Dataset ID

NHA000190

Name: NHA000190: GWAS for gut microbiome, GWAS for plasma metabolite, GWAS for KEGG Gene Ortholog and KEGG Pathway
Published: 2023-10-02

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

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201–300 / 732

File	Label	Size
metabo_N_0061_QCed_sumstats.tsv.gz	Fatty acid(22:3)-2	318 MB
metabo_N_0062_QCed_sumstats.tsv.gz	Fatty acid(22:2)	319 MB
metabo_N_0063_QCed_sumstats.tsv.gz	Erucic acid	318 MB
metabo_N_0064_QCed_sumstats.tsv.gz	Behenic acid	318 MB
metabo_N_0067_QCed_sumstats.tsv.gz	Tricosanoic acid-2	318 MB
metabo_N_0068_QCed_sumstats.tsv.gz	Fatty acid(24:5)	319 MB
metabo_N_0069_QCed_sumstats.tsv.gz	Fatty acid(24:4)	318 MB
metabo_N_0070_QCed_sumstats.tsv.gz	Fatty acid(24:2)	319 MB
metabo_N_0071_QCed_sumstats.tsv.gz	Nervonic acid-1	318 MB
metabo_N_0072_QCed_sumstats.tsv.gz	Nervonic acid-2	318 MB
metabo_N_0073_QCed_sumstats.tsv.gz	Dehydroisoandrosterone 3-sulfate-1	318 MB
metabo_N_0074_QCed_sumstats.tsv.gz	Dehydroisoandrosterone 3-sulfate-2	318 MB
metabo_N_0076_QCed_sumstats.tsv.gz	Fatty acid(24:0)-2	318 MB
metabo_N_0077_QCed_sumstats.tsv.gz	Lithocholic acid	318 MB
metabo_N_0080_QCed_sumstats.tsv.gz	Fatty acid(25:0)-2	319 MB
metabo_N_0081_QCed_sumstats.tsv.gz	Hyodeoxycholic acid	318 MB
metabo_N_0082_QCed_sumstats.tsv.gz	Ursodeoxycholic acid	318 MB
metabo_N_0083_QCed_sumstats.tsv.gz	Chenodeoxycholic acid	319 MB
metabo_N_0084_QCed_sumstats.tsv.gz	Deoxycholic acid	318 MB
metabo_N_0085_QCed_sumstats.tsv.gz	Fatty acid(26:2)-1	318 MB
metabo_N_0086_QCed_sumstats.tsv.gz	Fatty acid(26:2)-2	318 MB
metabo_N_0087_QCed_sumstats.tsv.gz	Pregnenolone sulfate	318 MB
metabo_N_0089_QCed_sumstats.tsv.gz	Fatty acid(26:0)-2	318 MB
metabo_N_0090_QCed_sumstats.tsv.gz	Cholic acid	319 MB
metabo_N_0091_QCed_sumstats.tsv.gz	Glycolithocholic acid	318 MB
metabo_N_0092_QCed_sumstats.tsv.gz	Glycodeoxycholic acid	318 MB
metabo_N_0093_QCed_sumstats.tsv.gz	Glycoursodeoxycholic acid	318 MB
metabo_N_0094_QCed_sumstats.tsv.gz	Glycochenodeoxycholic acid	318 MB
metabo_N_0095_QCed_sumstats.tsv.gz	Betulinic acid	319 MB
metabo_N_0096_QCed_sumstats.tsv.gz	Glycocholic acid	318 MB
metabo_N_0099_QCed_sumstats.tsv.gz	Cholesterol sulfate	318 MB
metabo_N_0105_QCed_sumstats.tsv.gz	Tauroursodeoxycholic acid	318 MB
metabo_N_0106_QCed_sumstats.tsv.gz	Taurodeoxycholic acid	318 MB
metabo_N_0107_QCed_sumstats.tsv.gz	Taurochenodeoxycholic acid	318 MB
metabo_N_0108_QCed_sumstats.tsv.gz	Taurocholic acid	318 MB
metabo_P_0002_QCed_sumstats.tsv.gz	Indole-3-carboxaldehyde-2	318 MB
metabo_P_0012_QCed_sumstats.tsv.gz	Retinol-1	318 MB
metabo_P_0013_QCed_sumstats.tsv.gz	Retinol-2	318 MB
metabo_P_0015_QCed_sumstats.tsv.gz	β-Estradiol	318 MB
metabo_P_0017_QCed_sumstats.tsv.gz	Androsterone-2	318 MB
metabo_P_0020_QCed_sumstats.tsv.gz	4-Androstene-3,17-dione-2	319 MB
metabo_P_0022_QCed_sumstats.tsv.gz	Testosterone-2	318 MB
metabo_P_0024_QCed_sumstats.tsv.gz	Testosterone-4	318 MB
metabo_P_0027_QCed_sumstats.tsv.gz	Palmitoylethanolamide-1	318 MB
metabo_P_0029_QCed_sumstats.tsv.gz	Sphingosine	318 MB
metabo_P_0031_QCed_sumstats.tsv.gz	Sphinganine	318 MB
metabo_P_0036_QCed_sumstats.tsv.gz	11β-Hydroxyandrost-4-ene-3,17-dione-3	318 MB
metabo_P_0038_QCed_sumstats.tsv.gz	Abietic acid-2	318 MB
metabo_P_0048_QCed_sumstats.tsv.gz	Acylcarnitine(10:0)	318 MB
