nstd203 (Borges-Monroy et al. 2021)

Organism:
Human
Study Type:
Collection
Submitter:
Rebeca Borges Monroy
Description:
In this study we detected polymorphic and de novo retrotransposons within the Simons Simplex Collection to study the role of retrotransposons in Autism Spectrum Disorder. Here, we provide polymorphic Alu, L1, and SVA insertions detected in 4,577 unaffected parental whole-genome sequenced samples of this cohort. These insertions were detected using a novel tool, xTea, which was specifically designed for detecting non-reference retrotransposon insertions with high sensitivity. See Variant Summary counts for nstd203 in dbVar Variant Summary.

Detailed Information: Download 140215 Variant Regions, Download 140215 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr110,59010,590SubmittedNC_000001.11
NC_000002.12Chr210,96910,969SubmittedNC_000002.12
NC_000003.12Chr39,8029,802SubmittedNC_000003.12
NC_000004.12Chr49,0919,091SubmittedNC_000004.12
NC_000005.10Chr58,4078,407SubmittedNC_000005.10
NC_000006.12Chr69,4159,415SubmittedNC_000006.12
NC_000007.14Chr78,2308,230SubmittedNC_000007.14
NC_000008.11Chr86,5616,561SubmittedNC_000008.11
NC_000009.12Chr95,6395,639SubmittedNC_000009.12
NC_000010.11Chr106,2806,280SubmittedNC_000010.11
NC_000011.10Chr116,5666,566SubmittedNC_000011.10
NC_000012.12Chr127,2137,213SubmittedNC_000012.12
NC_000013.11Chr134,9714,971SubmittedNC_000013.11
NC_000014.9Chr144,4664,466SubmittedNC_000014.9
NC_000015.10Chr154,1944,194SubmittedNC_000015.10
NC_000016.10Chr163,6113,611SubmittedNC_000016.10
NC_000017.11Chr174,8844,884SubmittedNC_000017.11
NC_000018.10Chr183,6233,623SubmittedNC_000018.10
NC_000019.10Chr194,1404,140SubmittedNC_000019.10
NC_000020.11Chr202,8962,896SubmittedNC_000020.11
NC_000021.9Chr211,9221,922SubmittedNC_000021.9
NC_000022.11Chr222,0222,022SubmittedNC_000022.11
NC_000023.11ChrX4,6104,610SubmittedNC_000023.11
NC_000024.10ChrY113113SubmittedNC_000024.10
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr110,53610,536RemappedNC_000001.10
NC_000002.11Chr210,95310,953RemappedNC_000002.11
NC_000003.11Chr39,7519,751RemappedNC_000003.11
NC_000004.11Chr49,1039,103RemappedNC_000004.11
NC_000005.9Chr58,4008,400RemappedNC_000005.9
NC_000006.11Chr69,3719,371RemappedNC_000006.11
NC_000007.13Chr78,1668,166RemappedNC_000007.13
NC_000008.10Chr86,5486,548RemappedNC_000008.10
NC_000009.11Chr95,6425,642RemappedNC_000009.11
NC_000010.10Chr106,2096,209RemappedNC_000010.10
NC_000011.9Chr116,5586,558RemappedNC_000011.9
NC_000012.11Chr127,2077,207RemappedNC_000012.11
NC_000013.10Chr134,9574,957RemappedNC_000013.10
NC_000014.8Chr144,4084,408RemappedNC_000014.8
NC_000015.9Chr154,1814,181RemappedNC_000015.9
NC_000016.9Chr163,6043,604RemappedNC_000016.9
NC_000017.10Chr174,7834,783RemappedNC_000017.10
NC_000018.9Chr183,6183,618RemappedNC_000018.9
NC_000019.9Chr194,0044,004RemappedNC_000019.9
NC_000020.10Chr202,6102,610RemappedNC_000020.10
NC_000021.8Chr211,8711,871RemappedNC_000021.8
NC_000022.10Chr221,8501,850RemappedNC_000022.10
