ALFRED: allele frequency database

The ALlele FREquency Database
ALFRED is a resource of gene frequency data on human populations
supported by the Yale Center for Medical Informatics.

00ALFRED detailed record information

Population Information

Name	ALFRED UID	Primary Language	Language Family
Japanese	PO000010B	JAPANESE	JAPANESE

Synonyms:
Geographic Location¹: 46N, 130E; 30N, 146E

Sites typed for this population: View List
Population Samples: See Sample Information
External Resources: Japan and Connecticut Record Ethnologue: Language Description Record Encarta: Country Description Record
References: See references
Population Description: Japan was first settled perhaps 30,000 years ago by hunter-gatherers who reached the islands via land bridges from Asia. Around 12,000 years ago, this population gave rise to the Jomon culture, a group of sedentary, ceramic-using village dwellers who hunted, fished, and practiced rudimentary agriculture. In the third century BC the Jomon were replaced by the Yayoi, metal-using rice farmers from the Asian mainland. The exact nature of this replacement is a subject of debate, but it is the Yayoi who may be the ancestors of the modern Japanese. Modern Japanese culture has been heavily influenced by China and Korea, but there do not appear to have been additional invasions or large-scale population replacements after the Yayoi period. Japanese, spoken by more than 99% of Japan's roughly 125,000,000 inhabitants, is considered by some linguists to be a language isolate, not closely related to any other languages. Others place it in the Altaic language family along with Turkish, Mongolian, and Korean.
References:
- Kitaoji H. "The structure of the Japanese family". American Anthropologist 73:1036-57. (1971)

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA000901K

Sample Description:This sample consists of healthy unrelated Japanese individuals from the Nagoya area.

Number of Chromosomes: 416

Relation to Other Samples:

References:
- Yoshimoto T, Tamaki K, Katsumata S, Huang XL, Uchihi R, Tanaka M, Uchida H, Yamamoto T, Chen S, Armour JA, Katsumata Y. "Sequence analysis of alleles at a microsatellite locus D14S299 (wg1c5) and population genetic comparisons". Int J Legal Med 113:15-18. (1999) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA000909S

Sample Description:This sample consists of unrelated Japanese from Sendai, in the Northeast region of Japan.

Number of Chromosomes: 240

Relation to Other Samples:

References:
- Nata M, Kimura T, Hashiyada M, He P, Yan W, Li X, Funayama M, Sagisaka K. "Allele frequencies of eight STRs in Japanese and Chinese". Int J Legal Med 112:396-399. (1999) Online citation.

Sample Information:

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Sample Name: Japanese, Yamanashi

Sample UID: SA000924P

Sample Description:This sample consists of unrelated Japanese from Yamanashi, Japan. This sample was collected from blood banks. Ethnic origin was determined by self declaration.

Number of Chromosomes: 198

Relation to Other Samples:

References:
- Hou YP, Jin ZM, Li YB, Wu J, Walter H, Kido A, Prinz M. "D20S161 data for three ethnic populations and forensic validation". Int J Legal Med 112:400-402. (1999) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA000733N

Sample Description:Collected by L.L. Cavalli-Sforza from Japanese-born individuals living in the San Francisco Bay area, and by K.K. Kidd and J. R. Kidd from Japanese-born individuals living in Connecticut.

Number of Chromosomes: 102

Relation to Other Samples: Subset of SA000010B

References:
- Barr CL, Kidd KK. "Population frequencies of the A1 allele at the dopamine D2 receptor locus". Biol.Psychiatry 34:204. (1993) Online citation.

- Chang FM, Kidd JR, Livak KJ, Pakstis AJ, Kidd KK. "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus". Hum. Genet. 98:91-101. (1996) Online citation.

- Kang AM, Palmatier MA, Kidd KK. "Global variation of a 40-bp VNTR in the 3'-untranslated region of the dopamine transporter gene (SLC6A3)". Biological Psychiatry 46:151-60. (1999) Online citation.

- Kidd JR, Black FL, Weiss KM, Balazs I, Kidd KK. "Studies of three Amerindian populations using nuclear DNA polymorphisms.". Human Biology 63:775. (1991) Online citation.

- Kidd JR, Pakstis AJ, Kidd KK. "Global levels of DNA variation". Proceedings of the 4th International Symposium on Human Identification 1993 (Promega) 21-30. (1993)

- Kidd KK et al. http://info.med.yale.edu/genetics/kkidd/pops.html

- Kidd KK, Morar B, Castiglione CM, Zhao H, Pakstis AJ, Speed WC, Bonne-Tamir B, Lu RB, Goldman D, Lee C, Nam YS, Grandy DK, Jenkins T, Kidd JR. "A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus". Hum. Genet. 103:211-27. (1998) Online citation.

- Mateu E, Calafell F, Bonne-Tamir B, Kidd JR, Casals T, Kidd KK, Bertranpetit J. "Allele Frequencies in a Worldwide Survey of a CA Repeat in the First Intron of the CFTR Gene". Human Heredity 49:15-20. (1999) Online citation.

