GWAS summary statistics of 220 deep phenotypes in European population.

General information:

Here, we provide summary statistics of either (i) meta-analysis result of UK Biobank and FinnGen or (ii) UK Biobank GWAS of disease endpoints without matching phenotype in FinnGen. In filenames, (i) is indicated as EUR and (ii) is indicated as UKB.
We do not directly provide summary statistics of UK Biobank or FinnGen if we just use raw data provided by each cohort or other labs.
Genotyping array: UK Biobank: either the Applied Biosystems UK BiLEVE Axiom Array or the Applied Biosystems UK Biobank Axiom Array. FinnGen: the FinnGen1 ThermoFisher array or other genotyping arrays in previous cohorts.
Sample population: UK Biobank: We analyzed individuals of white British genetic ancestry as determined by the PCA-based sample selection criteria. FinnGen: We excluded population outliers via PCA.
Phenotyping: UKB GWAS was conducted based on UKB ICD10/9 mapped to Phecode, and FinnGen GWAS was conducted based on FinnGen endpoint.
Phasing and imputation: UK Biobank: IMPUTE4 software. FinnGen: beagle4.1 software.
Imputation reference: UK Biobank: A combination of the Haplotype Reference Consortium, UK10K, and 1000 Genomes Phase 3 reference panels. FinnGen: A panel with whole-genome sequencing data from 3,775 Finnish individuals.
Post-imputation QC: UK Biobank: We excluded the variants with (i) INFO score ≤ 0.8, (ii) MAF ≤ 0.0001 (except for missense and protein-truncating variants annotated by VEP, which were excluded if MAF ≤ 1 × 10^-6), and (iii) P_HWE ≤ 1 × 10^-10. FinnGen: We excluded variants with an imputation INFO score < 0.8 or MAF < 0.0001.
Association test: SAIGE software was used with age, age², sex, age×sex, age²×sex, and top 20 principal components as covariates.
Meta-analysis: METAL software was used to conduct meta-analysis by the inverse-variance method.

Uploaded files

File name	Descriptions
GWASsummary_{TRAITNAME}_{EUR/UKB}_SakaueKanai2020.auto.txt.gz	Summary results for autosomal variants
GWASsummary_{TRAITNAME}_{EUR/UKB}_SakaueKanai2020.chrX.txt.gz	Summary results for X-chromosomal variants

Please note that UKB GWAS was conducted based on UKB ICD10/9 mapped to Phecode, and FinnGen GWAS was conducted based on FinnGen endpoint. We strongly recommend you to check the phenotype codings before using these summary statistics.

Columns

(i) Meta-analysis result of UK Biobank and FinnGen

We provide the summary statitics of meta-analysis (using METAL software) and allele frequency data from each of the cohorts.

#	column name	Descriptions
1	v	marker name (CHR:POS:REF:ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	Allele1	REF allele
5	Allele2	ALT allele (This allele is the effect allele.)
6	AF_Allele2_UKB	allele frequency of Allele2 (ALT) in UK Biobank
7	AF_Allele2_FG	allele frequency of Allele2 (ALT) in FinnGen
8	Direction	the signs of betas in UK Biobank (left) and FinnGen (right)
9	BETA	effect size of Allele2 in meta-analysis
10	SE	standard error of BETA in meta-analysis
11	p.value	P value in meta-analysis

(ii) UK Biobank GWAS of disease endpoints without matching phenotype in FinnGen

We provide the output from SAIGE software in autosome and sex-combined meta-analysis in X chromosome.
Please be careful with the header, and also refer to the SAIGE website.

Autosome summary

#	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

X chromosome summary

#	column name	Descriptions
1	v	marker name (CHR:POS:REF:ALT)
2	CHR	chromosome
3	POS	position (hg19)
4	Allele1	REF allele
5	Allele2	ALT allele (This allele is the effect allele.)
6	AF_Allele2	allele frequency of Allele2 (ALT) in UK Biobank
7	N	sample size
8	BETA	effect size of Allele2 in meta-analysis
9	SE	standard error of BETA in meta-analysis
10	p.value	P value in sex-combined meta-analysis

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.