Inversion Report: HsInv0573

Human Polymorphic Inversion DataBase

Inversion Report: HsInv0573

General information

Accession	HsInv0573	Region of the inversion	chr17:40928985-42139672
Status	Validated	Prediction type	Simple
Estimated Inversion Size	835,409 bp	Supporting predictions	3
Inverted allele frequency	0.0737	Mechanism of origin	NAHR
Functional effect	Intergenic breakpoints	Breakpoint 1	chr17:40928985-41060948
Ancestral orientation	Inverted	Breakpoint 2	chr17:41521078-42139672

- Region map

+ Predictions

- Frequency

+ Africa (AFR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
African American	African American in North America (Steinberg et al. 2012)	64	8	0.9375	0.0625	> 0.05
Bakola	Bakola from Cameroon, Central Africa (GYI) (Steinberg et al. 2012)	19	2	0.9474	0.0526	> 0.5
Bantu Kenya	North-Eastern Bantu from Kenya (Bantu_N.E.) (Steinberg et al. 2012)	11	0	1.0000	0.0000	NA
Bantu South Africa	Bantu speakers from South Africa (Bantu_S.E./S.W.) (Steinberg et al. 2012)	8	0	1.0000	0.0000	NA
Beja	Beja from Sudan, Saharan Africa (BEJ) (Steinberg et al. 2012)	18	4	0.8889	0.1111	> 0.5
Biaka	All samples and studies	23	2	0.9565	0.0435	> 0.5
Boni	Boni or Wata from Kenya, Eastern Africa (BOB) (Steinberg et al. 2012)	19	3	0.9211	0.0789	> 0.5
Borana	Borana from Kenya, Eastern Africa (GAX) (Steinberg et al. 2012)	19	1	0.9737	0.0263	> 0.5
Bulala	Bulala from Chad, Central Africa (MNE) (Steinberg et al. 2012)	15	0	1.0000	0.0000	NA
Chagga	Chagga (CGA) (Steinberg et al. 2012)	1	1	0.5000	0.5000	> 0.3
Datog	Datog from Tanzania, Eastern Africa (TCC) (Steinberg et al. 2012)	18	3	0.9167	0.0833	> 0.5
Fulani	Fulani from Cameroon, Central Africa (Steinberg et al. 2012)	19	0	1.0000	0.0000	NA
Hadza	Hadza from Arusha, Tanzania (Steinberg et al. 2012)	36	2	0.9722	0.0278	> 0.5
Iraqw	Iraqw from Tanzania, Eastern Africa (IRK) (Steinberg et al. 2012)	18	1	0.9722	0.0278	> 0.5
Lemande	Lemande from Cameroon, Central Africa (LEM) (Steinberg et al. 2012)	19	0	1.0000	0.0000	NA
Luhya	Luhya in Webuye, Kenya (LWK) (Steinberg et al. 2012)	100	0	1.0000	0.0000	NA
Luo	Luo from Kenya, Eastern Africa (LUO) (Steinberg et al. 2012)	19	0	1.0000	0.0000	NA
Maasai	Maasai in Kinyawa, Kenya (MKK) (Steinberg et al. 2012)	143	13	0.9545	0.0455	< 0.0001
Mandara	Mandara from Cameroon, Central Africa (MFI) (Steinberg et al. 2012)	18	0	1.0000	0.0000	NA
Mandenka	Mandenka from Senegal (Steinberg et al. 2012)	22	1	0.9773	0.0227	> 0.5
Mbuti	Mbuti Pygmy from Democratic Republic of Congo (Steinberg et al. 2012)	13	1	0.9615	0.0385	> 0.5
San	All samples and studies	40	1	0.9875	0.0125	> 0.5
Sandawe	All samples and studies	46	3	0.9674	0.0326	> 0.4
Sengwer	Sengwer from Kenya, Eastern Africa (KLN) (Steinberg et al. 2012)	18	3	0.9167	0.0833	> 0.5
Yoruba	All samples and studies	156	0	1.0000	0.0000	NA

