GWAS summary statistics of 58 quantitative traits in the BioBank Japan Project

This data set provides the summary statistics of 58 quantitative traits in the BioBank Japan Project (Kanai, M. et al. Nat Genet, 2018).

Analyzed traits

Category Trait (Abbr.) #samples Mean SD Unit
Metabolic Total cholesterol TC 128,305 199.17 38.56 mg/dL
Metabolic High density lipoprotein cholesterol HDL-C 70,657 54.75 15.43 mg/dL
Metabolic Low density lipoprotein cholesterol LDL-C 72,866 130.81 40.97 mg/dL
Metabolic Triglyceride TG 105,597 133.17 71.86 mg/dL
Metabolic Blood sugar BS 93,146 106.32 21.08 mg/dL
Metabolic Hemoglobin A1c HbA1c 42,790 5.49 0.60 %
Protein Total protein TP 113,509 7.11 0.56 g/dL
Protein Albumin Alb 102,223 4.22 0.42 g/dL
Protein Non-albumin protein NAP 98,538 2.88 0.45 g/dL
Protein Albumin/globulin ratio A/G 98,626 1.50 0.30 [ratio]
Kidney-related Blood urea nitrogen BUN 139,818 15.44 4.77 mg/dL
Kidney-related Serum creatinine sCr 142,097 0.77 0.22 mg/dL
Kidney-related Estimated glomerular filtration rate eGFR 143,658 73.93 15.42 mL/min/1.73 m2
Kidney-related Uric acid UA 109,029 5.32 1.45 mg/dL
Electrolyte Sodium Na 127,304 141.14 2.63 mEq/L
Electrolyte Potassium K 132,938 4.24 0.41 mEq/L
Electrolyte Chlorine Cl 126,402 104.38 2.92 mEq/L
Electrolyte Calcium Ca 71,701 9.19 0.52 mg/dL
Electrolyte Phosphorus P 42,793 3.35 0.61 mg/dL
Liver-related Total bilirubin TBil 110,207 0.62 0.29 mg/dL
Liver-related Zinc sulfate turbidity test ZTT 12,303 8.00 3.97 U
Liver-related Aspartate aminotransferase AST 134,154 22.96 7.79 IU/L
Liver-related Alanine aminotransferase ALT 134,182 22.33 11.94 IU/L
Liver-related Alkaline phosphatase ALP 105,030 234.20 83.13 IU/L
Liver-related Gamma-glutamyl transferase GGT 118,309 35.00 25.39 IU/L
Other biochemical Activated partial thromboplastin time APTT 37,767 30.07 4.78 sec
Other biochemical Prothrombin time PT 58,110 1.06 0.16 sec
Other biochemical Fibrinogen Fbg 18,348 323.06 104.48 mg/dL
Other biochemical Creatine kinase CK 106,080 101.40 55.85 IU/L
Other biochemical Lactate dehydrogenase LDH 126,319 223.43 89.46 IU/L
Other biochemical C-reactive protein CRP 75,391 0.24 0.27 mg/dL
Hematological White blood cell count WBC 107,964 6126.44 1856.41 /μL
Hematological Neutrophil count Neutro 62,076 3673.61 1501.73 /μL
Hematological Eosinophil count Eosino 62,076 189.13 191.08 /μL
Hematological Basophil count Baso 62,076 36.31 33.68 /μL
Hematological Monocyte count Mono 62,076 376.19 170.94 /μL
Hematological Lymphocyte count Lym 62,076 1791.08 702.76 /μL
Hematological Red blood cell count RBC 108,794 434.93 55.21 104/μL
Hematological Hemoglobin Hb 108,769 13.45 1.74 g/dL
Hematological Hematocrit Ht 108,757 40.27 4.82 %
Hematological Mean corpuscular volume MCV 108,256 92.88 5.19 fL
Hematological Mean corpuscular hemoglobin MCH 108,054 31.04 2.01 pg
Hematological Mean corpuscular hemoglobin concentration MCHC 108,728 33.38 1.07 %
Hematological Platelet count Plt 108,208 22.63 6.78 104/μL
Blood pressure Systolic blood pressure SBP 136,597 134.68 19.69 mmHg
Blood pressure Diastolic blood pressure DBP 136,615 79.35 12.13 mmHg
Blood pressure Mean arterial pressure MAP 136,482 97.76 13.51 mmHg
Blood pressure Pulse pressure PP 136,249 55.21 13.79 mmHg
Echocardiographic Interventricular septum thickness IVS 19,318 9.95 2.00 mm
Echocardiographic Posterior wall thickness PW 19,373 9.78 1.72 mm
Echocardiographic Left ventricular internal dimension in diastole LVDd 19,676 48.91 7.27 mm
Echocardiographic Left ventricular internal dimension in systole LVDs 19,586 32.44 8.06 mm
Echocardiographic Left ventricular mass LVM 19,076 174.40 53.86 g
Echocardiographic Left ventricular mass index LVMI 17,837 106.05 30.60 g/m2
Echocardiographic Relative wall thickness RWT 19,311 0.41 0.09 [ratio]
Echocardiographic Fractional shortening FS 19,580 34.11 8.75 %
Echocardiographic Ejection fraction EF 19,516 61.39 13.14 %
Echocardiographic E/A ratio E/A 8,600 0.86 0.32 [ratio]

* Detailed chracteristics of these traits were available in Supplementary Table 1 of the paper.

Files

The data set contains 116 files in total. For each trait, two files were provided as follows.

File name Chromosome # variants
BBJ.[TRAIT].autosome.txt.gz Autosome 5,961,600
BBJ.[TRAIT].chrX.txt.gz X chromosome 147,353

Column description

Column Description
1 SNP Marker name
2 CHR Chromosome
3 POS Position (hg19)
4 REF Reference allele
5 ALT Alternative allele
6 Frq a Alternative allele frequency
7 Rsq Imputation quality
8 BETA b Beta
9 SE Standard error
10 P c P-value
11 LOG10P −log10 (P)
12 N Sample size

a Allele frequency was calculated within the BioBank Japan Project (n = 200,849).
b Alternative alleles were tested as effect alleles.
c We conducted a GWAS using a linear regression model under the assumption of additive allelic effects of the SNP dosages via mach2qtl. Note that P-value might be less than DBL_MIN (the minimum double value).

Reference

When using these summary statistics, please cite the following paper.

Links