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

rs560581252
Alleles:
reference
T
ancestral
alternate
C
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  136,649,287  (GRCh37) Explore rs560581252 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 100.0%
0.0%
OCN 100.0%
0.0%
SAS 97.4%
2.6%
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 C allele # pairs = concordant + discordant Quality score
    Genomes in SGDP79.3 generations 100  =  1  +  991.000
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_Kalash-2A + S_Kalash-2B Concordant SGDP 130,869,783 – 138,406,587 7,536,804.0 7.85463352 10 9,902.3727 20.2
S_Kalash-2B + B_Australian-4B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Han-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Eskimo_Sireniki-1A Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 12 121.1271 1,981.4
S_Kalash-2B + S_Chane-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 98 552.7512 3,545.9
S_Kalash-2B + S_Jordanian-2A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 21 246.0346 1,707.1
S_Kalash-2B + S_Bulgarian-2A Discordant SGDP 136,556,402 – 136,784,130 227,728.0 0.03533949 15 138.5810 2,164.8
S_Kalash-2B + S_Madiga-2B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Oroqen-1B Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 13 121.1271 2,146.5
S_Kalash-2A + S_Even-1B Discordant SGDP 136,488,251 – 136,785,841 297,590.0 0.04973076 10 183.6278 1,089.2
S_Kalash-2A + S_Eskimo_Chaplin-1A Discordant SGDP 136,549,528 – 136,762,052 212,524.0 0.02737236 17 124.9094 2,722.0
S_Kalash-2A + S_Eskimo_Sireniki-1B Discordant SGDP 136,488,251 – 136,785,841 297,590.0 0.04973076 11 183.6278 1,198.1
S_Kalash-2A + S_Ulchi-2A Discordant SGDP 136,544,266 – 136,762,052 217,786.0 0.02797987 18 127.9212 2,814.2
S_Kalash-2A + S_Mixtec-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Mixtec-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Chukchi-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Kapu-1A Discordant SGDP 136,559,711 – 136,785,841 226,130.0 0.03650418 18 138.7457 2,594.7
S_Kalash-2A + S_Oroqen-2B Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 14 121.1271 2,311.6
S_Kalash-2B + S_Punjabi-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 186 552.7512 6,730.0
S_Kalash-2A + S_Uygur-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Icelandic-2A Discordant SGDP 135,760,098 – 136,649,318 889,220.0 0.08174625 164 493.2226 6,650.1
S_Kalash-2A + S_Dai-2B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + B_Crete-1B Discordant SGDP 135,760,098 – 136,649,318 889,220.0 0.08174625 171 493.2226 6,934.0
S_Kalash-2A + S_Xibo-2B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Zapotec-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 109 552.7512 3,943.9
S_Kalash-2A + S_Ami-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 114 552.7512 4,124.8
S_Kalash-2B + S_Even-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 119 575.9127 4,132.6
S_Kalash-2A + S_Thai-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Tu-2B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Papuan-14B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 93 575.9127 3,229.7
S_Kalash-2B + S_Papuan-4A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Eskimo_Naukan-2B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
S_Kalash-2B + S_Eskimo_Naukan-2B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
S_Kalash-2A + S_Kapu-1A Discordant SGDP 136,559,711 – 136,785,841 226,130.0 0.03650418 18 138.7457 2,594.7
S_Kalash-2B + S_Somali-1B Discordant SGDP 136,619,416 – 136,785,841 166,425.0 0.02865172 16 103.8054 3,082.7
S_Kalash-2A + S_Relli-2A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
S_Kalash-2B + S_Punjabi-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 96 552.7512 3,473.5
S_Kalash-2A + S_Irula-1A Discordant SGDP 136,549,528 – 136,649,318 99,790.0 0.02060201 11 65.3808 3,364.9
S_Kalash-2B + S_Abkhasian-1B Discordant SGDP 136,555,141 – 136,762,052 206,910.5 0.02601890 13 121.1322 2,146.4
S_Kalash-2A + S_Irula-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 94 552.7512 3,401.2
S_Kalash-2B + S_Saami-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 67 552.7512 2,424.2
S_Kalash-2A + S_Mala-3A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_BedouinB-1A Discordant SGDP 136,390,550 – 136,785,841 395,291.0 0.06761750 21 244.8337 1,715.5
S_Kalash-2A + S_Madiga-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 96 552.7512 3,473.5
S_Kalash-2B + S_Tajik-2A Discordant SGDP 136,544,266 – 136,739,216 194,950.0 0.02679905 16 116.0152 2,758.3
S_Kalash-2A + S_Kusunda-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + B_Yoruba-3B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Makrani-2B Discordant SGDP 136,115,467 – 136,762,052 646,585.0 0.06710173 70 365.0422 3,835.2
