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# Summary statistics - Cross-ancestry GWAS of Age at Menarche in the UK Biobank #
# Contact: chloesar@bu.edu                                                      #
# Citation: PMID: 34021356 PMCID: PMC8213450                                    #
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Sample
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Participants: women with diverse and predominantly non-European ancestry (exclusion based on the following self-reported ancestries: "White", "British", "Irish" and "Any other white background")
Phenotype: age at menarche (variable 2714) information at all of the three exams available
Exclusion of participants: age at menarche < 9 or > 17; samples with high heterozygosity and high missing rate, sex aneuploidy, or with different genomic and stated sex (based on the UK Biobank QC file)

Genotyping & association analysis
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Genotyping array: Applied Biosystems UKBB Lung Exome Variant Evaluation UKBB Axiom Arrays
Imputation panel: HRC / UK10K + 1kG phase 3
Software: Scalable and Accurate Implementation of Generalized mixed model (SAIGE) (Zhou et al., 2018)
Statistical model: linear mixed-effects model adjusted for birth cohort and PCs significantly associated with age at menarche
Variant QC: SAIGE minMAC=3, minMAF=10-6, post-analysis: imputation quality score >= 0.30,  effective number of minor alleles (minor allele count x imputation quality score) >= 20


Column names / Header
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CHR: chromosome
POS: genome position (build 37)
rsid: rsid
SNPID: variant ID (chromosome:position_al1_al2)
Allele1: allele 1
Allele2: allele 2 (effect allele)
AC_Allele2: allele count of allele 2
AF_Allele2: allele frequency of allele 2
imputationInfo: imputation info / quality score
N: sample size
BETA: effect size of allele 2
SE: standard error of BETA
Tstat: score statistic of allele 2
p.value: p value
varT: estimated variance of score statistic with sample relatedness incorporated
varTstar: variance of score statistic without sample relatedness incorporated