NBDC Research ID: hum0164.v1

 

SUMMARY

Aims: Identify the genetic factors related to tanning ability in Japanese

Methods: Genome-wide association study

Participants/Materials: Genotypedata and quetionnaire based skin tanning ability information of 9,187 participants of Tohoku Medical Megabank Organization cohort study

URL: https://www.megabank.tohoku.ac.jp/english/

URL: http://iwate-megabank.org/en/

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000160 GWAS for skin tanning ability of 9,187 participants Controlled Access (Type I) 2018/12/14

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000160

Participants/Materials 9,187 participants of Tohoku Medical Megabank Organization cohort study
Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Illumina [Infinium OmniExpressExome-8]
Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Illumina Infinium OmniExpressExome-8 Beadchip Kit
Genotype Call Methods (software) GenCall software (GenomeStudio)
Association Analysis (software)

linear mixed model (software: BOLT-LMM v2.3.2)

adjusted by age, sex and 1-10 principal component scores

Filtering Methods

Sample: Call rate > 0.98

SNP: HWE P < 0.0001, MAF < 0.01, Missing rate > 0.05

Marker Number (after QC) 6,193,994 SNPs (reference: hg19)
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000238

Dictionary file

* GWAS_summary_statistics_JST_Combined_set.txt.gz

GWAS summary statistics of Japanese Skin Type for 9,187 Japanese individuals in Miyagi and Iwate prefectures

* GWAS_summary_statistics_JST_Miyagi.txt.gz

GWAS summary statistics of Japanese Skin Type for 4,475 Japanese individuals in Miyagi prefecture

* GWAS_summary_statistics_JST_Iwate.txt.gz

GWAS summary statistics of Japanese Skin Type for 4,712 Japanese individuals in Iwate prefecture

Total Data Volume 463 MB (txt)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Masao Nagasaki

Affiliation: Tohoku Medical Megabank Organization・Genome Information Analysis

Project / Group Name: -

URL: https://www.megabank.tohoku.ac.jp/english/

URL: http://iwate-megabank.org/en/

Funds / Grants (Research Project Number):

NameTitleProject Number
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Tohoku University) Special account of the Great East Japan Earthquake disaster recovery JP18km0105001
Japan Agency for Medical Research and Development (AMED) Tohoku Medical Megabank Project (Tohoku University) General accounting JP18km0105002
Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) Facilitation of R&D Platform for AMED Genome Mecidine Support JP18km0405001

 

PUBLICATIONS

TitleDOIData Set ID
1
2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use