- Palmatier MA, Kang AM, Kidd KK. "Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles". Biol. Psychiatry. 46:557-67. (1999) Online citation.

- Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Cheung K, Kidd JR, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Watson E, Krings M, Paabo S, Risch N, Jenkins T, Kidd KK. "Global patterns of linkage disequilibrium at the CD4 locus and modern human origins". Science 271:1380-7. (1996) Online citation.

- Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK. "A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations". Am. J. Hum. Genet. 62:1389-402. (1998) Online citation.

- Tishkoff SA, Ruano G, Kidd JR, Kidd KK. "Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans". Hum. Genet. 97:759-64. (1996) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA000277Q

Sample Description:The Japanese sample was drawn from the Osaka area of Japan.

Number of Chromosomes: 96

Relation to Other Samples:

References:
- Parra E, Saha N, Soemantri AG, McGarvey ST, Hundrieser J, Shriver MD, Deka R. "Genetic Variation at 9 autosomal Microsatellite Loci in Asian and Pacific Populations". Hum. Biol. 71:757-779. (1999) Online citation.

Sample Information:

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Sample Name: Japanese American, Southern California

Sample UID: SA000197R

Sample Description:Japanese American sample of (n=78) volunteers from Southern California, all apparently healthy. Each subject provided a blood sample, after providing informed consent and self-report of his or her ethnicity.

Number of Chromosomes: 156

Relation to Other Samples:

References:
- Goddard KA, Hopkins PJ, Hall JM, Witte JS. "Linkage Disequilibrium and Allele-Frequency Distributions for 114 Single-Nucleotide Polymorphisms in Five Populations ". Am. J. Hum. Genet. 66:216-234. (2000) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA000120D

Number of Chromosomes: 38

Relation to Other Samples: subset of sample 10

References:
- Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD, Soodyall H, Jenkins T, Rogers AR. "Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.". Am. J. Hum. Genet. 57:523-538. (1995) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA000010B

Sample Description:This sample was collected by L.L. Cavalli-Sforza from Japanese-born individuals living in the San Francisco Bay area, and by K.K. Kidd and J. R. Kidd from Japanese-born individuals living in Connecticut. Several of the samples were also collected by Tetsuro Miki in Osaka,Japan.

Number of Chromosomes: 112

Relation to Other Samples:

References:
- Barr CL, Kidd KK. "Population frequencies of the A1 allele at the dopamine D2 receptor locus". Biol.Psychiatry 34:204. (1993) Online citation.

- Chang FM, Kidd JR, Livak KJ, Pakstis AJ, Kidd KK. "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus". Hum. Genet. 98:91-101. (1996) Online citation.

- Kidd JR, Black FL, Weiss KM, Balazs I, Kidd KK. "Studies of three Amerindian populations using nuclear DNA polymorphisms.". Human Biology 63:775. (1991) Online citation.

- Kidd JR, Pakstis AJ, Kidd KK. "Global levels of DNA variation". Proceedings of the 4th International Symposium on Human Identification 1993 (Promega) 21-30. (1993)

- Kidd KK et al. http://info.med.yale.edu/genetics/kkidd/pops.html

- Palmatier MA, Kang AM, Kidd KK. "Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles". Biol. Psychiatry. 46:557-67. (1999) Online citation.

- Tishkoff SA, Ruano G, Kidd JR, Kidd KK. "Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans". Hum. Genet. 97:759-64. (1996) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA000810J

Sample Description:This sample consists of unrelated Japapese men and women above the age of 45 years. All participants came from Kyushu, Japan. Informed consent was a requirement.

Number of Chromosomes: 300

Relation to Other Samples:

References:
- Ohmori O, Shinkai T, Kojima H, Terao T, Suzuki T, Mita T, Abe K. "Association study of a functional catechol-O-methyltransferase gene polymorphism in Japanese schizophrenics". Neurosci Lett. 243:109-12. (1998) Online citation.

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001022F

Sample Description:This sample consists of unrelated Japanese individuals from the Tokyo area (Japan).

Number of Chromosomes: 428

Relation to Other Samples:

References:
- Zhou HG, Sato K, Nishimaki Y, Fang L, Hasekura H "The HumD21S11 system of short tandem repeat DNA polymorphisms in Japanese and Chinese". Forensic Sci Int 86:109-18. (1997) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001031F

Sample Description:This sample consists of healthy Japanese volunteers, mostly medical staff members, recruited as control subjects. Only unaffected subjects whose first- and second-degree relatives had no history of schizophrenia or other psychiatric disorders were included. All individuals were over 45 years old and lived within a 30-km radius of the University of Occupational and Environmental Health located in the city of Kitakyushu, Japan.

Number of Chromosomes: 402

Relation to Other Samples:

References:
- Hori H, Ohmori O, Shinkai T, Kojima H, Nakamura J. "Association analysis between two functional dopamine D2 receptor gene polymorphisms and schizophrenia". Am J Med Genet. 105:176-178. (2001) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese, Kansai region

Sample UID: SA001063K

Sample Description:This sample consists of Japanese residing in the western region of Japan (Kansai region). Subjects were healthy individuals who were selected from medical personnel at institutions affiliated with Osaka Medical Collage. Individuals served as a control group for a study of schizophrenia and interviews were given to all subjects prior to blood collection in order to rule out the possibility of psychotic disorders and previous psychiatric treatment in first- and second-degree relatives. The average age of the sample group was 33.1 and ranged from 22.3 to 43.9 years.

