| Accession | HsInv0147 | Region of the inversion | chr12:70226101-70227930 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 1,691 bp | Supporting predictions | 3 |
| Inverted allele frequency | 0.1000 | Mechanism of origin | NAHR |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr12:70226101-70226240 |
| Ancestral orientation | NA | Breakpoint 2 | chr12:70227791-70227930 |
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Human Polymorphic Inversion DataBase
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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 | chr12:70226180-70226180 | Breakpoint 2 | chr12:70227839-70227839 |
| Individuals | 311 out of 2504 individuals
 | ||
| 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 | chr12:70224048-70224048 | Breakpoint 2 | chr12:70227458-70227458 | ||||||
| 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 | chr12:70178919-70227366 | Breakpoint 2 | chr12:70227930-70267977 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99185 | ||||||||||||||||||||
| Support | 2 probes | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| 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 8 STD/STD - 2 STD/INV |
- 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)
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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
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Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| East Asia (EAS)
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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 (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 0 | 1.0000 | 0.0000 | NA |
| Unknown
|
Unknown summary | 2 | 0 | 1.0000 | 0.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chr12:70226101-70226240 | Breakpoint 2 | chr12:70227791-70227930 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NAHR
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| Flexibility | 10.35 | GC content | 0.49 | Stability | 1.94 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 140 bp inverted repeats with 100% identity that consist of part of AluSx elements |
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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
- LGR5
| Gene position | chr12:70119816-70266355 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-18 00:00:00
| Breakpoint 1 | chr12:70221180-70227366 | Breakpoint 2 | chr12:70227930-70232839 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:27
| Breakpoint 1 | chr12:70217238-70227366 | Breakpoint 2 | chr12:70227930-70234268 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:27
| Breakpoint 1 | chr12:70226101-70226240 | Breakpoint 2 | chr12:70227791-70227930 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
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