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

rs370622934
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  31,793,510  (GRCh37) Explore rs370622934 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 Recombination clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP118.1 generations 97  =  1  +  960.990
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_Ami-1A + S_Igorot-1B Concordant SGDP 31,480,074 – 31,979,966 499,891.5 0.32484965 3 260.8797 230.0
S_Ami-1A + S_Saami-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Czech-2B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
S_Ami-1A + S_Punjabi-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + B_French-3A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Igorot-1B + S_Kalash-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Chane-1A Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Orcadian-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Ulchi-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Tubalar-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Altaian-1A Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Yakut-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Tubalar-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Quechua-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Iraqi_Jew-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Sardinian-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Even-3A Discordant SGDP 31,793,510 – 31,868,351 74,841.5 0.00585184 3 5.6815 10,560.6
S_Ami-1A + S_Yemenite_Jew-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Yakut-2B Discordant SGDP 31,134,695 – 31,793,555 658,860.0 0.24469808 3 196.7585 304.9
S_Igorot-1B + S_Ulchi-2A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 3 26.9148 2,229.3
S_Ami-1A + S_Tlingit-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Igorot-1B + S_French-2A Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 3 10.0637 5,962.0
S_Ami-1A + S_Aleut-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Sindhi-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Naxi-3B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Bulgarian-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Miao-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Finnish-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Han-1B Discordant SGDP 31,583,614 – 31,868,351 284,737.0 0.01207056 3 10.6565 5,630.4
S_Ami-1A + S_Iranian-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Tu-2A Discordant SGDP 31,793,510 – 31,795,978 2,468.0 0.00048212 3 1.3857 43,299.5
S_Ami-1A + S_BedouinB-2A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Uygur-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Jordanian-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Yi-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Turkish-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Uygur-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Ami-1A + B_Dai-4A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_She-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Pima-2A Discordant SGDP 31,697,077 – 31,793,555 96,478.5 0.00273832 3 3.1907 18,804.9
S_Ami-1A + S_Korean-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Igorot-1B + S_Papuan-9B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Burmese-2B Discordant SGDP 31,793,510 – 31,868,351 74,841.5 0.00585184 3 5.6815 10,560.6
S_Igorot-1B + S_English-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Burmese-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Polish-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Thai-1B Discordant SGDP 31,079,206 – 31,868,351 789,145.5 0.32163275 3 258.3062 232.3
S_Ami-1A + S_Mixe-2A Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Kinh-2B Discordant SGDP 31,793,510 – 31,795,978 2,468.0 0.00048212 3 1.3857 43,299.5
S_Ami-1A + S_Punjabi-4B Discordant SGDP 31,793,510 – 31,795,978 2,468.0 0.00048212 3 1.3857 43,299.5
S_Ami-1A + S_Kinh-1B Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Abkhasian-1A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Dusun-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Luhya-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Maori-1A Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Estonian-2A Discordant SGDP 31,565,428 – 31,841,841 276,413.0 0.01149221 3 10.1938 5,885.9
S_Ami-1A + S_Bougainville-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Finnish-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Papuan-14A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Saami-2A Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Papuan-9A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Iraqi_Jew-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Igorot-1A Discordant SGDP 31,079,206 – 31,868,351 789,145.5 0.32163275 3 258.3062 232.3
S_Ami-1A + S_Palestinian-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Hawaiian-1A Discordant SGDP 31,793,510 – 33,399,761 1,606,251.5 0.88818335 3 711.5467 84.3
S_Ami-1A + S_Bergamo-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Chukchi-1B Discordant SGDP 31,697,077 – 31,793,555 96,478.5 0.00273832 3 3.1907 18,804.9
S_Ami-1A + S_Jordanian-2A Discordant SGDP 31,697,077 – 31,793,555 96,478.5 0.00273832 3 3.1907 18,804.9
S_Ami-1A + S_Itelman-1B Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Ami-1A + S_Jordanian-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Bengali-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Russian-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Yadava-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Yemenite_Jew-2A Discordant SGDP 31,575,111 – 31,868,351 293,240.5 0.01288349 3 11.3068 5,306.5
S_Ami-1A + S_Mala-3B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Yemenite_Jew-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Brahmin-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + B_French-3B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Madiga-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Piapoco-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Madiga-2A Discordant SGDP 31,687,839 – 31,793,555 105,716.0 0.00318573 3 3.5486 16,908.2
S_Igorot-1B + S_Mozabite-1B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 3 16.8520 3,560.4
S_Ami-1A + S_Kusunda-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Even-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Kusunda-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Mala-2B Discordant SGDP 31,034,032 – 31,868,351 834,319.5 0.38828804 3 311.6304 192.5
S_Ami-1A + S_Makrani-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Albanian-1A Discordant SGDP 31,697,077 – 31,793,555 96,478.5 0.00273832 3 3.1907 18,804.9
S_Ami-1A + S_Pathan-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Finnish-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Brahui-1B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 3 11.9367 5,026.5
S_Igorot-1B + S_Druze-1A Discordant SGDP 31,793,510 – 31,795,978 2,468.0 0.00048212 3 1.3857 43,299.5
S_Ami-1A + S_Pathan-2B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_North_Ossetian-1B Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Kalash-2A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Igorot-1B + S_Karitiana-1A Discordant SGDP 31,793,510 – 31,793,555 45.5 0.00001486 3 1.0119 59,294.9
S_Ami-1A + S_Sindhi-2A Discordant SGDP 31,565,428 – 31,795,978 230,549.5 0.00830117 3 7.6409 7,852.4
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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