| Accession | HsInv0379 | Region of the inversion | chr19:21621973-22037101 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 415,128 bp | Supporting predictions | 1 |
| Inverted allele frequency | 0.0114 | Mechanism of origin | NHEJ |
| Functional effect | Breaks one gene | Breakpoint 1 | chr19:21621973^21621974 |
| Ancestral orientation | Standard | Breakpoint 2 | chr19:22037100^22037101 |
| Comments | Asian-specific inversion that disrupts the ZNF257 gene and creates a new fusion transcript
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
- 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 | chr19:21606515-21625294 | Breakpoint 2 | chr19:22034588-22059648 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.15258 | ||||||||||||||||||||
| Support | 5 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Functional impact and evolution of a novel human polymorphic inversion that disrupts a gene and creates a fusion transcript | ||||||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 548 individuals: 547 HapMap/1000GP, 1 Other 530 STD/STD - 11 STD/INV - 1 INV/INV - 6 ND |
| Method | Genotype predicted by tag-SNPs |
| Status | Genotyping |
| Genotyping | 2173 individuals: 2077 HapMap/1000GP, 96 Other 2126 STD/STD - 47 STD/INV |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
African American
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African American in North America (Puig et al. 2015) | 62 | 0 | 1.0000 | 0.0000 | NA |
| African Caribbeans
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African Caribbeans in Barbados (ACB) (Puig et al. 2015) | 86 | 0 | 1.0000 | 0.0000 | NA |
| Esan
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Esan in Nigeria (ESN) (Puig et al. 2015) | 99 | 0 | 1.0000 | 0.0000 | NA |
| Gambian
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Gambian in Western Divisions in the Gambia (GWD) (Puig et al. 2015) | 113 | 0 | 1.0000 | 0.0000 | NA |
| Luhya
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Luhya in Webuye, Kenya (LWK) (Puig et al. 2015) | 114 | 0 | 1.0000 | 0.0000 | NA |
| Mende
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Mende in Sierra Leone (MSL) (Puig et al. 2015) | 78 | 0 | 1.0000 | 0.0000 | NA |
| Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Puig et al. 2015) | 120 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 672 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| British
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British in England and Scotland (GBR) (Puig et al. 2015) | 98 | 0 | 1.0000 | 0.0000 | NA |
| Finnish
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Finnish in Finland (FIN) (Puig et al. 2015) | 103 | 0 | 1.0000 | 0.0000 | NA |
| Iberian
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Iberian Population in Spain (IBS) (Puig et al. 2015) | 107 | 0 | 1.0000 | 0.0000 | NA |
| Northwestern European
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Utah residents with Northern and Western European ancestry (CEU) (Puig et al. 2015) | 83 | 0 | 1.0000 | 0.0000 | NA |
| Toscan
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Toscani in Italia (TSI) (Puig et al. 2015) | 109 | 0 | 1.0000 | 0.0000 | NA |
| Europe (EUR)
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Europe (EUR) summary | 500 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ South Asia (SAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Bengali
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Bengali from Bangladesh (BEB) (Puig et al. 2015) | 86 | 1 | 0.9942 | 0.0058 | > 0.5 |
| Gujarati Indians
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Gujarati Indian from Houston, Texas (GIH) (Puig et al. 2015) | 111 | 0 | 1.0000 | 0.0000 | NA |
| Punjabi
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Punjabi from Lahore, Pakistan (PJL) (Puig et al. 2015) | 96 | 0 | 1.0000 | 0.0000 | NA |
| Sri Lankan
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Sri Lankan Tamil from the UK (STU) (Puig et al. 2015) | 99 | 0 | 1.0000 | 0.0000 | NA |
| Telugu Indians
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Indian Telugu from the UK (ITU) (Puig et al. 2015) | 100 | 0 | 1.0000 | 0.0000 | NA |
| South Asia (SAS)
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South Asia (SAS) summary | 492 | 1 | 0.9990 | 0.0010 | > 0.5 |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Dai Chinese