Number of Chromosomes: 206

Relation to Other Samples:

References:
- Himei A, Koh J, Sakai J, Inada Y, Akabame K, Yoneda H. "The influence on the schizophrenic symptoms by the DRD2Ser/Cys311 and -141C Ins/Del polymorphisms". Psychiatry Clin Neurosci. 56:97-102. (2002) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001120E

Sample Description:This sample consists of rendomly selected unrelated healthy donors of the population living in Miyazaki, Southern Japan.

Number of Chromosomes: 200

Relation to Other Samples:

References:
- Waiyawuth W, Zhang L, Rittner C, Schneider PM. "Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations". Forensic Sci Int. 94:25-31. (1998) Online citation.

Sample Information:

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Sample Name: Japanese 1

Sample UID: SA001256O

Sample Description:This sample consists of Japanese living in the United States. Samples provided by hte California Department of Justice, Orange County Sheriff's-Coroner Laboratory, and the Oregon State Police.

Number of Chromosomes: 298

Relation to Other Samples:

References:
- Budowle B, Shea B, Niezgoda S, Chakraborty R. "CODIS STR loci data from 41 sample populations". J Forensic Sci. 46:453-489. (2001) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese 2

Sample UID: SA001257P

Number of Chromosomes: 314

Relation to Other Samples:

References:
- Budowle B, Shea B, Niezgoda S, Chakraborty R. "CODIS STR loci data from 41 sample populations". J Forensic Sci. 46:453-489. (2001) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001342K

Sample Description:This sample consists of healthy , unrelated individuals from Shiga area.

Number of Chromosomes: 272

Relation to Other Samples:

References:
- Brinkmann B, Junge A, Meyer E, Wiegand P. "Population genetic diversity in relation to microsatellite heterogeneity". Hum Mutat 11:135-144. (1998) Online citation.

- Rolf B, Waterkamp K, Huhne J. "Allele frequency data for the FGA locus in eight populations". Int J Legal Med. 111:55-6. (1998) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Fukuoka

Sample UID: SA001370L

Sample Description:This sample consists of randomly selected Japanese. Bloo samples were supplied by Japan Red Cross Blood Center in Fukuoka.

Number of Chromosomes: 282

Relation to Other Samples:

References:
- Koda Y, Soejima M, Liu Y, Kimura H. "Molecular basis for secretor type alpha(1,2)-fucosyltransferase gene deficiency in a Japanese population: a fusion gene generated by unequal crossover responsible for the enzyme deficiency". Am J Hum Genet. 59:343-350. (1996) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA000816P

Sample Description:This sample consists of healthy, unrelated Japenese men and women. Participants were medical staff and students. Informed, written consent was obtained from all individuals.

Number of Chromosomes: 270

Relation to Other Samples:

References:
- Ohara K, Nagai M, Suzuki Y, Ochiai M, Ohara K. "No association between anxiety disorders and catechol-O-methyltransferase polymorphism.". Psychiatry Res. 80:145-8. . (1998) Online citation.

Graph estimated heterozygosities for various sites

Sample Name: Okinawa Japanese

Sample UID: SA001412I

Sample Description:This sample consists of random donors from Okinawa, Japan (southern most island of the Japanese archipelago).

Number of Chromosomes: 272

Relation to Other Samples:

References:
- Liu YH, Koda Y, Soejima M, Pang H, Wang BJ, Kim DS, Oh HB, Kimura H. "The fusion gene at the ABO-secretor locus (FUT2): absence in Chinese populations". J Hum Genet. 44:181-184. (1999) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001382O

Sample Description:This sample consists of Japanese individuals who gave appropriate informed consent.

Number of Chromosomes: 108

Relation to Other Samples:

References:
- Chang JG, Ko YC, Lee JC, Chang SJ, Liu TC, Shih MC, Peng CT. "Molecular analysis of mutations and polymorphisms of the Lewis secretor type alpha(1,2)-fucosyltransferase gene reveals that Taiwan aborigines are of Austronesian derivation". J Hum Genet. 47:60-65. (2002) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002035K

Sample Description:This sample consists of Japanese individuals.

Number of Chromosomes: 48

Relation to Other Samples:

References:
- Nakajima T, Wooding S, Sakagami T, Emi M, Tokunaga K, Tamiya G, Ishigami T, Umemura S, Munkhbat B, Jin F, Guan-Jun J, Hayasaka I, Ishida T, Saitou N, Pavelka K, Lalouel JM, Jorde LB, Inoue I. "Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world". Am J Hum Genet 74:898-916. (2004) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002072L

Sample Description:This sample consists of Japanese individuals living in the Aichi prefecture, Japan. Residents aged 40-79 years old were randomly selected from the register in cooperation with the local government.

