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

rs563746196
Alleles:
reference
A
ancestral
alternate
G
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  31,663,150  (GRCh37) Explore rs563746196 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 Recombination clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP103.4 generations 98  =  1  +  970.990
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_Yakut-2B + S_Tu-1B Concordant SGDP 31,481,698 – 32,370,205 888,507.5 0.48068284 3 385.5463 155.6
S_Yakut-2B + S_Czech-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Punjabi-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Kusunda-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Tu-1B + S_Madiga-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Pima-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Lezgin-2A Discordant SGDP 31,296,226 – 31,663,157 366,931.0 0.21283276 3 171.2662 350.3
S_Yakut-2B + S_Palestinian-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Even-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Ulchi-1B Discordant SGDP 31,548,099 – 31,981,099 433,000.0 0.26903236 3 216.2259 277.5
S_Yakut-2B + S_Ulchi-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Ulchi-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Tubalar-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Altaian-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Mongola-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Finnish-2B Discordant SGDP 31,565,428 – 31,727,319 161,891.0 0.00557631 3 5.4610 10,986.9
S_Yakut-2B + S_Greek-1A Discordant SGDP 31,565,428 – 31,841,841 276,413.0 0.01149221 3 10.1938 5,885.9
S_Yakut-2B + S_Even-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Jordanian-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Yakut-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + B_Dai-4A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Even-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Tu-1B + S_Han-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Naxi-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Brahmin-1A Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 3 8.6709 6,919.7
S_Yakut-2B + S_Miao-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Burusho-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Miao-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Albanian-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Tu-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Estonian-2B Discordant SGDP 31,484,549 – 31,795,978 311,428.5 0.02702374 3 22.6190 2,652.6
S_Yakut-2B + S_Oroqen-2A Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 3 8.6709 6,919.7
S_Yakut-2B + S_French-1A Discordant SGDP 31,135,093 – 31,663,157 528,063.5 0.23800322 3 191.4026 313.5
S_Yakut-2B + S_Uygur-1A Discordant SGDP 31,620,012 – 31,868,351 248,339.5 0.01078264 3 9.6261 6,233.0
S_Yakut-2B + S_Iraqi_Jew-1A Discordant SGDP 31,601,307 – 31,795,978 194,671.0 0.00595989 3 5.7679 10,402.4
S_Yakut-2B + S_Uygur-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Sardinian-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Yi-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Yakut-2B + S_Orcadian-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Dai-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Yakut-2B + S_Spanish-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Uygur-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + B_Papuan-15A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Yakut-2B + S_Korean-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Tu-1B + S_Yakut-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Korean-1B Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 3 8.6709 6,919.7
S_Tu-1B + S_She-2B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 3 201.4281 297.9
S_Yakut-2B + S_Burmese-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Mozabite-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Thai-1B Discordant SGDP 31,134,695 – 31,663,157 528,461.5 0.24094651 3 193.7572 309.7
S_Yakut-2B + S_Madiga-2B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Yakut-2B + S_Thai-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Brahui-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Kinh-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Kalash-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Yakut-2B + S_Kinh-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Abkhasian-1B Discordant SGDP 31,663,142 – 31,841,841 178,699.0 0.00740992 3 6.9279 8,660.6
S_Yakut-2B + B_Australian-3B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Yakut-2B + S_Bulgarian-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + B_Australian-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_English-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Maori-1B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Yakut-2B + S_Estonian-1B Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 3 8.6709 6,919.7
S_Yakut-2B + S_Bougainville-2B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Yakut-2B + S_Finnish-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-3A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Yakut-2B + S_French-2B Discordant SGDP 31,548,099 – 31,795,978 247,878.5 0.01444522 3 12.5562 4,778.5
S_Yakut-2B + S_Papuan-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Hungarian-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Druze-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-5A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Yakut-2B + S_Bergamo-2B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 3 201.4281 297.9
S_Yakut-2B + S_Papuan-4A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Tuscan-2B Discordant SGDP 31,134,695 – 31,663,157 528,461.5 0.24094651 3 193.7572 309.7
S_Yakut-2B + S_Papuan-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Kyrgyz-1B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
S_Yakut-2B + S_Papuan-14B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Yakut-2B + S_Polish-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-7B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Adygei-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-9A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Turkish-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-9B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + B_French-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-12B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Karitiana-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Papuan-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Tu-1B + S_Tubalar-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Chukchi-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 3 1.8106 33,137.5
S_Tu-1B + S_Even-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Mansi-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Tu-1B + S_Oroqen-2A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 3 201.4281 297.9
S_Yakut-2B + S_Kapu-1A Discordant SGDP 31,663,142 – 32,451,906 788,763.5 0.48737286 3 390.8983 153.5
S_Tu-1B + S_Dusun-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Irula-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Tu-1B + S_Saami-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 3 1.0000 59,997.8
S_Yakut-2B + S_Mala-3A Discordant SGDP 31,548,099 – 31,841,841 293,742.0 0.01763626 3 15.1090 3,971.1
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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