Africa (AFR)	Africa (AFR) summary	882	49	0.9722	0.0278	< 0.0001

+ Middle East/North Africa (MENA)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Bedouin	Bedouin from Negev, Israel (Steinberg et al. 2012)	45	12	0.8667	0.1333	> 0.1
Druze	All samples and studies	42	15	0.8214	0.1786	< 0.05
Mozabite	Mozabite from M'Zab, Algeria (Steinberg et al. 2012)	29	3	0.9483	0.0517	> 0.3
Palestinian	Palestinian from central Israel (Steinberg et al. 2012)	46	13	0.8587	0.1413	< 0.01
Samaritan	Samaritan (SAM) (Steinberg et al. 2012)	2	4	0.0000	1.0000	NA

Middle East/North Africa (MENA)	Middle East/North Africa (MENA) summary	164	47	0.8567	0.1433	< 0.0001

+ Europe (EUR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Adygei	All samples and studies	18	4	0.8889	0.1111	< 0.05
British	British in England and Scotland (GBR) (Steinberg et al. 2012)	99	40	0.7980	0.2020	> 0.2
Danish	Danish (DAN) (Steinberg et al. 2012)	1	2	0.0000	1.0000	NA
Finnish	Finnish in Finland (FIN) (Steinberg et al. 2012)	100	19	0.9050	0.0950	< 0.05
French	French from various regions of France (Steinberg et al. 2012)	28	9	0.8393	0.1607	> 0.05
French Basque	Basque from France (Steinberg et al. 2012)	24	7	0.8542	0.1458	< 0.01
Hungarian	Hungarian (HGR) (Steinberg et al. 2012)	1	2	0.0000	1.0000	NA
Iberian	Iberian Population in Spain (IBS) (Steinberg et al. 2012)	46	28	0.6957	0.3043	> 0.5
North Italian	North Italian from Bergamo, Italy (Steinberg et al. 2012)	11	5	0.7727	0.2273	< 0.05
Northwestern European	All samples and studies	117	26	0.8889	0.1111	< 0.05
Orcadian	Orcadian from Orkney Islands, UK (Steinberg et al. 2012)	15	3	0.9000	0.1000	> 0.1
Russian	Russian from eastern Russia (Steinberg et al. 2012)	25	3	0.9400	0.0600	< 0.005
Sardinian	Sardinian from Sardinia, Italy (Steinberg et al. 2012)	30	15	0.7500	0.2500	> 0.2
Toscan	All samples and studies	110	51	0.7682	0.2318	< 0.0001

Europe (EUR)	Europe (EUR) summary	625	214	0.8288	0.1712	< 0.0001

+ Central Asia (CAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Yakut	Yakut from Siberia (Steinberg et al. 2012)	24	1	0.9792	0.0208	> 0.5

Central Asia (CAS)	Central Asia (CAS) summary	24	1	0.9792	0.0208	> 0.5

+ South Asia (SAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Balochi	Balochi from Pakistan (Steinberg et al. 2012)	24	0	1.0000	0.0000	NA
Brahui	Brahui from Pakistan (Steinberg et al. 2012)	25	3	0.9400	0.0600	> 0.5
Burusho	Burusho from Pakistan (Steinberg et al. 2012)	25	1	0.9800	0.0200	> 0.5
Hazara	Hazara from Afganistan (Steinberg et al. 2012)	22	0	1.0000	0.0000	NA
Kachari	Kachari (KCH) (Steinberg et al. 2012)	1	2	0.0000	1.0000	NA
Kalash	Kalash from Pakistan (Steinberg et al. 2012)	23	3	0.9348	0.0652	> 0.5
Makrani	Makrani from Pakistan (Steinberg et al. 2012)	25	3	0.9400	0.0600	> 0.3
Pathan	Pathan from Pakistan (Steinberg et al. 2012)	22	2	0.9545	0.0455	> 0.5
Sindhi	Sindhi from Pakistan (Steinberg et al. 2012)	24	2	0.9583	0.0417	> 0.5

