| Accession | HsInv0059 | Region of the inversion | chr6:89980347-89980670 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 316 bp | Supporting predictions | 4 |
| Inverted allele frequency | 0.7986 | Mechanism of origin | NH |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr6:89980347-89980355 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr6:89980662-89980670 |
| Comments | Derived allele includes two duplications of 2 bp and 7 bp and a deletion of 0.6 kb flanking the inverted region
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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 | chr6:89980309-89980309 | Breakpoint 2 | chr6:89980678-89980678 |
| Individuals | |||
| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr6:89979710-89980058 | Breakpoint 2 | chr6:89980640-89980759 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr6:89980114-89980352 | Breakpoint 2 | chr6:89980492-89980670 | ||||
| Individuals |
| ||||||
| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr6:89980353-89980353 | Breakpoint 2 | chr6:89980661-89980661 | ||||
| Individuals |
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+ 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 4 STD/STD - 29 STD/INV - 65 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 | Validated |
| Comment | Tested in sample A105c |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017) | 4 | 7 | 0.1250 | 0.8750 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 7 | 0.1250 | 0.8750 | > 0.5 |
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+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
Utah residents with Northern and Western European ancestry (CEU) (Vicente-Salvador et al. 2017) | 64 | 104 | 0.1875 | 0.8125 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 64 | 104 | 0.1875 | 0.8125 | > 0.5 |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
Han Chinese in Beijing, China (CHB) (Vicente-Salvador et al. 2017) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Vicente-Salvador et al. 2017) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
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+ Breakpoints
| Breakpoint 1 | chr6:89980347-89980355 | Breakpoint 2 | chr6:89980662-89980670 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NH
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| Flexibility | 10.94 | GC content | 0.24 | Stability | 1.67 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) of staggered breaks that generated duplications of 41 bp and 39 bp flanking the inverted region, plus a 0.6 deletion in BP2. Breakpoint positions comprise the staggered breaks plus the duplicated sequences. |
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+ 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) | Vicente-Salvador et al. 2017 |
| Gorilla | Inverted | Polymerase chain reaction (PCR) | Vicente-Salvador et al. 2017 |
| Rhesus macaque | Inverted | Genome sequence comparison | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
- GABRR1
| Gene position | chr6:89943941-89984215 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2018-10-26 17:37:22
| Breakpoint 1 | chr6:89980347-89980355 | Breakpoint 2 | chr6:89980662-89980670 |
| 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 | chr6:89979752-89980714 | Breakpoint 2 | chr6:89980070-89981092 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:01
| Breakpoint 1 | chr6:89979752-89980714 | Breakpoint 2 | chr6:89980070-89981092 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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