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Chinese Dai in Xishuangbanna, China (CDX) (Puig et al. 2015) | 93 | 15 | 0.9194 | 0.0806 | > 0.5 |
| Han Chinese
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Han Chinese in Beijing, China (CHB) (Puig et al. 2015) | 110 | 6 | 0.9727 | 0.0273 | > 0.5 |
| Han Chinese South
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Southern Han Chinese (CHS) (Puig et al. 2015) | 111 | 13 | 0.9414 | 0.0586 | > 0.5 |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Puig et al. 2015) | 104 | 5 | 0.9760 | 0.0240 | > 0.5 |
| Malay
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Malay from Malaisia (Puig et al. 2015) | 96 | 7 | 0.9635 | 0.0365 | > 0.5 |
| Vietnamese
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Kinh in Ho Chi Minh City, Vietnam (KHV) (Puig et al. 2015) | 99 | 12 | 0.9394 | 0.0606 | > 0.5 |
| East Asia (EAS)
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East Asia (EAS) summary | 613 | 58 | 0.9527 | 0.0473 | > 0.5 |
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+ America - Admixed (AMR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Colombian
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Colombians from Medellin, Colombia (CLM) (Puig et al. 2015) | 96 | 0 | 1.0000 | 0.0000 | NA |
| Mexican
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Mexican Ancestry from Los Angeles USA (MXL) (Puig et al. 2015) | 68 | 1 | 0.9926 | 0.0074 | > 0.5 |
| Peruvian
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Peruvians from Lima, Peru (PEL) (Puig et al. 2015) | 85 | 0 | 1.0000 | 0.0000 | NA |
| Puerto Ricans
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Puerto Ricans from Puerto Rico (PUR) (Puig et al. 2015) | 105 | 0 | 1.0000 | 0.0000 | NA |
| America - Admixed (AMR)
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America - Admixed (AMR) summary | 354 | 1 | 0.9986 | 0.0014 | > 0.5 |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Puig et al. 2015) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Unknown
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Unknown summary | 1 | 0 | 1.0000 | 0.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chr19:21621973^21621974 | Breakpoint 2 | chr19:22037100^22037101 | ||
| Study | Puig et al. 2015 | ||||
| Description | Breakpoints defined by comparison with a sequenced fosmid and sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
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| Flexibility | 10.85 | GC content | 0.3 | Stability | 1.73 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) with a clean break between two pairs of bases |
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+ Evolutionary history
| Ancestral allele | Standard | Age | 43,450 years |
| Derived allele | Inverted | Origin | Unique |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Genome sequence comparison | Puig et al. 2015 |
+ Age
| Age | Method | Study |
| 43,450 years | Divergence analysis | Puig et al. 2015 |
+ Origin
| Origin | Method | Study |
| Unique | Analysis of breakpoint sequences | Puig et al. 2015 |
+ Functional effects
- ZNF257
| Gene position | chr19:22027105-22065743 |
| Mechanism | Breaks one gene |
| Study | Puig et al. 2015 |
| Effect | 2.9-fold decrease (P = 0.0047) in ZNF257 expression level in lymphoblastoid cell lines of Std/Inv individuals compared to Std/Std ones and generation of a new 468-bp fusion transcript from inverted chromosomes |
| Functional consequences | ZNF257 expression change and new fusion transcript has been associated to other expression changes in multiple genes in trans across the genome |
+ Inversion phenotypical effects
| No significant association found with several general, hematological, metabolic and immunological traits in 3,787 Japanese individuals from the Nagahama cohort | Puig et al. 2015 |
+ Report history
- 2016-12-09 18:11:27
| Breakpoint 1 | chr19:21621973-21621974 | Breakpoint 2 | chr19:22037100-22037101 |
| Study | Puig et al. 2015 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with a sequenced fosmid and sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
- 2016-12-09 18:08:29
| Breakpoint 1 | chr19:21606515-21625294 | Breakpoint 2 | chr19:22034588-22059648 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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