Number of Chromosomes: 2252

Relation to Other Samples:

References:
- Suzuki Y, Fujisawa M, Ando F, Niino N, Ohsawa I, Shimokata H, Ohta S. "Alcohol dehydrogenase 2 variant is associated with cerebral infarction and lacunae". Neurology 63:1711-3.. (2004) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001972T

Sample Description:This sample consists of Japanese individuals from Tottori in western Japan.

Number of Chromosomes: 206

Relation to Other Samples:

References:
- Yuasa I, Umetsu K, Watanabe G, Nakamura H, Endoh M, Irizawa Y. "MATP polymorphisms in Germans and Japanese: the L374F mutation as a population marker for Caucasoids". Int J Legal Med. 118:364-366. (2004) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001809S

This sample is a subset of SA000010B.

Number of Chromosomes: 48

Relation to Other Samples: Subset of SA000010B

References:
- Verdu P, Barreiro LB, Patin E, Gessain A, Cassar O, Kidd JR, Kidd KK, Behar DM, Froment A, Heyer E, Sica L, Casanova J-L, Abel L, Quintana-Murci L. "Evolutionary Insights into the High Worldwide Prevalence of MBL2 Deficiency Alleles". Hum Mol Genet. 15:2650-2658. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001836S

Sample Description:This sample consists of unrelated Japanese individuals.

Number of Chromosomes: 354

Relation to Other Samples:

References:
- Okamoto O, Yamamoto Y, Inagaki S, Yoshitome K, Ishikawa T, Imabayashi K, Miyaishi S, Ishizu H. "Analysis of short tandem repeat (STR) polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice". Acta Med Okayama. 57:59-71. (2003) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001461M

Sample Description:This sample consists of unrelated individuals in Japan.

Number of Chromosomes: 2700

Relation to Other Samples:

References:
- Yoshida K, Takahashi K, Kasai K, "Allele frequencies of 15 Loci using AmpF1STR identifiler kit in Japanese population ". J Forensic Sci. 50:718-719. (2005)

Sample Information:

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Sample Name: Japanese

Sample UID: SA001608P

Sample Description:This sample consists of Japanese living in Nagasaki, western Japan.

Number of Chromosomes: 668

Relation to Other Samples:

References:
- Yoshiura KI et al. "A SNP in the ABCC11 gene is the determinant of human earwax type.". Nat Genet. 38:324-330. (2006) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA001609Q

Sample Description:This sample consists of Japanese living in Okinawa, southwestern Japan.

Number of Chromosomes: 116

Relation to Other Samples:

References:
- Yoshiura KI et al. "A SNP in the ABCC11 gene is the determinant of human earwax type.". Nat Genet. 38:324-330. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA001610I

Sample Description:This sample consists of Japanese living on Yonakuni, a western island of Japan.

Number of Chromosomes: 60

Relation to Other Samples:

References:
- Yoshiura KI et al. "A SNP in the ABCC11 gene is the determinant of human earwax type.". Nat Genet. 38:324-330. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Yamamnash Japanese

Sample UID: SA001451L

Sample Description:This sample consists of volunteer donors from Yamamnash, Japan.

Number of Chromosomes: 236

Relation to Other Samples:

References:
- Liang W, Lv M, Xu Y, Liao M, Zhou B, Jia Y, Lin Z "STR Loci D19S400's allele frequency distribution in ten populations.". J Forensic Sci 50:725. (2005)

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002321I

Sample Description:This sample consists of Japanese individuals from Japan.

Number of Chromosomes: 30

Relation to Other Samples:

References:
- Su B, Jin L, Hu F, Xiao J, Luo J, Lu D, Zhang W, Chu J, Du R, Geng Z, Qiu X, Xue J, Tan J, O'Brien SJ, Chakraborty R "Distribution of two HIV-1-resistant polymorphisms (SDF1-3'A and CCR2-64I) in East Asian and world populations and its implication in AIDS epidemiology". Am J Hum Genet. 65:1047-53. (1999) Online citation.

- Su B, Sun G, Lu D, Xiao J, Hu F, Chakraborty R, Deka R, Jin L "Distribution of three HIV-1 resistance-conferring polymorphisms (SDF1-3'A, CCR2-641, and CCR5-delta32) in global populations". Eur J Hum Genet. 8:975-9. (2000) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002720L

Sample Description:This sample consists of healthy individuals who were volunteers recruited from the National Hospital Organisation, Kurihama Alcoholism Center. Written informed consent was obtained from all individuals participating in the study and the approvals from the Ethics Committee in different medical facilities were obtained.

Number of Chromosomes: 84

Relation to Other Samples:

References:
- Maruyama K, Harada S, Yokoyama A, Naruse S, Hirota M, Nishimori I, Otsuki M "Association analysis among polymorphisms of the various genes and chronic alcoholic pancreatitis". J Gastroenterol Hepatol. 23:S69-72. (2008) Online citation.

Sample Information:

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Sample Name: Japanese (JP-ML)

Sample UID: SA003415N

Sample Description:This sample consists of Japanese from Tokyo, Japan.

