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Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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1000 Genomes Project
Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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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

rs925627898
Alleles:
reference
C
ancestral
alternate
A
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  136,612,005  (GRCh37) Explore rs925627898 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 96.0%
4.0%
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 A allele # pairs = concordant + discordant Quality score
    Genomes in SGDP313.2 generations 92  =  1  +  911.000
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_Papuan-1A + S_Papuan-11A Concordant SGDP 135,156,391 – 137,042,195 1,885,804.0 1.21814325 14 1,880.7005 148.9
S_Papuan-1A + S_Iranian-2B Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Hungarian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 37 562.7585 1,315.0
S_Papuan-1A + S_Georgian-1A Discordant SGDP 136,389,749 – 136,976,283 586,534.5 0.28476486 29 510.3485 1,136.5
S_Papuan-1A + S_Finnish-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 66 562.7585 2,345.6
S_Papuan-11A + S_Brahui-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 37 575.9127 1,284.9
S_Papuan-1A + S_Chechen-1A Discordant SGDP 136,493,766 – 136,762,052 268,286.0 0.03370694 26 156.7428 3,317.5
S_Papuan-1A + S_Tuscan-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 37 562.7585 1,315.0
S_Papuan-1A + S_Tlingit-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Tlingit-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 39 562.7585 1,386.0
S_Papuan-1A + S_Yakut-2A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Altaian-1B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Altaian-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 61 562.7585 2,167.9
S_Papuan-1A + S_BantuHerero-1B Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Mixtec-2A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Druze-2B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Palestinian-3A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 40 575.9127 1,389.1
S_Papuan-1A + S_Lahu-1B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Russian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 70 562.7585 2,487.7
S_Papuan-1A + S_Daur-2B Discordant SGDP 135,778,044 – 136,774,712 996,668.0 0.08469333 42 547.1553 1,535.2
S_Papuan-1A + B_Crete-2A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Tujia-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 45 552.7512 1,628.2
S_Papuan-1A + S_Mozabite-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 35 562.7585 1,243.9
S_Papuan-1A + S_Hezhen-1A Discordant SGDP 135,343,836 – 136,774,712 1,430,875.5 0.37964609 71 991.5371 1,432.1
S_Papuan-1A + S_Basque-2B Discordant SGDP 136,557,025 – 136,774,712 217,686.5 0.02752585 15 127.5102 2,352.8
S_Papuan-1A + S_Naxi-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Greek-1B Discordant SGDP 135,760,098 – 136,976,283 1,216,185.5 0.31932188 54 840.2265 1,285.4
S_Papuan-1A + S_She-1B Discordant SGDP 136,587,680 – 136,649,985 62,305.0 0.01255858 6 40.9533 2,930.2
S_Papuan-1A + S_Iranian-1B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Japanese-2B Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Iraqi_Jew-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 58 562.7585 2,061.3
S_Papuan-1A + S_Korean-2B Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Druze-1B Discordant SGDP 135,778,044 – 136,785,841 1,007,797.0 0.09445865 45 560.3095 1,606.3
S_Papuan-1A + S_Korean-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 42 562.7585 1,492.6
S_Papuan-1A + S_Sardinian-1B Discordant SGDP 136,500,227 – 136,785,841 285,613.5 0.04705139 10 175.7356 1,138.1
S_Papuan-1A + S_Burmese-1A Discordant SGDP 136,555,141 – 136,774,712 219,570.5 0.03093206 21 131.1395 3,202.7
S_Papuan-1A + S_Jordanian-1A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 61 780.7852 1,562.5
S_Papuan-1A + S_Ami-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 48 562.7585 1,705.9
S_Papuan-1A + S_Abkhasian-2A Discordant SGDP 136,389,749 – 136,642,220 252,471.5 0.04531508 16 158.4384 2,019.7
S_Papuan-1A + S_Thai-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 51 562.7585 1,812.5
S_Papuan-1A + S_Tajik-1B Discordant SGDP 135,760,098 – 136,612,021 851,923.0 0.07260582 67 468.0077 2,863.2
S_Papuan-1A + S_Thai-2A Discordant SGDP 135,978,431 – 136,762,052 783,620.5 0.07237876 46 435.0408 2,114.7
S_Papuan-1A + S_Karitiana-1B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 43 562.7585 1,528.2