metabo_P_0054_QCed_sumstats.tsv.gz	Linoleyl ethanolamide	318 MB
metabo_P_0055_QCed_sumstats.tsv.gz	Oleoyl ethanolamide;Arachidonoylethanolamide(18:1)-1	318 MB
metabo_P_0057_QCed_sumstats.tsv.gz	Stearoyl ethanolamide	319 MB
metabo_P_0060_QCed_sumstats.tsv.gz	17α-Hydroxyprogesterone-2	319 MB
metabo_P_0062_QCed_sumstats.tsv.gz	Testosterone acetate-2	318 MB
metabo_P_0063_QCed_sumstats.tsv.gz	21-Hydroxypregnenolone-1	318 MB
metabo_P_0069_QCed_sumstats.tsv.gz	Acylcarnitine(12:1)-1	318 MB
metabo_P_0070_QCed_sumstats.tsv.gz	Acylcarnitine(12:1)-2	319 MB
metabo_P_0071_QCed_sumstats.tsv.gz	Acylcarnitine(12:1)-3	318 MB
metabo_P_0073_QCed_sumstats.tsv.gz	Acylcarnitine(12:0)-2	318 MB
metabo_P_0075_QCed_sumstats.tsv.gz	Corticosterone-2;Cortexolone-2;21-Deoxycortisol-2	318 MB
metabo_P_0077_QCed_sumstats.tsv.gz	Acylcarnitine(13:1)	318 MB
metabo_P_0079_QCed_sumstats.tsv.gz	Cortisone	318 MB
metabo_P_0083_QCed_sumstats.tsv.gz	Cortisol-1;18-Hydroxycorticosterone-1	318 MB
metabo_P_0084_QCed_sumstats.tsv.gz	Cortisol-2;18-Hydroxycorticosterone-2	318 MB
metabo_P_0085_QCed_sumstats.tsv.gz	18-Hydroxycorticosterone-3	318 MB
metabo_P_0086_QCed_sumstats.tsv.gz	Cortisol-3;18-Hydroxycorticosterone-4	318 MB
metabo_P_0089_QCed_sumstats.tsv.gz	Acylcarnitine(14:3)-3	318 MB
metabo_P_0090_QCed_sumstats.tsv.gz	Acylcarnitine(14:3)-4	319 MB
metabo_P_0092_QCed_sumstats.tsv.gz	7-Dehydrocholesterol-1	318 MB
metabo_P_0094_QCed_sumstats.tsv.gz	Acylcarnitine(14:2)-1	319 MB
metabo_P_0095_QCed_sumstats.tsv.gz	Acylcarnitine(14:2)-2	318 MB
metabo_P_0096_QCed_sumstats.tsv.gz	Acylcarnitine(14:2)-3	318 MB
metabo_P_0099_QCed_sumstats.tsv.gz	Acylcarnitine(14:1)-2	318 MB
metabo_P_0100_QCed_sumstats.tsv.gz	Acylcarnitine(14:1)-3	319 MB
metabo_P_0101_QCed_sumstats.tsv.gz	Acylcarnitine(14:1)-4	318 MB
metabo_P_0102_QCed_sumstats.tsv.gz	Cholesterol	318 MB
metabo_P_0103_QCed_sumstats.tsv.gz	Arachidonoylethanolamide(22:6)	318 MB
metabo_P_0105_QCed_sumstats.tsv.gz	Acylcarnitine(14:0)-2	318 MB
metabo_P_0110_QCed_sumstats.tsv.gz	2-Arachidonoylglycerol-3	319 MB
metabo_P_0112_QCed_sumstats.tsv.gz	Campesterol-1	318 MB
metabo_P_0113_QCed_sumstats.tsv.gz	Campesterol-2	319 MB
metabo_P_0117_QCed_sumstats.tsv.gz	Stigmasterol-1	318 MB
metabo_P_0118_QCed_sumstats.tsv.gz	Stigmasterol-2	318 MB
metabo_P_0119_QCed_sumstats.tsv.gz	Acylcarnitine(16:2)	318 MB
metabo_P_0121_QCed_sumstats.tsv.gz	Sitosterol-2	318 MB
metabo_P_0122_QCed_sumstats.tsv.gz	Acylcarnitine(16:1)	318 MB
metabo_P_0124_QCed_sumstats.tsv.gz	Palmitoylcarnitine	318 MB
metabo_P_0125_QCed_sumstats.tsv.gz	Cycloartenol;Lanosterol	318 MB
metabo_P_0127_QCed_sumstats.tsv.gz	Acylcarnitine(17:1)-2	318 MB
metabo_P_0128_QCed_sumstats.tsv.gz	Acylcarnitine(17:0)-1	318 MB
metabo_P_0129_QCed_sumstats.tsv.gz	Acylcarnitine(17:0)-2	318 MB
metabo_P_0131_QCed_sumstats.tsv.gz	Diosgenin-2	318 MB
metabo_P_0133_QCed_sumstats.tsv.gz	γ-Tocopherol-2	318 MB
metabo_P_0136_QCed_sumstats.tsv.gz	Acylcarnitine(18:2)-3	318 MB
metabo_P_0138_QCed_sumstats.tsv.gz	Acylcarnitine(18:1)	318 MB
metabo_P_0139_QCed_sumstats.tsv.gz	Acylcarnitine(18:0)	318 MB
metabo_P_0141_QCed_sumstats.tsv.gz	Hydroxyprogesterone caproate-2	318 MB
metabo_P_0142_QCed_sumstats.tsv.gz	Hecogenin	318 MB
metabo_P_0143_QCed_sumstats.tsv.gz	α-Tocopherol	318 MB
metabo_P_0149_QCed_sumstats.tsv.gz	Acylcarnitine(20:1)-1	318 MB

201–300 / 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)