Note: This sample is part of the HUGO Pan-Asian SNP Consortium. The 71 samples from this Consortium were collected with informed consent and were approved by local ethics and institutional review boards (IRBs) in the respective countries from which the samples were collected. Copies of IRB approvals were reviewed with the Policy Review Board (PRB) of the Pan Asia SNP Consortium.

Number of Chromosomes: 142

Relation to Other Samples:

References:
- HUGO Pan-Asian SNP Consortium, Abdulla MA etal. "Mapping human genetic diversity in Asia". Science. 329:1541-5. (2009) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA003764U

Sample Description:This sample consists of healthy Japanese individuals (319 males and 473 females). This study was approved by the Ethics committee at Fujita Health University, Nagoya University School of Medicine and University of occupational and Environmental health.

Number of Chromosomes: 1584

Relation to Other Samples:

References:
- Fukuo Y, Kishi T, Kushima I, Yoshimura R, Okochi T, Kitajima T, Matsunaga S, Kawashima K, Umene-Nakano W, Naitoh H, Inada T, Nakamura J, Ozaki N, Iwata N. "Possible association between ubiquitin-specific peptidase 46 gene and major depressive disorders in the Japanese population". J Affect Disord. (2011) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA003716R

Sample Description:This sample consists of Japanese individuals. The DNA samples were provided by Kenneth and Judith Kidd, Yale School of Medicine.

Number of Chromosomes: 26

Relation to Other Samples: Subset of SA000733N

- Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, Jorde LB. "Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping". Genomics 96:199-210. (2010) Online citation.

- Xing J, Watkins WS, Witherspoon DJ, Zhang Y, Guthery SL, Thara R, Mowry BJ, Bulayeva K, Weiss RB, Jorde LB. "Fine-scaled human genetic structure revealed by SNP microarrays". Genome Res. 19:815-25. (2009) Online citation.

Sample Information:

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Graph estimated heterozygosities for various sites

Sample Name: Tokyo

Sample UID: SA003509R

Sample Description:This sample consists of Japanese individuals from Showa University Dental Hospital, Tokyo. All the subjects gave informed consent to participate in the study.

Number of Chromosomes: 204

Relation to Other Samples:

Sample Information:

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Sample Name: Japanese Brazilian

Sample UID: SA003845U

Sample Description:This sample consists of Japanese Brazilians.

Number of Chromosomes: 106

Relation to Other Samples:

References:
- Mattar R, Monteiro MS, Villares CA, Santos AF, Silva JM, Carrilho FJ. "Frequency of LCT -13910C>T single nucleotide polymorphism associated with adult-type hypolactasia/lactase persistence among Brazilians of different ethnic groups". Nutr J. 8:46. (2009) Online citation.

Sample Information:

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Sample Name: Japanese

Sample UID: SA003009M

Sample Description:This sample consists of Japanese from Fukui, Shimane and Gunma Prefectures, Japan. Written informed consent was obtained from each participant. The study was approved by the Human Ethics Committee of each institute.

Number of Chromosomes: 684

Relation to Other Samples:

References:
- Ueki M, Takeshita H, Fujihara J, Iida R, Yuasa I, Kato H, Panduro A, Nakajima T, Kominato Y, Yasuda T. "Caucasian-specific allele in non-synonymous single nucleotide polymorphisms of the gene encoding deoxyribonuclease I-like 3, potentially relevant to autoimmunity, produces an inactive enzyme". Clin Chim Acta. 407:20-4. (2009) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Sakishima

Sample UID: SA003510J

Sample Description:This sample consists of Japanese individuals in Sakishima Islands (Miyako and Ishigaki) the southernmost Ryukyu Islands. The subjects were selected as individuals who had no ancestor derived from other regions for atleast three generations.

Number of Chromosomes: 200

Relation to Other Samples:

Sample Information:

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Sample Name: Hondo

Sample UID: SA003513M

Sample Description:This sample consists of Japanese individuals from the Hondo cluster of Islands. The 'Hondo' cluster includes the Japanese main islands other than Okinawa. The islands included in the cluster are Hokkaido (514 individuals), Tohoku (466 individuals), Kanto-Koshinetsu (3978 individuals), Tokai-Hokuriku (358 individuals), Kinki (908 individuals) and Kyushu (628 individuals).This project was approved by the ethical committees at the Institute of Medical Science, The University of Tokyo and the Center for Genomics Medicine, Institutes of Physical and Chemical Research (RIKEN).

Number of Chromosomes: 13464

Relation to Other Samples:

References:
- Yamaguchi-Kabata Y, Nakazono K, Takahashi A, Saito S, Hosono N, Kubo M, Nakamura Y, Kamatani N "Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies.". Am J Hum Genet. 83:445-56. (2008) Online citation.

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Sample Name: Shibata

Sample UID: SA003297V

Sample Description:This sample consists of Japanese individuals.

Note: This sample information is not fully curated. For additional information about the sample, consult the publications under "References". The sample was entered as part of data submission by Eisenberg DA.