South Asia (SAS)	South Asia (SAS) summary	191	16	0.9581	0.0419	> 0.1

+ East Asia (EAS)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Cambodian	Cambodians from Cambodia (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Dai Chinese	Dai minority from China (Dai) (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Daur	Daur minority from China (Steinberg et al. 2012)	9	0	1.0000	0.0000	NA
Han Chinese	All samples and studies	145	1	0.9966	0.0034	> 0.5
Han Chinese South	Southern Han Chinese (CHS) (Steinberg et al. 2012)	100	0	1.0000	0.0000	NA
Hezhen	Hezhen minority from China (Steinberg et al. 2012)	8	0	1.0000	0.0000	NA
Japanese	All samples and studies	129	2	0.9922	0.0078	> 0.5
Lahu	Lahu minority from China (Steinberg et al. 2012)	8	0	1.0000	0.0000	NA
Miaozu	Miaozu (Miao) minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Mongola	Mongola minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Naxi	Naxi minority from China (Steinberg et al. 2012)	8	0	1.0000	0.0000	NA
Oroqen	Oroqen minority from China (Steinberg et al. 2012)	9	0	1.0000	0.0000	NA
She	She minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Taiwan Chinese	Chinese from Taiwan (CHT) (Steinberg et al. 2012)	1	1	0.5000	0.5000	> 0.3
Tu	Tu minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Tujia	Tujia minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Uygur	Uygur minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Xibo	Xibo minority from China (Steinberg et al. 2012)	9	0	1.0000	0.0000	NA
Yizu	Yizu (Yi) minority from China (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA

East Asia (EAS)	East Asia (EAS) summary	516	4	0.9961	0.0039	> 0.5

+ Oceania (OCE)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Melanesian	NAN Melanesian from Bougainville, Papua New Guinea (NAN Melanesian) (Steinberg et al. 2012)	10	0	1.0000	0.0000	NA
Papuan	Papuan from New Guinea (Steinberg et al. 2012)	17	0	1.0000	0.0000	NA

Oceania (OCE)	Oceania (OCE) summary	27	0	1.0000	0.0000	NA

+ America - Admixed (AMR)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Colombian	Colombians from Medellin, Colombia (CLM) (Steinberg et al. 2012)	72	25	0.8264	0.1736	> 0.2
Mexican	Mexican Ancestry from Los Angeles USA (MXL) (Steinberg et al. 2012)	70	20	0.8571	0.1429	< 0.05
Puerto Ricans	Puerto Ricans from Puerto Rico (PUR) (Steinberg et al. 2012)	61	16	0.8689	0.1311	> 0.2

America - Admixed (AMR)	America - Admixed (AMR) summary	203	61	0.8498	0.1502	> 0.1

+ America - Natives (AMN)

Population	Sample and Study	Independent individuals	Inverted alleles	Standard frequency	Inverted frequency	HWE p-value
Colombia natives	Piapoco and Curripaco from Colombia (Steinberg et al. 2012)	7	0	1.0000	0.0000	NA
Karitiana	Karitiana from Brazil (Steinberg et al. 2012)	14	0	1.0000	0.0000	NA
Maya	All samples and studies	22	4	0.9091	0.0909	< 0.0001
Pima	All samples and studies	15	1	0.9667	0.0333	> 0.5
Quechua	Quechua (QUE) (Steinberg et al. 2012)	1	1	0.5000	0.5000	> 0.3
Surui	Surui from Brazil (Steinberg et al. 2012)	8	0	1.0000	0.0000	NA

America - Natives (AMN)	America - Natives (AMN) summary	67	6	0.9552	0.0448	< 0.0001

+ Breakpoints

Breakpoint 1	chr17:40928985-41060948	Breakpoint 2	chr17:41521078-42139672
Study	INVFEST curation
Description	Breakpoints defined by InvFEST curators as the largest blocks of inverted segmental duplications
Definition method	Manual curation
Mechanism of origin	NAHR

Flexibility

10.76

GC content

0.38

Stability

1.82

Comments

Inversion generated by non-allelic homologous recombination (NAHR) between large blocks of inverted SDs with high identity

Sequence features

Segmental duplications:

Position SD1	Size (bp)	Position SD2	Size (bp)	Identity	Relative orientation
chr17:40928985-40949277	20,293	chr17:41980250-41997758	17,509	0.982	Inverted
chr17:40928985-40949277	20,293	chr17:41762833-41780263	17,431	0.982	Inverted
chr17:40949281-41006704	57,424	chr17:41922092-41984234	62,143	0.984	Inverted
chr17:40949281-40986574	37,294	chr17:41725190-41766827	41,638	0.980	Inverted
chr17:41018854-41025889	7,036	chr17:41686947-41693926	6,980	0.984	Inverted
chr17:41026708-41060948	34,241	chr17:41650183-41685507	35,325	0.988	Inverted
chr17:41029737-41033098	3,362	chr17:41971263-41974749	3,487	0.910	Inverted
chr17:41029737-41033098	3,362	chr17:41753858-41757343	3,486	0.909	Inverted

+ Evolutionary history

Ancestral allele	Inverted	Age	13,600-3,000,000 years
Derived allele	Standard	Origin	ND

+ Orientation in other species

+ Age

+ Origin

+ Functional effects

- CRHR1

Gene position	chr17:41053492-41268975
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Lower expression associated with STD/STD genotype in cerebellum
Functional consequences	Unknown

- LRRC37A

Gene position	chr17:41728273-41770918
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Decreased expression associated with the STD/STD genotype in frontal cortex, temporal cortex and pons
Functional consequences	Unknown

- LRRC37A4P

Gene position	chr17:40939031-40953672
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Positive association of the expression level with the number of STD alleles in blood
Functional consequences	Unknown

- MAPT

Gene position	chr17:41327541-41461546
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Increased expression associated with the STD/STD genotype in frontal cortex and cerebellum
Functional consequences	Unknown

- MGC57346

Gene position	chr17:41053763-41071112
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Lower expression associated with the STD/STD genotype in blood. Three exons (out of a total of 4) of this gene are shared with the long isoform of gene CRHR1, and it is possible that MGC57346 corresponds to a different splice form of the same gene
Functional consequences	Unknown

- PLEKHM1

Gene position	chr17:40869048-40923929
Mechanism	Intergenic breakpoints
Study	De Jong et al. 2012
Effect	Increased expression associated to STD/STD genotype in cerebellum
Functional consequences	Unknown

+ Inversion phenotypical effects

+ Report history

Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Description	Characterization of a 900-kb inversion polymorphism in human populations
Method	Chromosome-specific assembly

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)

Method	Genotype predicted by tag-SNPs
Status	Validated
Genotyping	2700 individuals: 1392 HapMap/1000GP, 936 HGDP, 372 Other 2203 STD/STD - 434 STD/INV - 63 INV/INV

Method	Fluorescence in situ hybridization (FISH)
Status	Validated
Genotyping	30 individuals: 23 HapMap/1000GP, 7 Other 6 STD/STD - 13 STD/INV - 11 INV/INV

Method	Fluorescence in situ hybridization (FISH)
Status	Validated
Genotyping	27 individuals: 27 HapMap/1000GP 24 STD/STD - 3 STD/INV

Method	Haplotype definition by microsatellite loci genotyping
Status	Validated

Species	Orientation	Method	Study
Rhesus macaque	Inverted	Fluorescence in situ hybridization (FISH)	Zody et al. 2008
Chimpanzee	Polymorphic	Fluorescence in situ hybridization (FISH)	Zody et al. 2008
Bonobo	Polymorphic	Fluorescence in situ hybridization (FISH)	Zody et al. 2008
Orangutan	Polymorphic	Fluorescence in situ hybridization (FISH)	Zody et al. 2008

Age	Method	Study
3,000,000 years	Coalescense analysis	Stefansson et al. 2005
2,300,000 years	Coalescense analysis	Zody et al. 2008
13,600-108,400 years	Short tandem repeat polymorphism data analysis	Donnelly et al. 2010

Breakpoint 1	chr17:40937225-41046061	Breakpoint 2	chr17:41711127-41999689
Assembly	hg18
Definition method	Default informatic definition