GWAS summary statistics of 220 deep phenotypes in Japanese.

General information:

Genotyping array: the Illumina HumanOmniExpressExome BeadChip or a combination of the Illumina HumanOmniExpress and HumanExome BeadChips.
Sample QC: We excluded samples with low genotyping call rates (call rate < 98%). We included samples of the estimated East Asian ancestry using PCA.
Variant QC: We excluded variants with (1) genotyping call rate < 99%, (2) P value for Hardy–Weinberg equilibrium < 1.0 × 10⁻⁶, and (3) number of heterozygotes < 5.
Phasing and imputation: Eagle and Minimac3
Imputation reference: Combined panel of WGS data from the BioBank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504).
Post-imputation QC: We here report results of whole-genome imputed variants with Rsq > 0.7.
Association test: For binary traits (disease endpoints and medications), SAIGE software was used with age, age², sex, age×sex, age²×sex, and top 20 principal components as covariates. For quantitative traits (biomarkers),BOLT-LMM software was used with the same covariates.

Uploaded files

File name	Descriptions
GWASsummary_{TRAITNAME}_Japanese_SakaueKanai2020.auto.txt.gz	Summary results for autosomal variants
GWASsummary_{TRAITNAME}_Japanese_SakaueKanai2020.chrX.txt.gz	Summary results for X-chromosomal variants

Columns

Binary traits (disease endpoints and medications)

We provide the output from SAIGE software.
Please also refer to the SAIGE website.

#	column name	Descriptions
1	v	marker name (CHR:POS:REF:ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	SNPID	rsID (if present) or equivalent ID
5	Allele1	REF allele
6	Allele2	ALT allele (This allele is the effect allele.)
7	AC_Allele2	allele count of Allele2 (ALT)
8	AF_Allele2	allele frequency of Allele2 (ALT)
9	imputationInfo	RSQ value in imputation
10	N	sample size
11	BETA	effect size of Allele2
12	SE	standard error f BETA
13	Tstat	score statistic
14	p.value	P value with SPA (suddle point approximation) applied
15	p.value.NA	P value when SPA is not applied
16	Is.SPA.converge	whether SPA is converged or not
17	varT	estimated variance of score statistic with sample related incorporated
18	varTstar	variance of score statistic without sample related incorporated
19	AF.Cases	allele frequency of Allele2 in cases
20	AF.Controls	allele frequency of Allele2 in controls

Quantitative traits (biomarkers)

We provide the output from BOLT software.
Please also refer to the BOLT website.

#	column name	Descriptions
1	v	marker name (CHR:POS:REF:ALT)
2	SNP	rsID (if present) or equivalent ID
3	CHR	chromosome
4	BP	position (hg19)
5	GENPOS	genetic position
6	ALLELE1	the effect allele
7	ALLELE0	the other allele
8	A1FREQ	the frequency of ALLELE1
9	INFO	RSQ value in imputation
10	CHISQ_LINREG	chi-squared value in linear regression
11	P_LINREG	P value in linear regression
12	BETA	effect size from BOLT-LMM approximation to infinitesimal mixed model
13	SE	standard error of effect size
14	CHISQ_BOLT_LMM_INF	infinitesimal mixed model association test chi-squared value
15	P_BOLT_LMM_INF	infinitesimal mixed model association test P value

Reference

If you use these summary statistics, please cite the following paper;
Sakaue S and Kanai M et al. A global atlas of genetic associations of 220 deep phenotypes. medRxiv 2020.