Number of Chromosomes: 2656

Relation to Other Samples:

References:
- Eisenberg DA, Kuzawa, CW, Hayes MG "Worldwide allele frequencies of the human apolipoprotein E (APOE) gene: climate, local adaptations and evolutionary history". American Journal of Physical Anthropology 143:100-11. (2010) Online citation.

- Zaman MM, Ikemoto S, Yoshiike N, Date C, Yokoyama T, Tanaka H. "Association of apolipoprotein genetic polymorphisms with plasma cholesterol in a Japanese rural population. The Shibata Study". Arterioscler Thromb Vasc Biol. 17:3495-504. (1997) Online citation.

Sample Information:

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Sample Name: Mie

Sample UID: SA003298W

Sample Description:This sample consists of Japanese individuals.

Number of Chromosomes: 1888

Relation to Other Samples:

- Nakayama S, Kuzuhara S "Apolipoprotein E phenotypes in healthy normal controls and demented subjects with Alzheimer's disease and vascular dementia in Mie Prefecture of Japan". Psychiatry Clin Neurosci. 53:643-8. (1999) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Sendai

Sample UID: SA003304K

Sample Description:This sample consists of Japanese individuals from Sendai area, Japan.

Number of Chromosomes: 214

Relation to Other Samples:

- Sano R, Abe R, Oikawa S, Fujii Y, Hori S, Suzuki N, Toyota T, Goto Y. "Apolipoprotein E phenotypes of normo- and hyperlipoproteinemia in Japanese". Tohoku J Exp Med. 154:297-303. (1988) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002719T

Sample Description:This sample consists of Japanese subjects from Akita Prefecture, northeast Japan. A Self-reported questionnaire with detailed explanations of the study purpose was distributed to salespersons at motor vehicle dealerships in the central area of Akita Prefecture. Blood samples were taken from the subjects who returned the questionnaire with written informed consent. This study protocol was approved by the ethical review committes of the Akita Health Insurance Union of the Motor Vehicle Stores and the Akita University School of Medicine.

Number of Chromosomes: 1350

Relation to Other Samples:

References:
- Dakeishi M, Murata K, Sasaki M, Tamura A, Iwata T "Association of alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 genotypes with fasting plasma glucose levels in Japanese male and female workers". Alcohol Alcohol. 43:143-7. (2008) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA003533O

Sample Description:This sample consists of Japanese from Japan.Written informed consent was obtained from each participant. The study was approved by the Human Ethics Committees of the participating institutes.

Number of Chromosomes: 220

Relation to Other Samples:

References:
- Fujihara J, Ueki M, Yasuda T, Iida R, Soejima M, Koda Y, Kimura-Kataoka K, Kato H, Panduro A, Tongu M, Takeshita H. "Functional and Genetic Survey of All Known Single-Nucleotide Polymorphisms Within the Human Deoxyribonuclease I Gene in Wide-Ranging Ethnic Groups". DNA Cell Biol. (Epub, ahead of print) (2011) Online citation.

- Yasuda T, Ueki M, Takeshita H, Fujihara J, Kimura-Kataoka K, Iida R, Tsubota E, Soejima M, Koda Y, Kato H, Panduro A. "A biochemical and genetic study on all non-synonymous single nucleotide polymorphisms of the gene encoding human deoxyribonuclease I potentially relevant to autoimmunity". Int J Biochem Cell Biol. 42:1216-25. (2010) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002728T

Sample Description:This sample consists of Japanese subjects from Kanazawa, Japan. Written informed consent was obtained from each subject.

Number of Chromosomes: 98

Relation to Other Samples:

References:
- Nishimura FT, Kimura Y, Abe S, Fukunaga T, Minami J, Tanii H, Saijoh K. "Effects of Functional Polymorphisms Related to Catecholaminergic Systems on Changes in Blood Catecholamine and Cardiovascular Measures After Alcohol Ingestion in the Japanese Population". Alcohol Clin Exp Res. (Epub Ahead of print) (2008) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002867X

Sample Description:This sample consists of unrelated Japanese individuals, mainly living in Tottori, Japan. The donors were selected at random, irrespective of skin color, and their phenotypic data were unavailable.

Number of Chromosomes: 358

Relation to Other Samples:

References:
- Yuasa I, Umetsu K, Harihara S, Kido A, Miyoshi A, Saitou N, Dashnyam B, Jin F, Lucotte G, Chattopadhyay PK, Henke L, Henke J. "Distribution of two Asian-related coding SNPs in the MC1R and OCA2 genes". Biochem Genet. 45:535-42. (2007) Online citation.

- Yuasa I, Umetsu K, Harihara S, Miyoshi A, Saitou N, Park KS, Dashnyam B, Jin F, Lucotte G, Chattopadhyay PK, Henke L, Henke J "OCA2 481Thr, a hypofunctional allele in pigmentation, is characteristic of northeastern Asian populations". J Hum Genet 52:690-3.. (2007) Online citation.

- Yuasa I, Umetsu K, Matsusue A, Nishimukai H, Harihara S, Fukumori Y, Saitou N, Jin F, Chattopadhyay PK, Henke L, Henke J. "A Japanese-specific allele in the GALNT11 gene". Leg Med (Tokyo). 12:208-11. (2010) Online citation.

