GWAS summary statistics of 220 deep phenotypes in trans-ethnic meta-analysis.

General information:

Uploaded files

File name Descriptions
GWASsummary_{TRAITNAME} Summary results for autosomal variants
GWASsummary_{TRAITNAME}_META_SakaueKanai2020.chrX.txt.gz Summary results for X-chromosomal variants

Please always be aware 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.


We provide the summary statitics of trans-ethnic meta-analysis (using METAL software) and allele frequency data from each of the cohorts. Please always carefully check the header before using the summary statistics. Column numbers are different according to the phenotypes!

# 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_BBJ allele frequency of Allele2 (ALT) in BBJ
X AF_Allele2_UKB allele frequency of Allele2 (ALT) in UK Biobank
X AF_Allele2_FG allele frequency of Allele2 (ALT) in FinnGen
X Direction the signs of betas in each of the cohorts in the order of BBJ, UK Biobank and FinnGen*
X BETA effect size of Allele2 in meta-analysis
X SE standard error of BETA in meta-analysis
X p.value P value in meta-analysis

* The directions are consisted of the meta-analyzed cohorts only (either (i) BBJ + UKB + FinnFen, (ii) BBJ + UKB, or (iii) BBJ + FinnGen).
X; the column number can be different according to the combination of the cohorts where the meta-analysis has been performed.


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.