NC_000023.10ChrX4,5694,569RemappedNC_000023.10
NC_000024.9ChrY125125RemappedNC_000024.9
NT_113923.1Unplaced|NT_113923.188RemappedNT_113923.1
NT_167227.1Unplaced|NT_167227.122RemappedNT_167227.1
NT_167213.1Unplaced|NT_167213.144RemappedNT_167213.1
NT_167225.1Unplaced|NT_167225.11010RemappedNT_167225.1
NT_167226.1Unplaced|NT_167226.17575RemappedNT_167226.1
NT_167229.1Unplaced|NT_167229.11212RemappedNT_167229.1
NT_167211.1Unplaced|NT_167211.144RemappedNT_167211.1
NT_167223.1Unplaced|NT_167223.111RemappedNT_167223.1
NT_167228.1Unplaced|NT_167228.11717RemappedNT_167228.1
NT_167231.1Unplaced|NT_167231.133RemappedNT_167231.1
NT_167233.1Unplaced|NT_167233.199RemappedNT_167233.1
NT_167207.1Chr1|NT_167207.11212RemappedNT_167207.1
NW_003315903.1Chr1|NW_003315903.111RemappedNW_003315903.1
NW_003315904.1Chr1|NW_003315904.144RemappedNW_003315904.1
NW_003571030.1Chr1|NW_003571030.199RemappedNW_003571030.1
NW_003871055.3Chr1|NW_003871055.3115115RemappedNW_003871055.3
NW_003871056.3Chr1|NW_003871056.32323RemappedNW_003871056.3
NW_003871057.1Chr1|NW_003871057.12525RemappedNW_003871057.1
NW_004070865.1Chr1|NW_004070865.144RemappedNW_004070865.1
NW_003571032.1Chr2|NW_003571032.188RemappedNW_003571032.1
NW_004504299.1Chr2|NW_004504299.12626RemappedNW_004504299.1
NW_003315910.1Chr3|NW_003315910.166RemappedNW_003315910.1
NW_003315911.1Chr3|NW_003315911.188RemappedNW_003315911.1
NW_003315912.1Chr3|NW_003315912.122RemappedNW_003315912.1
NW_003871058.1Chr3|NW_003871058.11111RemappedNW_003871058.1
NW_003871059.1Chr3|NW_003871059.177RemappedNW_003871059.1
NW_003871060.1Chr3|NW_003871060.111RemappedNW_003871060.1
NW_004775426.1Chr3|NW_004775426.166RemappedNW_004775426.1
NT_113885.1Chr4|NT_113885.11919RemappedNT_113885.1
NT_167250.1Chr4|NT_167250.111RemappedNT_167250.1
NW_003315916.1Chr4|NW_003315916.144RemappedNW_003315916.1
NW_003571034.1Chr4|NW_003571034.133RemappedNW_003571034.1
NW_003571035.1Chr4|NW_003571035.155RemappedNW_003571035.1
NW_004775427.1Chr4|NW_004775427.14040RemappedNW_004775427.1
NT_113948.1Chr5|NT_113948.111RemappedNT_113948.1
NW_003871061.1Chr5|NW_003871061.11414RemappedNW_003871061.1
NW_004775428.1Chr5|NW_004775428.11818RemappedNW_004775428.1
NT_167246.1Chr6|NT_167246.199RemappedNT_167246.1
NT_167248.1Chr6|NT_167248.199RemappedNT_167248.1
NT_167249.1Chr6|NT_167249.111RemappedNT_167249.1
NW_003871062.1Chr6|NW_003871062.12121RemappedNW_003871062.1
NW_004070866.1Chr6|NW_004070866.155RemappedNW_004070866.1
NW_004504300.1Chr6|NW_004504300.15656RemappedNW_004504300.1
NW_004775429.1Chr6|NW_004775429.133RemappedNW_004775429.1
NW_003571037.1Chr7|NW_003571037.12525RemappedNW_003571037.1
NW_003571038.1Chr7|NW_003571038.11818RemappedNW_003571038.1
NW_003571039.1Chr7|NW_003571039.122RemappedNW_003571039.1
NW_003571040.1Chr7|NW_003571040.14242RemappedNW_003571040.1
NW_003571041.1Chr7|NW_003571041.11111RemappedNW_003571041.1
NW_003871064.1Chr7|NW_003871064.1156156RemappedNW_003871064.1
NW_003871065.1Chr7|NW_003871065.13232RemappedNW_003871065.1
NW_004775430.1Chr7|NW_004775430.11616RemappedNW_004775430.1
NW_003315923.1Chr8|NW_003315923.12323RemappedNW_003315923.1
NW_003315924.1Chr8|NW_003315924.12727RemappedNW_003315924.1
NW_003571042.1Chr8|NW_003571042.177RemappedNW_003571042.1
NW_003871066.2Chr8|NW_003871066.222RemappedNW_003871066.2
NW_004775431.1Chr8|NW_004775431.166RemappedNW_004775431.1
NT_113914.1Chr9|NT_113914.111RemappedNT_113914.1
NT_113916.2Chr9|NT_113916.211RemappedNT_113916.2
NW_003315925.1Chr9|NW_003315925.11313RemappedNW_003315925.1
NW_003871067.1Chr9|NW_003871067.155RemappedNW_003871067.1
NW_004070868.1Chr9|NW_004070868.111RemappedNW_004070868.1
NW_004070869.1Chr9|NW_004070869.111RemappedNW_004070869.1
NW_004504301.1Chr9|NW_004504301.133RemappedNW_004504301.1
NW_003315932.1Chr10|NW_003315932.12727RemappedNW_003315932.1
NW_003315933.1Chr10|NW_003315933.122RemappedNW_003315933.1
NW_003571043.1Chr10|NW_003571043.111RemappedNW_003571043.1
NW_003871068.1Chr10|NW_003871068.14545RemappedNW_003871068.1
NW_003871069.1Chr10|NW_003871069.111RemappedNW_003871069.1
NW_003871070.1Chr10|NW_003871070.199RemappedNW_003871070.1
NW_003871071.1Chr10|NW_003871071.11515RemappedNW_003871071.1
NW_004070870.1Chr10|NW_004070870.122RemappedNW_004070870.1
NW_004504302.1Chr10|NW_004504302.11010RemappedNW_004504302.1
NW_004775432.1Chr10|NW_004775432.16666RemappedNW_004775432.1
NW_003571045.1Chr11|NW_003571045.188RemappedNW_003571045.1
NW_003571046.1Chr11|NW_003571046.11313RemappedNW_003571046.1
NW_003871072.2Chr11|NW_003871072.25858RemappedNW_003871072.2
NW_003871075.1Chr11|NW_003871075.11818RemappedNW_003871075.1
NW_003871076.1Chr11|NW_003871076.11616RemappedNW_003871076.1
NW_003871078.1Chr11|NW_003871078.11010RemappedNW_003871078.1
NW_003871079.1Chr11|NW_003871079.11313RemappedNW_003871079.1
NW_003871080.1Chr11|NW_003871080.11919RemappedNW_003871080.1
NW_003871081.1Chr11|NW_003871081.122RemappedNW_003871081.1
NW_003871082.1Chr11|NW_003871082.111RemappedNW_003871082.1
NW_004070871.1Chr11|NW_004070871.11717RemappedNW_004070871.1
NW_003571048.1Chr12|NW_003571048.11010RemappedNW_003571048.1
NW_003871083.2Chr12|NW_003871083.22626RemappedNW_003871083.2
NW_004504303.2Chr12|NW_004504303.299RemappedNW_004504303.2
NW_003571051.1Chr13|NW_003571051.111RemappedNW_003571051.1
NW_004166863.1Chr14|NW_004166863.17070RemappedNW_004166863.1
NW_003871084.1Chr15|NW_003871084.133RemappedNW_003871084.1
NW_003871085.1Chr16|NW_003871085.133RemappedNW_003871085.1
NT_113941.1Chr17|NT_113941.199RemappedNT_113941.1
NW_003315947.1Chr17|NW_003315947.11313RemappedNW_003315947.1
NW_003315948.2Chr17|NW_003315948.233RemappedNW_003315948.2
NW_003315949.1Chr17|NW_003315949.155RemappedNW_003315949.1
NW_003315950.2Chr17|NW_003315950.22323RemappedNW_003315950.2
NW_003571052.1Chr17|NW_003571052.12626RemappedNW_003571052.1
NW_003871087.1Chr17|NW_003871087.199RemappedNW_003871087.1
NW_003871088.1Chr17|NW_003871088.12222RemappedNW_003871088.1
NW_003871089.1Chr17|NW_003871089.11111RemappedNW_003871089.1
NW_003871090.1Chr17|NW_003871090.155RemappedNW_003871090.1
NW_004070872.2Chr17|NW_004070872.21010RemappedNW_004070872.2
NW_004166864.2Chr17|NW_004166864.266RemappedNW_004166864.2
NW_004775433.1Chr17|NW_004775433.12323RemappedNW_004775433.1
NW_003571053.2Chr19|NW_003571053.26868RemappedNW_003571053.2
NW_003871094.1Chr19|NW_003871094.13030RemappedNW_003871094.1
NW_004166865.1Chr19|NW_004166865.1122122RemappedNW_004166865.1
NW_004775434.1Chr19|NW_004775434.12323RemappedNW_004775434.1
NW_003871095.1Chr20|NW_003871095.111RemappedNW_003871095.1
NW_004504304.1Chr20|NW_004504304.11010RemappedNW_004504304.1
NW_003315968.1Chr21|NW_003315968.11111RemappedNW_003315968.1
NW_003315970.1Chr21|NW_003315970.111RemappedNW_003315970.1
NW_004775435.1Chr21|NW_004775435.188RemappedNW_004775435.1
NT_113961.1Chr22|NT_113961.122RemappedNT_113961.1
NW_003871096.1Chr22|NW_003871096.11717RemappedNW_003871096.1
NT_167235.1Chr22|NT_167235.14949RemappedNT_167235.1
NW_003571064.2ChrX|NW_003571064.2100100RemappedNW_003571064.2
NW_003871098.1ChrX|NW_003871098.11414RemappedNW_003871098.1
NW_003871099.1ChrX|NW_003871099.11111RemappedNW_003871099.1
NW_003871100.1ChrX|NW_003871100.15151RemappedNW_003871100.1
NW_003871101.3ChrX|NW_003871101.366RemappedNW_003871101.3
NW_003871102.1ChrX|NW_003871102.111RemappedNW_003871102.1
NW_003871103.3ChrX|NW_003871103.35757RemappedNW_003871103.3
NW_004070877.1ChrX|NW_004070877.19393RemappedNW_004070877.1
NW_004070878.1ChrX|NW_004070878.11616RemappedNW_004070878.1
NW_004070879.1ChrX|NW_004070879.11111RemappedNW_004070879.1
NW_004070880.2ChrX|NW_004070880.27575RemappedNW_004070880.2
NW_004070881.1ChrX|NW_004070881.11212RemappedNW_004070881.1
NW_004070882.1ChrX|NW_004070882.11414RemappedNW_004070882.1
NW_004070883.1ChrX|NW_004070883.11010RemappedNW_004070883.1
NW_004070884.1ChrX|NW_004070884.11010RemappedNW_004070884.1
NW_004070885.1ChrX|NW_004070885.155RemappedNW_004070885.1
NW_004070886.1ChrX|NW_004070886.11313RemappedNW_004070886.1
NW_004070887.1ChrX|NW_004070887.11414RemappedNW_004070887.1
NW_004070888.1ChrX|NW_004070888.188RemappedNW_004070888.1
NW_004070889.1ChrX|NW_004070889.13434RemappedNW_004070889.1
NW_004070890.2ChrX|NW_004070890.2167167RemappedNW_004070890.2
NW_004070891.1ChrX|NW_004070891.14747RemappedNW_004070891.1
NW_004070892.1ChrX|NW_004070892.188RemappedNW_004070892.1
NW_004070893.1ChrX|NW_004070893.122RemappedNW_004070893.1
NW_004166866.1ChrX|NW_004166866.199RemappedNW_004166866.1

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.11Chr110,59010,419022014910,59010,4190220149
NC_000002.12Chr210,96910,907310173210,96910,9073101732
NC_000003.12Chr39,8029,70101057349,8029,7010105734
NC_000004.12Chr49,0919,037002529,0919,03700252
NC_000005.10Chr58,4078,370006318,4078,37000631
NC_000006.12Chr69,4159,27801636859,4159,2780163685
NC_000007.14Chr78,2307,938512222538,2307,93851222253
NC_000008.11Chr86,5616,502212546,5616,50221254
NC_000009.12Chr95,6395,5970020225,6395,597002022
NC_000010.11Chr106,2806,06700551586,2806,0670055158
NC_000011.10Chr116,5666,3990001676,5666,399000167
NC_000012.12Chr127,2137,163005457,2137,16300545
NC_000013.11Chr134,9714,96400704,9714,9640070
NC_000014.9Chr144,4664,443124164,4664,44312416
NC_000015.10Chr154,1944,177101334,1944,17710133
NC_000016.10Chr163,6113,598001123,6113,59800112
NC_000017.11Chr174,8844,7620526914,8844,762052691
NC_000018.10Chr183,6233,61800503,6233,6180050
NC_000019.10Chr194,1404,01010111184,1404,0101011118
NC_000020.11Chr202,8962,695233155112,8962,69523315511
NC_000021.9Chr211,9221,894021881,9221,89402188
NC_000022.11Chr222,0221,96252415162,0221,9625241516
NC_000023.11ChrX4,6103,84111107574,6103,8411110757
NC_000024.10ChrY11311000301131100030

Samplesets

Number of Samplesets: 1

Name:
SSC Parents Transposable Elements Insertions
Size:
4,577
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
  • Download Samples as CSV file
  • Samples for sampleset 1 (displaying 100 of the 4577 samples)
    Sample IDSubject ID SexSubject Phenotype
    SSC00397.finalSSC00397.finalFemaleNot reported
    SSC00327.finalSSC00327.finalFemaleNot reported
    SSC00139.finalSSC00139.finalMaleNot reported
    SSC00138.finalSSC00138.finalFemaleNot reported
    SSC00265.finalSSC00265.finalFemaleNot reported
    SSC00100.finalSSC00100.finalFemaleNot reported
    SS0012978.finalSS0012978.finalFemaleNot reported
    SSC00091.finalSSC00091.finalFemaleNot reported
    SSC00351.finalSSC00351.finalFemaleNot reported
    SSC00398.finalSSC00398.finalMaleNot reported
    SSC00118.finalSSC00118.finalFemaleNot reported
    SSC00078.finalSSC00078.finalFemaleNot reported
    SS0013016.finalSS0013016.finalMaleNot reported
    SS0013035.finalSS0013035.finalMaleNot reported
    SSC00182.finalSSC00182.finalFemaleNot reported
    SSC00400.finalSSC00400.finalMaleNot reported
    SSC00321.finalSSC00321.finalFemaleNot reported
    SSC00369.finalSSC00369.finalMaleNot reported
    SSC00047.finalSSC00047.finalMaleNot reported
    SSC00255.finalSSC00255.finalFemaleNot reported
    SSC00229.finalSSC00229.finalMaleNot reported
    SSC00059.finalSSC00059.finalMaleNot reported
    SSC00134.finalSSC00134.finalFemaleNot reported
    SSC00101.finalSSC00101.finalMaleNot reported
    SSC00381.finalSSC00381.finalFemaleNot reported
    SSC00253.finalSSC00253.finalFemaleNot reported
    SSC00235.finalSSC00235.finalFemaleNot reported
    SSC00318.finalSSC00318.finalFemaleNot reported
    SSC00367.finalSSC00367.finalFemaleNot reported
    SSC00236.finalSSC00236.finalMaleNot reported
    SSC00008.finalSSC00008.finalFemaleNot reported
    SSC00350.finalSSC00350.finalMaleNot reported
    SSC00046.finalSSC00046.finalFemaleNot reported
    SSC00151.finalSSC00151.finalMaleNot reported
    SSC00354.finalSSC00354.finalMaleNot reported
    SSC00347.finalSSC00347.finalFemaleNot reported
    SSC00341.finalSSC00341.finalMaleNot reported
    SSC00133.finalSSC00133.finalMaleNot reported
    SSC00362.finalSSC00362.finalFemaleNot reported
    SSC00256.finalSSC00256.finalMaleNot reported
    SSC00333.finalSSC00333.finalMaleNot reported
    SSC00104.finalSSC00104.finalMaleNot reported
    SSC00095.finalSSC00095.finalMaleNot reported
    SSC00297.finalSSC00297.finalFemaleNot reported
    SS0013015.finalSS0013015.finalFemaleNot reported