Graph estimated heterozygosities for various sites

Sample Name: Gunma

Sample UID: SA002947W

Sample Description:This sample consists of unrelated Japanese individuals from Gunma district, Japan.

Number of Chromosomes: 384

Relation to Other Samples:

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Shimane

Sample UID: SA002948X

Sample Description:This sample consists of unrelated Japanese individuals from Shimane district, Japan.

Number of Chromosomes: 384

Relation to Other Samples:

Sample Information:

Graph estimated heterozygosities for various sites

Number of Chromosomes: 58

Relation to Other Samples: Subset of SA001499X

References:
- Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK. "A worldwide survey of haplotype variation and linkage disequilibrium in the human genome". Nat Genet. 38:1251-1260. (2006) Online citation.

- Rosenberg NA. "Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.". Ann Hum Genet. 70:841-847. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA002003F

Sample Description:This sample consists of unrelated individuals from Japan.

Number of Chromosomes: 14

Relation to Other Samples:

References:
- Sánchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. "A multiplex assay with 52 single nucleotide polymorphisms for human identification". Electrophoresis. 27:1713-1724. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Graph estimated heterozygosities for various sites

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA003044L

Sample Description:This sample consists of Japanese (174 males and 70 females) living in Honshu Island. The subjects volunteered to participate in the study.

Number of Chromosomes: 488

Relation to Other Samples:

References:
- Sadewa AH, Sunarti, Sutomo R, Hayashi C, Lee MJ, Ayaki H, Sofro AS, Matsuo M, Nishio H "The C677T mutation in the methylenetetrahydrofolate reductase gene among the Indonesian Javanese population". Kobe J Med Sci. 48:137-44. (2002) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Kumamoto

Sample UID: SA003305L

Sample Description:This sample consists of Japanese individuals from Kumamato, Japan.

Number of Chromosomes: 376

Relation to Other Samples:

- Kobori S, Nakamura N, Uzawa H, Shichiri M. "Influence of apolipoprotein E polymorphism on plasma lipid and apolipoprotein levels, and clinical characteristics of type III hyperlipoproteinemia due to apolipoprotein E phenotype E2/2 in Japan". Atherosclerosis. 69:81-8. (1988) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Niigata

Sample UID: SA003313K

Sample Description:This sample consists of Japanese individuals.

Number of Chromosomes: 258

Relation to Other Samples:

- Miida T. "Apolipoprotein E phenotypes in patients with coronary artery disease". Tohoku J Exp Med. 160:177-87. (1990) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Hyogo

Sample UID: SA003319Q

Sample Description:This sample consists of Japanese individuals.

Number of Chromosomes: 240

Relation to Other Samples:

- Nakata Y, Katsuya T, Rakugi H, Takami S, Ohishi M, Kamino K, Higaki J, Tabuchi Y, Kumahara Y, Miki T, Ogihara T. "Polymorphism of the apolipoprotein E and angiotensin-converting enzyme genes in Japanese subjects with silent myocardial ischemiaHypertension.". Hypertension. 27:1205-9.. (1996) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Iwate prefecture

Sample UID: SA003353O

Sample Description:This sample consists of Japanese individuals.

Number of Chromosomes: 844

Relation to Other Samples:

- Nakai K, Fusazaki T, Zhang T, Shiroto T, Osawa M, Kamata J, Itoh M, Nakai K, Habano W, Kiuchi T, Yamamori S, Hiramori K. "Polymorphism of the apolipoprotein E and angiotensin I converting enzyme genes in Japanese patients with myocardial infarction". Coron Artery Dis. 9:329-34.. (1998) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA003466T

Sample Description:This sample consists of unrelated Japanese volunteers at Tohoku Pharmaceutical University and Tohoku University Hospital. The ethics committee of the university and the Hospital approved the study and written informed consent was obtained from all the donors.

Number of Chromosomes: 128

Relation to Other Samples:

References:
- Hiratsuka M, Tsukamoto N, Konno Y, Nata M, Hashiyada M, Funayama M, Mizugaki M. "Forensic assessment of 16 single nucleotide polymorphisms analyzed by hybridization probe assay". Tohoku J Exp Med. 207:255-61. (2005) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Asahikawa

Sample UID: SA003332L

Sample Description:This sample consists of Japanese individuals from Asahikawa district of Hokkaido.

Number of Chromosomes: 1152

Relation to Other Samples:

- Eto M, Watanabe K, Ishii K. "A racial difference in apolipoprotein E allele frequencies between the Japanese and Caucasian populations". Clin Genet. 30:422-7.. (1986) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA003746U

Sample Description:This sample consists of Japanese individuals from Yamagata, Japan.

Number of Chromosomes: 578

Relation to Other Samples:

References:
- Yuasa I, Umetsu K, Harihara S, Miyoshi A, Saitou N, Park KS, Dashnyam B, Jin F, Lucotte G, Chattopadhyay PK, Henke L, Henke J "OCA2 481Thr, a hypofunctional allele in pigmentation, is characteristic of northeastern Asian populations". J Hum Genet 52:690-3.. (2007) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004448U

Sample Description:This sample consists of 251 unrelated, healthy, adult Japanese individuals.This study was approved by the ethics committee of Shinshu University.

