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 Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP866.2 generations 94  =  1  +  931.000
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_Ami-1B + S_Hawaiian-1B Concordant SGDP 135,757,046 – 136,825,844 1,068,798.0 0.25986017 24 721.9112 664.9
S_Ami-1B + S_Palestinian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 69 552.7512 2,496.6
S_Ami-1B + S_Druze-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 52 562.7585 1,848.0
S_Ami-1B + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 59 562.7585 2,096.8
S_Ami-1B + S_Georgian-1A Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 24 232.8804 2,061.1
S_Hawaiian-1B + S_Jordanian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 72 562.7585 2,558.8
S_Hawaiian-1B + B_Australian-3B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 59 564.6453 2,089.8
S_Ami-1B + S_Tajik-1B Discordant SGDP 135,760,098 – 136,585,834 825,736.5 0.06906363 65 452.6044 2,872.3
S_Ami-1B + S_Lahu-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Tlingit-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Tlingit-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Yakut-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 39 564.6453 1,381.4
S_Ami-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 562.7585 1,919.1
S_Ami-1B + S_Quechua-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 43 564.6453 1,523.1
S_Ami-1B + S_BantuHerero-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 75 552.7512 2,713.7
S_Ami-1B + S_Tuscan-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 47 552.7512 1,700.6
S_Ami-1B + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 23 158.4384 2,903.3
S_Ami-1B + S_Tu-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Tujia-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Daur-2B Discordant SGDP 135,782,261 – 136,776,467 994,206.0 0.08490211 48 546.1406 1,757.8
S_Hawaiian-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 71 562.7585 2,523.3
S_Ami-1B + S_Hezhen-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 47 575.9127 1,632.2
S_Hawaiian-1B + S_Turkish-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Naxi-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Hungarian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 56 562.7585 1,990.2
S_Ami-1B + S_She-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 37 575.9127 1,284.9
S_Ami-1B + S_Iraqi_Jew-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 56 575.9127 1,944.7
S_Ami-1B + S_Japanese-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Palestinian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 30 232.8804 2,576.4
S_Ami-1B + S_Korean-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 51 575.9127 1,771.1
S_Ami-1B + S_Sardinian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Korean-1A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 51 780.7852 1,306.4
S_Ami-1B + S_Kyrgyz-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Burmese-1A Discordant SGDP 136,555,141 – 136,785,841 230,699.5 0.04069738 18 144.2937 2,494.9
S_Ami-1B + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 26 156.7428 3,317.5
S_Ami-1B + S_Thai-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Mandenka-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 73 562.7585 2,594.4
S_Ami-1B + S_Kinh-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 49 552.7512 1,772.9
S_Hawaiian-1B + S_Thai-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 43 575.9127 1,493.3
S_Ami-1B + B_Australian-4B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 44 562.7585 1,563.7
S_Hawaiian-1B + S_Papuan-10B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Dusun-1B Discordant SGDP 135,942,298 – 136,785,841 843,542.5 0.08827139 36 476.5175 1,511.0
S_Hawaiian-1B + S_Iranian-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Bougainville-2A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Russian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 58 562.7585 2,061.3
S_Ami-1B + S_Bougainville-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 47 552.7512 1,700.6
S_Ami-1B + S_Mozabite-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Bougainville-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 62 562.7585 2,203.4
S_Ami-1B + S_Greek-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 70 562.7585 2,487.7
S_Ami-1B + S_Papuan-11A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 51 562.7585 1,812.5
S_Ami-1B + S_Iranian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Papuan-6A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Iraqi_Jew-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 62 562.7585 2,203.4
S_Ami-1B + S_Papuan-7B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 562.7585 1,919.1
S_Ami-1B + S_Samaritan-1B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 23 232.8804 1,975.3
S_Ami-1B + S_Papuan-9B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 45 493.9515 1,822.0
S_Ami-1B + S_Druze-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Mansi-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 57 562.7585 2,025.7
S_Ami-1B + S_Palestinian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 59 562.7585 2,096.8
S_Ami-1B + S_Bengali-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Sardinian-1B Discordant SGDP 136,500,227 – 136,774,712 274,484.5 0.03728607 12 162.5814 1,476.2
S_Ami-1B + S_Yadava-1B Discordant SGDP 135,954,725 – 136,762,052 807,326.5 0.07313183 47 447.0222 2,102.8
S_Ami-1B + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 56 562.7585 1,990.2
S_Ami-1B + S_Yadava-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 63 575.9127 2,187.8
S_Ami-1B + S_Jordanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 58 552.7512 2,098.6
S_Ami-1B + S_Irula-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Russian-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 61 562.7585 2,167.9
S_Ami-1B + S_Khonda_Dora-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 40 575.9127 1,389.1
S_Ami-1B + S_Abkhasian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 55 562.7585 1,954.7
S_Ami-1B + S_Mala-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Ami-1B + S_Saharawi-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Brahmin-2A Discordant SGDP 135,782,261 – 136,762,052 979,790.5 0.07868380 59 534.2465 2,208.7
S_Ami-1B + B_Crete-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 50 562.7585 1,777.0
S_Ami-1B + S_Brahui-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 53 562.7585 1,883.6
S_Hawaiian-1B + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 57 562.7585 2,025.7
S_Ami-1B + S_Balochi-1B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 57 493.9515 2,307.9
S_Hawaiian-1B + S_Tujia-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Luo-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 71 552.7512 2,569.0
S_Hawaiian-1B + B_Australian-3A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 54 562.7585 1,919.1
S_Ami-1B + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 57 562.7585 2,025.7
S_Hawaiian-1B + S_Papuan-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Albanian-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Madiga-2B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 42 564.6453 1,487.7
S_Ami-1B + S_Armenian-2B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 53 488.3165 2,170.7
S_Ami-1B + S_Atayal-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Masai-1B Discordant SGDP 136,391,342 – 136,762,052 370,710.0 0.05242810 38 220.8833 3,440.7
S_Ami-1B + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 56 562.7585 1,990.2
S_Hawaiian-1B + S_Russian-2A Discordant SGDP 135,597,516 – 136,774,712 1,177,196.0 0.25197117 73 767.6310 1,902.0
S_Ami-1B + S_French-1B Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Hawaiian-1B + S_Lezgin-1A Discordant SGDP 136,585,810 – 136,585,834 24.0 0.00001198 4 1.0211 78,346.6
S_Ami-1B + S_Basque-2B Discordant SGDP 136,557,025 – 136,785,841 228,815.5 0.03729117 16 140.6644 2,274.9
S_Hawaiian-1B + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,776,467 1,016,369.5 0.09473490 45 564.6453 1,593.9
S_Ami-1B + S_Georgian-2B Discordant SGDP 136,389,749 – 136,774,712 384,963.0 0.05887274 26 232.8804 2,232.9
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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