| Accession | HsInv0004 | Region of the inversion | chr1:196023412-196024609 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 1,197 bp | Supporting predictions | 5 |
| Inverted allele frequency | 0.1875 | Mechanism of origin | NHEJ |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr1:196023412-196023413 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr1:196024608-196024609 |
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chr1:196023411-196023411 | Breakpoint 2 | chr1:196024609-196024609 |
| Individuals | |||
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||||||||
| Method | Paired-end mapping (PEM), Long-read sequencing | ||||||||||
| Name | |||
| Breakpoint 1 | chr1:196023407-196023407 | Breakpoint 2 | chr1:196024605-196024605 |
| Individuals | 574 out of 2504 individuals
 | ||
| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:196014660-196023411 | Breakpoint 2 | chr1:196024609-196035436 | ||||
| Individuals |
| ||||||
| Description | Next-generation sequencing and analysis by paired-end mapping of a male Han Chinese individual genome | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chr1:196023411-196023411 | Breakpoint 2 | chr1:196024627-196024627 |
| Individuals | |||
| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:196023846-196023846 | Breakpoint 2 | chr1:196024607-196024607 | ||||
| Individuals |
| ||||||
+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 66 STD/STD - 27 STD/INV - 5 INV/INV |
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Inconclusive |
| Comment | Tested in samples A19c and A97b. PCR assay failed. |
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||
| Method | Sequence analysis |
| Status | Validated |
| Comment | Simple inversion validated by sequence analysis of PacBio long reads from long-range PCR amplicons, PacBio long reads from fosmids |
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 42 individuals (No genotypes available) |
| Comment | Inversion genotyped in 42 individuals of diverse origin ( 72 STD alleles/12 INV alleles) |
| Method | Genotype predicted by tag-SNPs |
| Status | Genotyping |
| Genotyping | 208 individuals (No genotypes available) |
| Comment | Inversion genotypes estimated from association with tag SNP rs1627999 (r2 > 0.8) |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
All samples and studies | 4 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
All samples and studies | 64 | 25 | 0.8047 | 0.1953 | > 0.2 |
| Europe (EUR)
|
Europe (EUR) summary | 64 | 25 | 0.8047 | 0.1953 | > 0.2 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
All samples and studies | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
|
All samples and studies | 1 | 0 | 1.0000 | 0.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Vicente-Salvador et al. 2017) | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
| Unknown
|
Unknown summary | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
|---|
+ Breakpoints
| Breakpoint 1 | chr1:196023412-196023413 | Breakpoint 2 | chr1:196024608-196024609 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
|
||||
| Flexibility | 10.05 | GC content | 0.52 | Stability | 1.99 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) mediated by a 2-bp microhomology |
||
+ Evolutionary history
| Ancestral allele | Inverted | Age | ND |
| Derived allele | Standard | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Inverted | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Orangutan | Inverted | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Rhesus macaque | Inverted | Genome sequence comparison | Vicente-Salvador et al. 2017 |
| Chimpanzee | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2018-10-08 15:43:20
| Breakpoint 1 | chr1:196023412-196023413 | Breakpoint 2 | chr1:196024608-196024609 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:04
| Breakpoint 1 | chr1:196023411-196023412 | Breakpoint 2 | chr1:196024608-196024609 |
| Study | Pang et al. 2013 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:15:04
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:04
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:04
| Breakpoint 1 | chr1:196022846-196024291 | Breakpoint 2 | chr1:196023747-196025507 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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