| Accession | HsInv0006 | Region of the inversion | chr1:203445230-203445457 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 157 bp | Supporting predictions | 3 |
| Inverted allele frequency | 0.5833 | Mechanism of origin | NHEJ |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr1:203445230-203445294 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr1:203445378-203445457 |
| Comments | Derived allele includes two duplications of 41-bp and 39-bp flanking the inverted region
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Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| 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 | chr1:203445149-203445149 | Breakpoint 2 | chr1:203445430-203445430 |
| Individuals | 1386 out of 2504 individuals
 | ||
| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:203444971-203445391 | Breakpoint 2 | chr1:203445288-203445653 | ||||
| Individuals |
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| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr1:203445294-203445294 | Breakpoint 2 | chr1:203445397-203445397 | ||||
| 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 20 STD/STD - 44 STD/INV - 34 INV/INV |
| 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 fosmids |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
Yoruba in Ibadan, Nigeria (YRI) (Vicente-Salvador et al. 2017) | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
|---|
+ 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 | 76 | 0.4062 | 0.5938 | > 0.4 |
| Europe (EUR)
|
Europe (EUR) summary | 64 | 76 | 0.4062 | 0.5938 | > 0.4 |
|---|
+ 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 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
|
Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 4 | 0.0000 | 1.0000 | 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 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Unknown
|
Unknown summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ Breakpoints
| Breakpoint 1 | chr1:203445230-203445294 | Breakpoint 2 | chr1:203445378-203445457 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
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| Flexibility | 10.77 | GC content | 0.33 | Stability | 1.74 |
| 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. 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
- DSTYK
| Gene position | chr1:203378253-203447350 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2018-10-08 16:25:54
| Breakpoint 1 | chr1:203445230-203445294 | Breakpoint 2 | chr1:203445378-203445457 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr1:203444791-203445571 | Breakpoint 2 | chr1:203445053-203445888 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:15:05
| Breakpoint 1 | chr1:203445230-203445294 | Breakpoint 2 | chr1:203445378-203445457 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:15:05
| Breakpoint 1 | chr1:203444791-203445571 | Breakpoint 2 | chr1:203445053-203445888 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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