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 Joint clock
Data source Estimated age of G allele # pairs = concordant + discordant Quality score
    Genomes in SGDP510.6 generations 98  =  1  +  971.000
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_Yakut-2B + S_Tu-1B Concordant SGDP 31,481,698 – 32,370,205 888,507.5 0.48068284 13 812.0299 320.2
S_Yakut-2B + S_Czech-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Punjabi-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Kusunda-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Tu-1B + S_Madiga-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Pima-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Lezgin-2A Discordant SGDP 31,296,226 – 31,663,157 366,931.0 0.21283276 45 347.3931 2,590.7
S_Yakut-2B + S_Palestinian-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Even-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Ulchi-1B Discordant SGDP 31,548,099 – 31,981,099 433,000.0 0.26903236 22 424.0659 1,037.6
S_Yakut-2B + S_Ulchi-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 211.1397 1,231.4
S_Yakut-2B + S_Ulchi-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Tubalar-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Altaian-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Mongola-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Finnish-2B Discordant SGDP 31,565,428 – 31,727,319 161,891.0 0.00557631 11 83.1687 2,645.2
S_Yakut-2B + S_Greek-1A Discordant SGDP 31,565,428 – 31,841,841 276,413.0 0.01149221 13 142.8720 1,819.8
S_Yakut-2B + S_Even-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Jordanian-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Yakut-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + B_Dai-4A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 16 211.1397 1,515.6
S_Yakut-2B + S_Even-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Tu-1B + S_Han-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Naxi-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Brahmin-1A Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 10 107.1712 1,866.2
S_Yakut-2B + S_Miao-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 211.1397 1,231.4
S_Yakut-2B + S_Burusho-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 16 211.1397 1,515.6
S_Yakut-2B + S_Miao-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Albanian-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Tu-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Estonian-2B Discordant SGDP 31,484,549 – 31,795,978 311,428.5 0.02702374 13 172.1047 1,510.7
S_Yakut-2B + S_Oroqen-2A Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 13 107.1712 2,426.0
S_Yakut-2B + S_French-1A Discordant SGDP 31,135,093 – 31,663,157 528,063.5 0.23800322 72 444.8731 3,236.9
S_Yakut-2B + S_Uygur-1A Discordant SGDP 31,620,012 – 31,868,351 248,339.5 0.01078264 13 128.8291 2,018.2
S_Yakut-2B + S_Iraqi_Jew-1A Discordant SGDP 31,601,307 – 31,795,978 194,671.0 0.00595989 14 99.2100 2,822.3
S_Yakut-2B + S_Uygur-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 13 211.1397 1,231.4
S_Yakut-2B + S_Sardinian-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Yi-2B Discordant SGDP 31,548,099 – 31,868,351 320,252.0 0.01981494 12 170.5729 1,407.0
S_Yakut-2B + S_Orcadian-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Dai-2B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 11 157.3398 1,398.2
S_Yakut-2B + S_Spanish-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Uygur-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + B_Papuan-15A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 17 157.3398 2,160.9
S_Yakut-2B + S_Korean-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Tu-1B + S_Yakut-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Korean-1B Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 15 107.1712 2,799.3
S_Tu-1B + S_She-2B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 70 553.5829 2,529.0
S_Yakut-2B + S_Burmese-1B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 15 211.1397 1,420.9
S_Yakut-2B + S_Mozabite-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Thai-1B Discordant SGDP 31,134,695 – 31,663,157 528,461.5 0.24094651 55 447.4187 2,458.5
S_Yakut-2B + S_Madiga-2B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Yakut-2B + S_Thai-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Brahui-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Kinh-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Kalash-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Yakut-2B + S_Kinh-1A Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 12 211.1397 1,136.7
S_Yakut-2B + S_Abkhasian-1B Discordant SGDP 31,663,142 – 31,841,841 178,699.0 0.00740992 9 92.7035 1,941.7
S_Yakut-2B + B_Australian-3B Discordant SGDP 31,484,549 – 31,868,351 383,802.0 0.03239346 18 211.1397 1,705.0
S_Yakut-2B + S_Bulgarian-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + B_Australian-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_English-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Maori-1B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Yakut-2B + S_Estonian-1B Discordant SGDP 31,663,142 – 31,868,351 205,209.0 0.00958860 9 107.1712 1,679.6
S_Yakut-2B + S_Bougainville-2B Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Yakut-2B + S_Finnish-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-3A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 17 157.3398 2,160.9
S_Yakut-2B + S_French-2B Discordant SGDP 31,548,099 – 31,795,978 247,878.5 0.01444522 13 131.5379 1,976.6
S_Yakut-2B + S_Papuan-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Hungarian-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Druze-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-5A Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 20 157.3398 2,542.3
S_Yakut-2B + S_Bergamo-2B Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 67 553.5829 2,420.6
S_Yakut-2B + S_Papuan-4A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Tuscan-2B Discordant SGDP 31,134,695 – 31,663,157 528,461.5 0.24094651 52 447.4187 2,324.4
S_Yakut-2B + S_Papuan-4B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Kyrgyz-1B Discordant SGDP 31,601,307 – 31,868,351 267,044.5 0.01132961 14 138.2450 2,025.4
S_Yakut-2B + S_Papuan-14B Discordant SGDP 31,565,428 – 31,868,351 302,923.0 0.01367089 17 157.3398 2,160.9
S_Yakut-2B + S_Polish-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-7B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Adygei-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-9A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Turkish-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-9B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + B_French-3B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-12B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Karitiana-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Papuan-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Tu-1B + S_Tubalar-2A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Chukchi-1A Discordant SGDP 31,663,142 – 31,697,077 33,934.5 0.00101330 5 18.0992 5,525.1
S_Tu-1B + S_Even-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Mansi-2B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Tu-1B + S_Oroqen-2A Discordant SGDP 31,134,695 – 31,868,351 733,656.0 0.25053506 75 553.5829 2,709.6
S_Yakut-2B + S_Kapu-1A Discordant SGDP 31,663,142 – 32,451,906 788,763.5 0.48737286 55 769.5048 1,429.5
S_Tu-1B + S_Dusun-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Irula-1B Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Tu-1B + S_Saami-1A Discordant SGDP 31,663,142 – 31,663,157 14.5 0.00000005 4 1.0070 79,444.2
S_Yakut-2B + S_Mala-3A Discordant SGDP 31,548,099 – 31,841,841 293,742.0 0.01763626 12 156.1052 1,537.4
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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