| Accession | HsInv0260 | Region of the inversion | chr2:184277421-184280256 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 2,334 bp | Supporting predictions | 4 |
| Inverted allele frequency | 0.2778 | Mechanism of origin | FoSTeS or NHEJ |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr2:184277421-184277442 |
| Ancestral orientation | NA | Breakpoint 2 | chr2:184279274-184280256 |
| Comments | Inverted allele includes a 1.0 kb inverted duplication and a small deletion 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 | chr2:184277442-184277442 | Breakpoint 2 | chr2:184278918-184278918 |
| Individuals | |||
| Name | |||
| Breakpoint 1 | chr2:184277524-184277524 | Breakpoint 2 | chr2:184280259-184280259 |
| 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 | chr2:184277324-184277324 | Breakpoint 2 | chr2:184280313-184280313 |
| Individuals | 742 out of 2504 individuals
 | ||
- Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr2:184246706-184277779 | Breakpoint 2 | chr2:184280255-184312212 | ||||||||||||||||||||
| D/C Score | 0.29 | Disc. Support Prob. | 0.99603 | ||||||||||||||||||||
| Support | 5 probes | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| 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 sample A139c. PCR assay failed. |
| Method | Polymerase chain reaction (PCR) |
| Status | Inconclusive |
| Comment | Tested in sample A139c. PCR assay failed. |
-Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 5 STD/STD - 3 STD/INV - 1 INV/INV - 1 ND |
- 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) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
| Africa (AFR)
|
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) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
| Europe (EUR)
|
Europe (EUR) summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
|---|
+ 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) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
|
Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| Unknown
|
Unknown summary | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
|---|
+ Breakpoints
| Breakpoint 1 | chr2:184277421-184277442 | Breakpoint 2 | chr2:184279274-184280256 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with two sequenced fosmids and sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS or NHEJ
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| Flexibility | 11.06 | GC content | 0.27 | Stability | 1.74 |
| Comments |
Inverted region is flanked by a 1.0 kb inverted duplication and a small deletion and was probably generated by several FoSTeS events mediated by microhomology or NHEJ of staggered breaks. |
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+ Evolutionary history
| Ancestral allele | NA | Age | ND |
| Derived allele | NA | Origin | ND |
+ Orientation in other species
Not defined
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-29 00:00:00
| Breakpoint 1 | chr2:184272442-184277779 | Breakpoint 2 | chr2:184280255-184283918 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr2:184272524-184277779 | Breakpoint 2 | chr2:184280255-184283918 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr2:184272324-184277779 | Breakpoint 2 | chr2:184280255-184285313 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:31
| Breakpoint 1 | chr2:184246706-184277779 | Breakpoint 2 | chr2:184280255-184312212 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:31
| Breakpoint 1 | chr2:184277421-184277442 | Breakpoint 2 | chr2:184279274-184280256 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with two sequenced fosmids and sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
Hosted by the Comparative and Functional Genomics group at the Hospital del Mar Research Institute
Contact us at invfestdb@researchmar.net
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