S_Papuan-1A + S_Kinh-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 58 552.7512 2,098.6
S_Papuan-11A + S_Kyrgyz-1A Discordant SGDP 136,494,791 – 136,774,712 279,920.5 0.03837478 15 166.0617 1,806.6
S_Papuan-1A + B_Australian-3B Discordant SGDP 135,344,664 – 136,762,052 1,417,388.0 0.37401540 59 980.5586 1,203.4
S_Papuan-1A + S_Saharawi-1A Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 19 246.0346 1,544.5
S_Papuan-1A + B_Australian-4A Discordant SGDP 136,603,542 – 136,612,021 8,479.0 0.00024899 4 5.2691 15,182.8
S_Papuan-1A + S_Finnish-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 65 562.7585 2,310.0
S_Papuan-1A + S_Dusun-1B Discordant SGDP 135,978,431 – 136,774,712 796,280.5 0.07729192 36 445.0482 1,617.8
S_Papuan-1A + S_Georgian-2B Discordant SGDP 136,389,749 – 136,785,841 396,092.0 0.06863806 21 246.0346 1,707.1
S_Papuan-1A + S_Bougainville-2A Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Greek-1A Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 29 488.3165 1,187.8
S_Papuan-1A + S_Bougainville-1A Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 36 780.7852 922.1
S_Papuan-1A + S_Masai-2B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 77 552.7512 2,786.1
S_Papuan-1A + S_Papuan-10A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 21 562.7585 746.3
S_Papuan-1A + S_Hungarian-1B Discordant SGDP 135,760,098 – 136,642,220 882,122.5 0.07987209 31 488.3165 1,269.7
S_Papuan-1A + S_Papuan-7A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Masai-1A Discordant SGDP 135,343,836 – 136,976,283 1,632,447.0 0.60553821 71 1,269.0051 1,119.0
S_Papuan-1A + S_Papuan-9A Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Iraqi_Jew-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 38 575.9127 1,319.6
S_Papuan-1A + S_Hawaiian-1A Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 43 493.9515 1,741.1
S_Papuan-1A + S_Samaritan-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Bengali-2A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 47 552.7512 1,700.6
S_Papuan-1A + S_Masai-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 76 552.7512 2,749.9
S_Papuan-1A + S_Yadava-1B Discordant SGDP 135,978,431 – 136,762,052 783,620.5 0.07237876 44 435.0408 2,022.8
S_Papuan-1A + S_Palestinian-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 40 575.9127 1,389.1
S_Papuan-1A + S_Yadava-2A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Palestinian-3B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 50 552.7512 1,809.1
S_Papuan-1A + S_Irula-2B Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Sardinian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 56 562.7585 1,990.2
S_Papuan-1A + S_Khonda_Dora-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Tuscan-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 54 552.7512 1,953.9
S_Papuan-1A + S_Mala-3A Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 26 552.7512 940.7
S_Papuan-1A + S_Russian-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Brahmin-2B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Russian-2B Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 36 562.7585 1,279.4
S_Papuan-1A + S_Madiga-2A Discordant SGDP 136,602,042 – 136,612,021 9,979.0 0.00077011 4 6.4060 12,488.3
S_Papuan-1A + S_Abkhasian-2B Discordant SGDP 135,597,516 – 136,785,841 1,188,325.0 0.26173649 44 780.7852 1,127.1
S_Papuan-1A + S_Makrani-1A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 37 562.7585 1,315.0
S_Papuan-1A + S_Lezgin-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Balochi-1B Discordant SGDP 135,760,098 – 136,649,985 889,887.5 0.08225686 38 493.9515 1,538.6
S_Papuan-1A + S_Turkish-1A Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Luhya-2B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Mandenka-1A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 55 575.9127 1,910.0
S_Papuan-1A + S_Luo-2A Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 61 575.9127 2,118.4
S_Papuan-11A + S_Mansi-2B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 39 575.9127 1,354.4
S_Papuan-1A + S_Sindhi-1B Discordant SGDP 135,760,098 – 136,785,841 1,025,743.0 0.10319507 38 575.9127 1,319.6
S_Papuan-11A + S_French-1A Discordant SGDP 135,395,583 – 136,774,712 1,379,128.5 0.37267562 66 961.1222 1,373.4
S_Papuan-1A + S_Albanian-1B Discordant SGDP 135,760,098 – 136,762,052 1,001,954.0 0.08851659 34 552.7512 1,230.2
S_Papuan-11A + S_Yemenite_Jew-1B Discordant SGDP 136,611,932 – 136,612,021 89.0 0.00000066 4 1.0432 76,683.6
S_Papuan-1A + S_Armenian-2A Discordant SGDP 135,760,098 – 136,774,712 1,014,614.0 0.09342975 61 562.7585 2,167.9
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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