| Accession | HsInv0105 | Region of the inversion | chr7:40845900-40846995 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 1,095 bp | Supporting predictions | 7 |
| Inverted allele frequency | 0.7500 | Mechanism of origin | NHEJ |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr7:40845900-40845901 |
| Ancestral orientation | NA | Breakpoint 2 | chr7:40846994-40846995 |
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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 | chr7:40845900-40845900 | Breakpoint 2 | chr7:40846995-40846995 |
| 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 | chr7:40845796-40845796 | Breakpoint 2 | chr7:40847004-40847004 |
| Individuals | 1823 out of 2504 individuals
 | ||
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||||||||||||
| Method | Long-read sequencing | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr7:40845900-40845900 | Breakpoint 2 | chr7:40846995-40846995 | ||||
| Individuals |
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| 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 | chr7:40845882-40845914 | Breakpoint 2 | chr7:40846985-40846995 | ||||
| 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 | chr7:40845669-40846159 | Breakpoint 2 | chr7:40846782-40847137 | ||||
| Individuals |
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| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||
| Name | |||||||||
| Breakpoint 1 | chr7:40844335-40844335 | Breakpoint 2 | chr7:40846241-40846241 | ||||||
| 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 | chr7:40813121-40845928 | Breakpoint 2 | chr7:40846563-40885604 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99734 | ||||||||||||||||||||
| Support | 3 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 | Validated |
| Comment | Tested in sample R11c |
| 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 |
-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 1 STD/STD - 3 STD/INV - 6 INV/INV |
- 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) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 6 | 0.2500 | 0.7500 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 6 | 0.2500 | 0.7500 | > 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
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Utah residents with Northern and Western European ancestry (CEU) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 2 | 3 | 0.2500 | 0.7500 | > 0.5 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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Han Chinese in Beijing, China (CHB) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 2 | 0.0000 | 1.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 2 | 0.0000 | 1.0000 | NA |
| East Asia (EAS)
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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
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Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
| Unknown
|
Unknown summary | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
|---|
+ Breakpoints
| Breakpoint 1 | chr7:40845900-40845901 | Breakpoint 2 | chr7:40846994-40846995 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with a sequenced fosmid, a fosmid split read, and sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
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| Flexibility | 11.01 | GC content | 0.31 | Stability | 1.73 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) with a 2 bp deletion in breakpoint 1 that is located within a small duplication in tandem |
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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
- C7orf10
| Gene position | chr7:40141099-40866891 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-29 00:00:00
| Breakpoint 1 | chr7:40845559-40845928 | Breakpoint 2 | chr7:40846563-40847382 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr7:40845559-40845928 | Breakpoint 2 | chr7:40846563-40847382 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr7:40845559-40845928 | Breakpoint 2 | chr7:40846563-40847382 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-03-12 08:53:11
| Breakpoint 1 | chr7:40845900-40845901 | Breakpoint 2 | chr7:40846994-40846995 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with a sequenced fosmid, a fosmid split read, and sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:34
| Breakpoint 1 | chr7:40845559-40845928 | Breakpoint 2 | chr7:40846563-40847382 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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