S_Kalash-2B + S_Surui-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 47 575.9127 1,632.2
S_Kalash-2A + S_Burusho-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Aleut-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 38 575.9127 1,319.6
S_Kalash-2A + S_Punjabi-4B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Even-3A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Armenian-1A Discordant SGDP 136,389,749 – 136,649,318 259,569.0 0.04718923 16 163.3445 1,959.0
S_Kalash-2B + S_Aleut-2B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Armenian-2B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 19 246.0346 1,544.5
S_Kalash-2B + S_Han-1A Discordant SGDP 136,080,619 – 136,784,130 703,510.5 0.08025028 65 402.8853 3,226.7
S_Kalash-2A + S_Finnish-1B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 19 246.0346 1,544.5
S_Kalash-2B + S_Hezhen-2A Discordant SGDP 135,760,098 – 136,649,318 889,220.0 0.08174625 154 493.2226 6,244.6
S_Kalash-2A + S_French-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Papuan-8B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 63 575.9127 2,187.8
S_Kalash-2A + S_Hungarian-2B Discordant SGDP 136,555,141 – 136,762,052 206,910.5 0.02601890 16 121.1322 2,641.7
S_Kalash-2B + S_Papuan-9B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Iranian-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Itelman-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Samaritan-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Bengali-1B Discordant SGDP 136,555,141 – 136,712,944 157,802.5 0.02457048 18 96.4016 3,734.4
S_Kalash-2A + S_Druze-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Kapu-2A Discordant SGDP 136,619,416 – 136,649,318 29,902.0 0.00720290 5 21.1153 4,735.9
S_Kalash-2A + S_BedouinB-1B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
S_Kalash-2B + S_Brahmin-1B Discordant SGDP 136,544,266 – 136,762,052 217,786.0 0.02797987 19 127.9212 2,970.6
S_Kalash-2A + S_BedouinB-2B Discordant SGDP 136,390,550 – 136,785,841 395,291.0 0.06761750 20 244.8337 1,633.8
S_Kalash-2B + S_Kalash-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + S_Sardinian-1A Discordant SGDP 136,555,141 – 136,784,130 228,988.5 0.03775564 16 141.1190 2,267.6
S_Kalash-2B + S_Punjabi-3A Discordant SGDP 136,493,766 – 136,785,841 292,075.0 0.04838542 13 179.9043 1,445.2
S_Kalash-2A + S_Sardinian-2A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Punjabi-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 111 552.7512 4,016.3
S_Kalash-2A + S_Tuscan-1A Discordant SGDP 136,544,266 – 136,762,052 217,786.0 0.02797987 16 127.9212 2,501.5
S_Kalash-2B + S_Armenian-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 40 575.9127 1,389.1
S_Kalash-2A + S_Russian-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Saharawi-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2A + B_Dai-4B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Hungarian-2B Discordant SGDP 136,555,141 – 136,762,052 206,910.5 0.02601890 16 121.1322 2,641.7
S_Kalash-2A + B_Karitiana-3A Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 17 121.1271 2,807.0
S_Kalash-2B + S_Palestinian-1A Discordant SGDP 135,597,516 – 136,762,052 1,164,536.0 0.24705801 100 757.6237 2,639.8
S_Kalash-2A + S_Piapoco-1A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_BedouinB-2A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 21 246.0346 1,707.1
S_Kalash-2A + S_Piapoco-1B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
S_Kalash-2B + S_Jordanian-2B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 21 246.0346 1,707.1
S_Kalash-2A + S_Mayan-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 106 552.7512 3,835.4
S_Kalash-2B + S_Yemenite_Jew-2B Discordant SGDP 136,544,266 – 136,762,052 217,786.0 0.02797987 16 127.9212 2,501.5
S_Kalash-2B + S_Mixe-2A Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 13 121.1271 2,146.5
S_Kalash-2B + B_Han-3A Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Quechua-1A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 47 552.7512 1,700.6
S_Kalash-2B + S_Saharawi-2A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 21 246.0346 1,707.1
S_Kalash-2B + S_Yakut-1B Discordant SGDP 135,760,098 – 136,781,557 1,021,459.5 0.09819052 71 569.8530 2,491.9
S_Kalash-2B + S_Chane-1B Discordant SGDP 136,590,087 – 136,785,841 195,753.5 0.03270679 15 121.1271 2,476.7
S_Kalash-2B + S_Ulchi-1B Discordant SGDP 136,649,280 – 136,649,318 38.0 0.00002907 4 1.0415 76,812.6
S_Kalash-2B + S_Mayan-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 106 552.7512 3,835.4
S_Kalash-2B + S_Aleut-1A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 20 246.0346 1,625.8
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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