Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000190

Type of data
GWAS for gut microbiome
GWAS for plasma metabolite
GWAS for KEGG Gene Ortholog and KEGG Pathway
Access criteria
Unrestricted-access
Total data volume
320 GB
File formats
  • TSV
  • DOCX
Research
hum0197
Date published
2023-10-02
Date modified
2023-10-02
Secondary ID
hum0197.v18.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
Per page
20
2050100

261–280 / 732

FileLabelSizeCopy URL
metabo_P_0077_QCed_sumstats.tsv.gzAcylcarnitine(13:1)318 MB
metabo_P_0079_QCed_sumstats.tsv.gzCortisone318 MB
metabo_P_0083_QCed_sumstats.tsv.gzCortisol-1;18-Hydroxycorticosterone-1318 MB
metabo_P_0084_QCed_sumstats.tsv.gzCortisol-2;18-Hydroxycorticosterone-2318 MB
metabo_P_0085_QCed_sumstats.tsv.gz18-Hydroxycorticosterone-3318 MB
metabo_P_0086_QCed_sumstats.tsv.gzCortisol-3;18-Hydroxycorticosterone-4318 MB
metabo_P_0089_QCed_sumstats.tsv.gzAcylcarnitine(14:3)-3318 MB
metabo_P_0090_QCed_sumstats.tsv.gzAcylcarnitine(14:3)-4319 MB
metabo_P_0092_QCed_sumstats.tsv.gz7-Dehydrocholesterol-1318 MB
metabo_P_0094_QCed_sumstats.tsv.gzAcylcarnitine(14:2)-1319 MB
metabo_P_0095_QCed_sumstats.tsv.gzAcylcarnitine(14:2)-2318 MB
metabo_P_0096_QCed_sumstats.tsv.gzAcylcarnitine(14:2)-3318 MB
metabo_P_0099_QCed_sumstats.tsv.gzAcylcarnitine(14:1)-2318 MB
metabo_P_0100_QCed_sumstats.tsv.gzAcylcarnitine(14:1)-3319 MB
metabo_P_0101_QCed_sumstats.tsv.gzAcylcarnitine(14:1)-4318 MB
metabo_P_0102_QCed_sumstats.tsv.gzCholesterol318 MB
metabo_P_0103_QCed_sumstats.tsv.gzArachidonoylethanolamide(22:6)318 MB
metabo_P_0105_QCed_sumstats.tsv.gzAcylcarnitine(14:0)-2318 MB
metabo_P_0110_QCed_sumstats.tsv.gz2-Arachidonoylglycerol-3319 MB
metabo_P_0112_QCed_sumstats.tsv.gzCampesterol-1318 MB

261–280 / 732

Analysis method

genome wide SNPs

Materials and participants
524 Japanese individuals (423 species in the gut microbiome)
306 Japanese individuals (306 plasma metabolites)
524 Japanese individuals (KEGG Gene Ortholog and KEGG Pathway)
  • Subject count
    524 (Individual)
  • Population
    Japanese
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Experimental method
Genotyping by array
WGS
Reagent kit
Infinium Asian Screening Array Kit
KAPA Hyper Prep Kit
TruSeq DNA PCR-Free Library Prep Kit
Platform
Illumina HiSeq 2500
Illumina HiSeq 3000
Illumina HiSeq X
Illumina Infinium Asian Screening Array
Illumina NovaSeq 6000
Reference genome
GRCh37
QC and filtering
SNP array data:
Sample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian ancestry using PCA.
Variant QC: We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10^−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project.
Post-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 1%.
WGS:
We excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10
After imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%.
Imputation
Haplotype phasing: shapeit4
Imputation: minimac4
Analysis method
SNP array:
Genotyping: GenomeStudio
WGS:
WA-MEM v0.7.13 + GATK v3.8-0
PLINK2
Variant count
Gut microbiota/KEGG (SNP array): 7,213,470 variants
Blood metabolites (WGS): 6,840,258 variants
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)