[ File names ]
- GWAS using both sexes
*.auto.rsq07.mac10.txt.gz
*.chrx.rsq07.mac10.txt.gz

- Sex stratified GWAS
*.auto_sex_stratified.txt.gz
*.chrx_sex_stratified.txt.gz


[ Information ]
- Removed variants with MAC < 10
- Effect allele = alternative allele
- Positions are based on hg19
- Association test was performed using SAIGE (v 0.29.4.2; Wei Zhou et al. Nature Genetics 2018)
- Please visit wiki page of SAIGE for more information (https://github.com/weizhouUMICH/SAIGE/wiki)

[ Header ]
CHR: chromosome
POS: genome position
SNPID: variant ID
Allele1: reference allele
Allele2: alternative allele
AC_Allele2: allele count of alternative allele
AF_Allele2: allele frequency of alternative allele
N: sample size
BETA: effect size (effect of alternative allele)
SE: standard error of BETA
Tstat: t statistic
p.value: p value with the saddlepoint approximation method (SPA) applied
p.value.NA: p value when SPA is not applied
Is.SPA.converge: whether SPA is converged (1) or not (0)
varT: estimated variance of score statistic with sample related incorporated
varTstar: variance of score statistic without sample related incorporated
AF.Cases/AF.Controls: allele frequency of alternative allele
Rsq: imputation quality measure in minimac3
MAC: minor allele count
Rsq.male: imputation quality for male
Rsq.female: imputation quality for female
**.x/**.y; male data and female data (e.g. BETA.x is BETA in male GWAS. In single sex diseases, **.x suggests target sex data, and **.y is set to NA)
single sex diseases: Breast cancer, Cervical cancer, Endometrial cancer, Endometriosis, Ovarian cancer, Uterine fibroid, and Prostate cancer


[ Additional header in *sex_stratified.txt.gz ]
metabeta: beta estimated by fixed effect meta-analysis between male and female specific GWAS.
metase: se of metabeta
metap: p of metabeta
Qpvalue: heterogeneity in effect size between male and female specific GWAS (Cochran’s Q test).

Sample sizes in each GWAS (sex_stratified) are shown in the file named "hum0014_v21_sample_size.xlsx" 
(Click "Sample size file" [under "Dictionary file" at the hum0014.v17/hum0014.v18/hum0014.v21 MOLECULAR DATA table] to download the file).