README_2019_BBJ_Height

2019 Biobank Japan Height GWAS summary statistics

General information:

Number of analyzed samples: N = 159,095 (Male: 86,257, Female: 72,838)
Eligibility criteria: 1) age>= 18, 2) available height information, and 3) height within 3 times the IQR of the upper/lower quartile.
Sample QCs: Exclusion criteria: 1) call rate < 98%, 2) closely related samples (PI_HAT > 0.175), and 3) outlier from Japanese cluster determined by PCA using GCTA.
Phenotype: We calculated Z-score from the residuals of linear regression analysis against height using age, age^2, and sex, and excluded individuals who fell outside of +/- 4 standard deviations.
Number of analyzed variants : M = 27,211,524 (autosomal variants), and 684,533 (X-chromosomal variants). Variants with low imputation quality score (Rsq < 0.3) were excluded.
Genotyping array: Illumina HumanOmniExpressExome or a combination of Illumina OmniExpress and Illumina Human Exome.
Haplotype phasing : Eagle2.
Genotype imputation: Minimac3.
Imputation reference panel: Newly constructed reference panel using WGS data of the biobank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504).

Uploaded file name:

File name	Number of samples	Number of variants
2019_BBJ_Height_autosomes_BOLT.txt.gz	159,095	27,211,524
2019_BBJ_Height_Xchromosome_male_mach2qtl.txt.gz	86,257	684,533
2019_BBJ_Height_Xchromosome_female_mach2qtl.txt.gz	72,838	684,533

Column:

■ Autosomal variants

Number of column	column	Description
1	Variants	marker name (CHR:POS_REF_ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	REF	reference allele
5	ALT	alternative allele
6	ALT_freq	alternative allele frequency
7	MAF	minor allele frequency
8	Rsq	imputation quality
9	BETA	beta
10	SE	standard error
11	P_INF	P-value estimated by standard infinitesimal mixed model
12	P_BOLT	P-value estimated by BOLT-LMM

・　Alternative alleles were used as effect alleles.
・　Association analysis was performed using BOLT-LMM software (ver2.2).

■ X-chromosomal variants

Number of column	column	Description
1	Variants	marker name (CHR:POS_REF_ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	REF	reference allele
5	ALT	alternative allele
6	ALT_freq	alternative allele frequency
7	MAF	minor allele frequency
8	Rsq	imputation quality
9	BETA	beta
10	SE	standard error
11	P	P-value estimated by mach2qtl software

・　Alternative alleles were used as effect alleles.
・　Association analysis was performed using mach2qtl software.

URLs:

National Bioscience Database Center Human Database
The biobank Japan project
RIKEN Center for Integrative Medical Sciences

Reference:

If you use these date, please cite the following paper:
Akiyama M et al. Characterizing rare and low-frequency height-asssociated variants in the Japanese population (Nat. Commun., 2019). doi:10.1038/s41467-019-12276-5