + S_Quechua-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 41 488.8574 1,677.4
S_Ami-1B + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 73 481.9379 3,029.4
S_Ami-1B + S_Tuscan-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 481.9379 1,867.5
S_Ami-1B + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 21 122.1863 3,437.4
S_Ami-1B + S_Tu-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Tujia-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Daur-2B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 46 478.2189 1,923.8
S_Hawaiian-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 69 488.0147 2,827.8
S_Ami-1B + S_Hezhen-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 45 493.3566 1,824.2
S_Hawaiian-1B + S_Turkish-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Naxi-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Hungarian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 488.0147 2,213.0
S_Ami-1B + S_She-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 35 493.3566 1,418.9
S_Ami-1B + S_Iraqi_Jew-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 54 493.3566 2,189.1
S_Ami-1B + S_Japanese-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Palestinian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 28 185.7822 3,014.3
S_Ami-1B + S_Korean-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 49 493.3566 1,986.4
S_Ami-1B + S_Sardinian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Korean-1A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 49 571.3960 1,715.1
S_Ami-1B + S_Kyrgyz-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Burmese-1A Discordant SGDP 136,555,141 – 136,785,841 230,699.5 0.04069738 16 111.7358 2,863.9
S_Ami-1B + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 24 129.7773 3,698.6
S_Ami-1B + S_Thai-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 71 488.0147 2,909.7
S_Ami-1B + S_Kinh-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 47 481.9379 1,950.5
S_Hawaiian-1B + S_Thai-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 41 493.3566 1,662.1
S_Ami-1B + B_Australian-4B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 42 488.0147 1,721.3
S_Hawaiian-1B + S_Papuan-10B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Dusun-1B Discordant SGDP 135,942,298 – 136,785,841 843,542.5 0.08827139 34 405.9004 1,675.3
S_Hawaiian-1B + S_Iranian-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Bougainville-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Russian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 56 488.0147 2,295.0
S_Ami-1B + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 481.9379 1,867.5
S_Ami-1B + S_Mozabite-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Bougainville-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 60 488.0147 2,458.9
S_Ami-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 68 488.0147 2,786.8
S_Ami-1B + S_Papuan-11A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 49 488.0147 2,008.1
S_Ami-1B + S_Iranian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Papuan-6A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Iraqi_Jew-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 60 488.0147 2,458.9
S_Ami-1B + S_Papuan-7B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 52 488.0147 2,131.1
S_Ami-1B + S_Samaritan-1B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 21 185.7822 2,260.7
S_Ami-1B + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 43 428.1460 2,008.7
S_Ami-1B + S_Druze-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Mansi-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 55 488.0147 2,254.0
S_Ami-1B + S_Palestinian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 57 488.0147 2,336.0
S_Ami-1B + S_Bengali-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Sardinian-1B Discordant SGDP 136,500,227 – 136,774,712 274,484.5 0.03728607 10 132.7526 1,506.6
S_Ami-1B + S_Yadava-1B Discordant SGDP 135,954,725 – 136,762,052 807,326.5 0.07313183 45 388.5167 2,316.5
S_Ami-1B + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 488.0147 2,213.0
S_Ami-1B + S_Yadava-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 61 493.3566 2,472.9
S_Ami-1B + S_Jordanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 56 481.9379 2,324.0
S_Ami-1B + S_Irula-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Russian-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 59 488.0147 2,418.0
S_Ami-1B + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 38 493.3566 1,540.5
S_Ami-1B + S_Abkhasian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 53 488.0147 2,172.1
S_Ami-1B + S_Mala-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 43 481.9379 1,784.5
S_Ami-1B + S_Saharawi-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Brahmin-2A Discordant SGDP 135,782,261 – 136,762,052 979,790.5 0.07868380 57 471.2994 2,418.8
S_Ami-1B + B_Crete-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 48 488.0147 1,967.2
S_Ami-1B + S_Brahui-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 51 488.0147 2,090.1
S_Hawaiian-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 55 488.0147 2,254.0
S_Ami-1B + S_Balochi-1B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 55 428.1460 2,569.2
S_Hawaiian-1B + S_Tujia-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Luo-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 69 481.9379 2,863.4
S_Hawaiian-1B + B_Australian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 52 488.0147 2,131.1
S_Ami-1B + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 55 488.0147 2,254.0
S_Hawaiian-1B + S_Papuan-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Albanian-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Madiga-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 40 488.8574 1,636.5
S_Ami-1B + S_Armenian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 51 424.4188 2,403.3
S_Ami-1B + S_Atayal-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Masai-1B Discordant SGDP 136,391,342 – 136,762,052 370,710.0 0.05242810 36 178.9408 4,023.7
S_Ami-1B + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 488.0147 2,213.0
S_Hawaiian-1B + S_Russian-2A Discordant SGDP 135,597,516 – 136,774,712 1,177,196.0 0.25197117 71 566.0541 2,508.6
S_Ami-1B + S_French-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Hawaiian-1B + S_Lezgin-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 2 1.0115 39,544.4
S_Ami-1B + S_Basque-2B Discordant SGDP 136,557,025 – 136,785,841 228,815.5 0.03729117 14 110.8314 2,526.4
S_Hawaiian-1B + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 43 488.8574 1,759.2
S_Ami-1B + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 24 185.7822 2,583.7
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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