Number of Chromosomes: 452

Relation to Other Samples:

References:
- Nunotani M, Shiozaki T, Sato N, Kamei S, Takatsu K, Hayashi T, Ota M, Asamura H "Analysis of 30 insertion-deletion polymorphisms in the Japanese population using the Investigator DIPplex� kit.". Leg Med (Tokyo). 17:467-70. (2015) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004708T

Sample Description:This sample consists of Japanese individuals in East Asia. Written informed consent was obtained from all individuals. This sample is part of Caixia Li's group in Institute of Forensic Science, Beijing, China. It was provided by the Kenneth K. Kidd's laboratory to Caixia lab.

Number of Chromosomes: 92

Relation to Other Samples:

References:
- Jiang L, Wei YL, Zhao L, Li N, Liu T, Liu HB, Ren LJ, Li JL, Hao HF, Li Q, Li CX. "Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs". Forensic Sci Int Genet. 35:e10-e12. (2018) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Mainland Japanese

Sample UID: SA004525Q

Sample Description:This sample consists of 49 unrelated individuals from mainland Japan living in 34 different prefectures.

Number of Chromosomes: 98

Relation to Other Samples:

References:
- Nakanishi H, Pereira V, Borsting C, Yamamoto T, Tvedebrink T, Hara M, Takada A, Saito K, Morling N. "Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel". Forensic Sci Int Genet. 33:106-109. (2018) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004113J

Sample Description:This sample consists of Japanese individuals at Showa University Dental Hospital, Tokyo.

Number of Chromosomes: 546

Relation to Other Samples:

References:
- Lee WC, Yamaguchi T, Watanabe C, Kawaguchi A, Takeda M, Kim YI, Haga S, Tomoyasu Y, Ishida H, Maki K, Park SB, Kimura R. "Association of common PAX9 variants with permanent tooth size variation in non-syndromic East Asian populations". J Hum Genet. (Epub, ahead of print) (2012) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004025L

Sample Description:This sample consists of Japanese.

Number of Chromosomes: 72

Relation to Other Samples:

References:
- Tikkanen MJ, Huttunen JK, Ehnholm C, Pietinen P. "Apolipoprotein E4 homozygosity predisposes to serum cholesterol elevation during high fat diet". Arteriosclerosis 10:285-8.. (1990) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004167S

Sample Description:This sample consists of unrelated Japanese subjects from the Tokyo metropolitan area.

Number of Chromosomes: 334

Relation to Other Samples:

References:
- Tomoyasu Y, Yamaguchi T, Tajima A, Nakajima T, Inoue I, Maki K. "Further evidence for an association between mandibular height and the growth hormone receptor gene in a Japanese population". Am J Orthod Dentofacial Orthop. 136:536-41. (2009) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese in East Asia(JEA)

Sample UID: SA004401J

Sample Description:This sample is part of KiddLab sample collection. This sample was provided by K.K. Kidd, Yale University to Caixia Li's group for typing their markers

Number of Chromosomes: 74

Relation to Other Samples: Subset of sample SA000010B

References:
- Wei YL, Wei L, Zhao L, Sun QF, Jiang L, Zhang T, Liu HB, Chen JG, Ye J, Hu L, Li CX "A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents". Int J Legal Med. 130:27-37. (2016) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: JPT_Hapmap

Sample UID: SA004359V

Sample Description:

Number of Chromosomes: 120

Relation to Other Samples: Subset of SA002088S

References:
- Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, Jorde LB. "Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping". Genomics 96:199-210. (2010) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese in Tokyo, Japan (JPT)

Sample UID: SA004060K

Sample Description:This sample consists of unrelated Japanese from Tokyo metropolitan area.

This sample is part of 1000 Genomes Collections.

Number of Chromosomes: 208

Relation to Other Samples: Superset of sample SA002088S

References:
- 1000 genomes phase1 samples data Online citation.

- 1000genomes project samples page Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Japanese

Sample UID: SA004180N

Sample Description:This sample consists of Japanese individuals from Shimane and Hokkaido prefectures in japan. Written informed consent was obtained from each participant. The study was approved by the Ethical committee of the university.

Number of Chromosomes: 282

Relation to Other Samples:

References:
- Fujihara J, Soejima M, Yasuda T, Koda Y, Agusa T, Kunito T, Tongu M, Yamada T, Takeshita H. "Global analysis of genetic variation in human arsenic (+3 oxidation state) methyltransferase (AS3MT)". Toxicol Appl Pharmacol. 243:292-9. (2010) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Okinawa Japanese

Sample UID: SA004526R

Sample Description:This sample consists of 47 unrelated residents of the Okinawa prefecture.

Number of Chromosomes: 94

Relation to Other Samples:

¹Geographic Coordinates represent two opposite corners of a rectangle encompassing the area where the population lives.This data is preliminary and changing.

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© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan