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nstd169 (Giner-Delgado et al. 2019)

Organism:
Human
Study Type:
Collection
Submitter:
Mario Caceres
Description:
Inversions are structural variants that are difficult to detect. We studied 45 common human inversions of 0.1-415 kb in 551 individuals of 7 populations with a new high-throughput genotyping method based on probe hybridization and inverse PCR. We found that most inversions promoted by homologous recombination occur recurrently in humans and great apes and are not tagged by SNPs. Also, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects like gene disruption or gene-expression changes, or association with phenotypic traits. Thus, our results indicate that human inversions have important functional and evolutionary consequences. See Variant Summary counts for nstd169 in dbVar Variant Summary.
Project:
PRJNA531903
Publication(s):
Giner-Delgado et al. 2019

Detailed Information: Download 45 Variant Regions, Download 45 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37.p13 (hg19)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr133RemappedNC_000001.11
NC_000002.12Chr244RemappedNC_000002.12
NC_000003.12Chr322RemappedNC_000003.12
NC_000004.12Chr433RemappedNC_000004.12
NC_000005.10Chr533RemappedNC_000005.10
NC_000006.12Chr655RemappedNC_000006.12
NC_000007.14Chr722RemappedNC_000007.14
NC_000009.12Chr933RemappedNC_000009.12
NC_000011.10Chr1122RemappedNC_000011.10
NC_000013.11Chr1322RemappedNC_000013.11
NC_000014.9Chr1422RemappedNC_000014.9
NC_000016.10Chr1622RemappedNC_000016.10
NC_000017.11Chr1722RemappedNC_000017.11
NC_000019.10Chr1911RemappedNC_000019.10
NC_000021.9Chr2111RemappedNC_000021.9
NC_000023.11ChrX77RemappedNC_000023.11
NC_000024.10ChrY11RemappedNC_000024.10
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr133SubmittedNC_000001.10
NC_000002.11Chr244SubmittedNC_000002.11
NC_000003.11Chr322SubmittedNC_000003.11
NC_000004.11Chr433SubmittedNC_000004.11
NC_000005.9Chr533SubmittedNC_000005.9
NC_000006.11Chr655SubmittedNC_000006.11
NC_000007.13Chr722SubmittedNC_000007.13
NC_000009.11Chr933SubmittedNC_000009.11
NC_000011.9Chr1122SubmittedNC_000011.9
NC_000013.10Chr1322SubmittedNC_000013.10
NC_000014.8Chr1422SubmittedNC_000014.8
NC_000016.9Chr1622SubmittedNC_000016.9
NC_000017.10Chr1722SubmittedNC_000017.10
NC_000019.9Chr1911SubmittedNC_000019.9
NC_000021.8Chr2111SubmittedNC_000021.8
NC_000023.10ChrX77SubmittedNC_000023.10
NC_000024.9ChrY11SubmittedNC_000024.9

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr1330000330000
NC_000002.11Chr2440000440000
NC_000003.11Chr3220000220000
NC_000004.11Chr4330000330000
NC_000005.9Chr5330000330000
NC_000006.11Chr6550000550000
NC_000007.13Chr7220000220000
NC_000009.11Chr9330000330000
NC_000011.9Chr11220000220000
NC_000013.10Chr13220000220000
NC_000014.8Chr14220000220000
NC_000016.9Chr16220000220000
NC_000017.10Chr17220000220000
NC_000019.9Chr19110000110000
NC_000021.8Chr21110000110000
NC_000023.10ChrX752000752000
NC_000024.9ChrY110000110000

Samplesets

Number of Samplesets: 1

Description:
551 individuals from 7 populations of HapMap and 1000 Genomes Projects
Size:
551
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
  • Download Samples as CSV file
  • Samples for sampleset 1 (displaying 100 of the 551 samples)
    Sample IDCell TypeSubject ID SexEthnicitySubject AgeSubject Phenotype
    SAMN11392436Epstein-Barr virus transformed B-LymphocyteGM12044FemaleCEU70 YearsNot reported
    SAMN11392485Epstein-Barr virus transformed B-LymphocyteGM18505FemaleYRINot reported
    SAMN11392464Epstein-Barr virus transformed B-LymphocyteGM12802FemaleCEUNot reported
    SAMN11392448Epstein-Barr virus transformed B-LymphocyteGM12248MaleCEU89 YearsNot reported
    SAMN11392430Epstein-Barr virus transformed B-LymphocyteGM11995FemaleCEU84 YearsNot reported
    SAMN11392392Epstein-Barr virus transformed B-LymphocyteGM07000FemaleCEU66 YearsNot reported
    SAMN11392486Epstein-Barr virus transformed B-LymphocyteGM18506MaleYRINot reported
    SAMN11392463Epstein-Barr virus transformed B-LymphocyteGM12801MaleCEUNot reported
    SAMN11392451Epstein-Barr virus transformed B-LymphocyteGM12707MaleCEUNot reported
    SAMN11392397Epstein-Barr virus transformed B-LymphocyteGM07048MaleCEU43 YearsNot reported
    SAMN11392484Epstein-Barr virus transformed B-LymphocyteGM18504MaleYRINot reported
    SAMN11392476Epstein-Barr virus transformed B-LymphocyteGM12891MaleCEUNot reported
    SAMN11392415Epstein-Barr virus transformed B-LymphocyteGM10859FemaleCEU41 YearsNot reported
    SAMN11392427Epstein-Barr virus transformed B-LymphocyteGM11992MaleCEU86 YearsNot reported
    SAMN11392487Epstein-Barr virus transformed B-LymphocyteGM18507MaleYRINot reported
    SAMN11392454Epstein-Barr virus transformed B-LymphocyteGM12740FemaleCEUNot reported
    SAMN11392410Epstein-Barr virus transformed B-LymphocyteGM10851MaleCEU52 YearsNot reported
    SAMN11392419Epstein-Barr virus transformed B-LymphocyteGM11829MaleCEU72 YearsNot reported
    SAMN11392467Epstein-Barr virus transformed B-LymphocyteGM12814MaleCEUNot reported
    SAMN11392442Epstein-Barr virus transformed B-LymphocyteGM12154MaleCEU92 YearsNot reported
    SAMN11392429Epstein-Barr virus transformed B-LymphocyteGM11994MaleCEU80 YearsNot reported
    SAMN11392444Epstein-Barr virus transformed B-LymphocyteGM12156FemaleCEU81 YearsNot reported
    SAMN11392402Epstein-Barr virus transformed B-LymphocyteGM07357MaleCEU69 YearsNot reported
    SAMN11392479Epstein-Barr virus transformed B-LymphocyteGM18498MaleYRINot reported
    SAMN11392472Epstein-Barr virus transformed B-LymphocyteGM12873FemaleCEUNot reported
    SAMN11392401Epstein-Barr virus transformed B-LymphocyteGM07348FemaleCEU45 YearsNot reported
    SAMN11392468Epstein-Barr virus transformed B-LymphocyteGM12815FemaleCEUNot reported
    SAMN11392452Epstein-Barr virus transformed B-LymphocyteGM12716MaleCEUNot reported
    SAMN11392407Epstein-Barr virus transformed B-LymphocyteGM10839FemaleCEU55 YearsNot reported
    SAMN11392405Epstein-Barr virus transformed B-LymphocyteGM10835MaleCEU39 YearsNot reported
    SAMN11392423Epstein-Barr virus transformed B-LymphocyteGM11839MaleCEU67 YearsNot reported
    SAMN11392420Epstein-Barr virus transformed B-LymphocyteGM11830FemaleCEU63 YearsNot reported
    SAMN11392481Epstein-Barr virus transformed B-LymphocyteGM18501MaleYRINot reported
    SAMN11392428Epstein-Barr virus transformed B-LymphocyteGM11993FemaleCEU80 YearsNot reported
    SAMN11392421Epstein-Barr virus transformed B-LymphocyteGM11831MaleCEU73 YearsNot reported
    SAMN11392475Epstein-Barr virus transformed B-LymphocyteGM12878FemaleCEUNot reported
    SAMN11392441Epstein-Barr virus transformed B-LymphocyteGM12146MaleCEU61 YearsNot reported
    SAMN11392438Epstein-Barr virus transformed B-LymphocyteGM12057FemaleCEU75 YearsNot reported
    SAMN11392406Epstein-Barr virus transformed B-LymphocyteGM10838MaleCEU60 YearsNot reported
    SAMN11392426Epstein-Barr virus transformed B-LymphocyteGM11882FemaleCEU61 YearsNot reported
    SAMN11392446Epstein-Barr virus transformed B-LymphocyteGM12236FemaleCEU86 YearsNot reported
    SAMN11392435Epstein-Barr virus transformed B-LymphocyteGM12043MaleCEU74 YearsNot reported
    SAMN11392456Epstein-Barr virus transformed B-LymphocyteGM12751FemaleCEUNot reported
    SAMN11392425Epstein-Barr virus transformed B-LymphocyteGM11881MaleCEU62 YearsNot reported
    SAMN11392393Epstein-Barr virus transformed B-LymphocyteGM07019FemaleCEU45 YearsNot reported
    SAMN11392453Epstein-Barr virus transformed B-LymphocyteGM12717FemaleCEUNot reported
    SAMN11392483Epstein-Barr virus transformed B-LymphocyteGM18503MaleYRINot reported
    SAMN11392450Epstein-Barr virus transformed B-LymphocyteGM12264MaleCEU72 YearsNot reported
    SAMN11392432Epstein-Barr virus transformed B-LymphocyteGM12004FemaleCEU92 YearsNot reported
    SAMN11392388Epstein-Barr virus transformed B-LymphocyteGM06985FemaleCEU69 YearsNot reported
    SAMN11392447Epstein-Barr virus transformed B-LymphocyteGM12239FemaleCEU61 YearsNot reported
    SAMN11392434Epstein-Barr virus transformed B-LymphocyteGM12006FemaleCEU75 YearsNot reported
    SAMN11392389Epstein-Barr virus transformed B-LymphocyteGM06991FemaleCEU42 YearsNot reported
    SAMN11392470Epstein-Barr virus transformed B-LymphocyteGM12865FemaleCEUNot reported
    SAMN11392455Epstein-Barr virus transformed B-LymphocyteGM12750MaleCEUNot reported
    SAMN11392403Epstein-Barr virus transformed B-LymphocyteGM10830MaleCEU66 YearsNot reported
    SAMN11392457Epstein-Barr virus transformed B-LymphocyteGM12752MaleCEUNot reported
    SAMN11392449Epstein-Barr virus transformed B-LymphocyteGM12249FemaleCEU77 YearsNot reported
    SAMN11392394Epstein-Barr virus transformed B-LymphocyteGM07022MaleCEU63 YearsNot reported
    SAMN11392458Epstein-Barr virus transformed B-LymphocyteGM12753FemaleCEUNot reported
    SAMN11392474Epstein-Barr virus transformed B-LymphocyteGM12875FemaleCEUNot reported
    SAMN11392417Epstein-Barr virus transformed B-LymphocyteGM10861FemaleCEU49 YearsNot reported
    SAMN11392399Epstein-Barr virus transformed B-LymphocyteGM07056FemaleCEU65 YearsNot reported
    SAMN11392408Epstein-Barr virus transformed B-LymphocyteGM10846MaleCEU43 YearsNot reported
    SAMN11392469Epstein-Barr virus transformed B-LymphocyteGM12864MaleCEUNot reported
    SAMN11392437Epstein-Barr virus transformed B-LymphocyteGM12056MaleCEU79 YearsNot reported
    SAMN11392443Epstein-Barr virus transformed B-LymphocyteGM12155MaleCEU86 YearsNot reported
    SAMN11392473Epstein-Barr virus transformed B-LymphocyteGM12874MaleCEUNot reported
    SAMN11392461Epstein-Barr virus transformed B-LymphocyteGM12762MaleCEUNot reported
    SAMN11392431Epstein-Barr virus transformed B-LymphocyteGM12003MaleCEU97 YearsNot reported
    SAMN11392395Epstein-Barr virus transformed B-LymphocyteGM07029MaleCEU47 YearsNot reported
    SAMN11392433Epstein-Barr virus transformed B-LymphocyteGM12005MaleCEU77 YearsNot reported
    SAMN11392418Epstein-Barr virus transformed B-LymphocyteGM10863FemaleCEU43 YearsNot reported
    SAMN11392445Epstein-Barr virus transformed B-LymphocyteGM12234FemaleCEU74 YearsNot reported
    SAMN11392398Epstein-Barr virus transformed B-LymphocyteGM07055FemaleCEU70 YearsNot reported
    SAMN11392465Epstein-Barr virus transformed B-LymphocyteGM12812MaleCEUNot reported
    SAMN11392460Epstein-Barr virus transformed B-LymphocyteGM12761FemaleCEUNot reported
    SAMN11392440Epstein-Barr virus transformed B-LymphocyteGM12145FemaleCEU70 YearsNot reported
    SAMN11392404Epstein-Barr virus transformed B-LymphocyteGM10831FemaleCEU59 YearsNot reported
    SAMN11392412Epstein-Barr virus transformed B-LymphocyteGM10855FemaleCEU37 YearsNot reported
    SAMN11392480Epstein-Barr virus transformed B-LymphocyteGM18500MaleYRINot reported
    SAMN11392422Epstein-Barr virus transformed B-LymphocyteGM11832FemaleCEU58 YearsNot reported
    SAMN11392439Epstein-Barr virus transformed B-LymphocyteGM12144MaleCEU71 YearsNot reported
    SAMN11392411Epstein-Barr virus transformed B-LymphocyteGM10854FemaleCEU42 YearsNot reported
    SAMN11392477Epstein-Barr virus transformed B-LymphocyteGM12892FemaleCEUNot reported
    SAMN11392482Epstein-Barr virus transformed B-LymphocyteGM18502FemaleYRINot reported
    SAMN11392396Epstein-Barr virus transformed B-LymphocyteGM07034MaleCEU71 YearsNot reported
    SAMN11392391Epstein-Barr virus transformed B-LymphocyteGM06994MaleCEU68 YearsNot reported
    SAMN11392424Epstein-Barr virus transformed B-LymphocyteGM11840FemaleCEU67 YearsNot reported
    SAMN11392471Epstein-Barr virus transformed B-LymphocyteGM12872MaleCEUNot reported
    SAMN11392466Epstein-Barr virus transformed B-LymphocyteGM12813FemaleCEUNot reported
    SAMN11392413Epstein-Barr virus transformed B-LymphocyteGM10856MaleCEU46 YearsNot reported
    SAMN11392390Epstein-Barr virus transformed B-LymphocyteGM06993MaleCEU74 YearsNot reported
    SAMN11392459Epstein-Barr virus transformed B-LymphocyteGM12760MaleCEUNot reported
    SAMN11392416Epstein-Barr virus transformed B-LymphocyteGM10860MaleCEU50 YearsNot reported
    SAMN11392409Epstein-Barr virus transformed B-LymphocyteGM10847FemaleCEU38 YearsNot reported
    SAMN11392478Epstein-Barr virus transformed B-LymphocyteGM15510FemaleNot reported
    SAMN11392462Epstein-Barr virus transformed B-LymphocyteGM12763FemaleCEUNot reported
    SAMN11392414Epstein-Barr virus transformed B-LymphocyteGM10857MaleCEU47 YearsNot reported
    SAMN11392400Epstein-Barr virus transformed B-LymphocyteGM07345FemaleCEU69 YearsNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisNumber of Variant Calls
    1GenotypingMLPAGenotyping45

    Validations

    No validation data were submitted for this study.

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