    SSC00013.finalSSC00013.finalMaleNot reported
    SSC00005.finalSSC00005.finalFemaleNot reported
    SSC00150.finalSSC00150.finalFemaleNot reported
    SSC00162.finalSSC00162.finalFemaleNot reported
    SS0012997.finalSS0012997.finalMaleNot reported
    SSC00034.finalSSC00034.finalMaleNot reported
    SSC00266.finalSSC00266.finalMaleNot reported
    SSC00090.finalSSC00090.finalMaleNot reported
    SSC00353.finalSSC00353.finalFemaleNot reported
    SSC00336.finalSSC00336.finalFemaleNot reported
    SS0013022.finalSS0013022.finalMaleNot reported
    SSC00257.finalSSC00257.finalMaleNot reported
    SSC00103.finalSSC00103.finalFemaleNot reported
    SSC00298.finalSSC00298.finalMaleNot reported
    SSC00030.finalSSC00030.finalFemaleNot reported
    SSC00163.finalSSC00163.finalMaleNot reported
    SSC00382.finalSSC00382.finalMaleNot reported
    SSC00334.finalSSC00334.finalFemaleNot reported
    SSC00178.finalSSC00178.finalMaleNot reported
    SSC00096.finalSSC00096.finalFemaleNot reported
    SSC00112.finalSSC00112.finalFemaleNot reported
    SSC00113.finalSSC00113.finalMaleNot reported
    SSC00186.finalSSC00186.finalMaleNot reported
    SSC00326.finalSSC00326.finalFemaleNot reported
    SSC00183.finalSSC00183.finalMaleNot reported
    SSC00033.finalSSC00033.finalFemaleNot reported
    SSC00174.finalSSC00174.finalFemaleNot reported
    SSC00232.finalSSC00232.finalMaleNot reported
    SSC00084.finalSSC00084.finalFemaleNot reported
    SSC00083.finalSSC00083.finalMaleNot reported
    SSC00252.finalSSC00252.finalMaleNot reported
    SS0013002.finalSS0013002.finalFemaleNot reported
    SSC00117.finalSSC00117.finalMaleNot reported
    SSC00058.finalSSC00058.finalFemaleNot reported
    SSC00012.finalSSC00012.finalFemaleNot reported
    SSC00175.finalSSC00175.finalMaleNot reported
    SSC00007.finalSSC00007.finalMaleNot reported
    SS0013028.finalSS0013028.finalFemaleNot reported
    SS0013004.finalSS0013004.finalMaleNot reported
    SSC00322.finalSSC00322.finalMaleNot reported
    SSC00258.finalSSC00258.finalFemaleNot reported
    SSC00276.finalSSC00276.finalMaleNot reported
    SSC00031.finalSSC00031.finalMaleNot reported
    SSC00228.finalSSC00228.finalFemaleNot reported
    SSC00361.finalSSC00361.finalMaleNot reported
    SSC00348.finalSSC00348.finalMaleNot reported
    SSC00231.finalSSC00231.finalFemaleNot reported
    SSC00299.finalSSC00299.finalFemaleNot reported
    SSC00004.finalSSC00004.finalMaleNot reported
    SSC00177.finalSSC00177.finalFemaleNot reported
    SSC00238.finalSSC00238.finalFemaleNot reported
    SSC00185.finalSSC00185.finalFemaleNot reported
    SSC00273.finalSSC00273.finalMaleNot reported
    SSC00079.finalSSC00079.finalMaleNot reported
    SS0013001.finalSS0013001.finalFemaleNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisNumber of Variant Calls
    1DiscoverySequencingSplit read and paired-end mapping140,215

    Validations

    No validation data were submitted for this study.

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