Sex-specific GWAS results format

There are two sets of results files for the sex-specific analyses. The first are the sex-specific results, output by REGENIE. These files are TSV tabix-indexed, compressed with bgzip and share the GWAS results format.

The second set of files are those produced by meta-analysing the female- and male-specific results, conveniently combining both sexes into a single file along with a heterogeneity statistic. The format of these meta-analysis files is described in the table below.

The sex-difference results are available in the FinnGen sex-difference PheWeb (currently requires an active finngen.fi account). The sex-difference beta reported on PheWeb is calculated as female_beta minus male_beta, the sex-difference standard error (SE) is sqrt(female_se^2 + male_se^2) and the sex-difference P-value is the Cochran's Q P-value (all_inv_var_het_p in meta-analysis results files).

Column name	Description
#CHR	Chromosome
POS	Chromosomal position (GRCh38)
REF	Reference (non-effect) allele
ALT	Alternative (effect) allele
SNP	Unique CHR:POS:REF:ALT variant ID
female_beta	female-only per-allele effect of the ALT allele on endpoint (units are SDs if endpoint is continuous or logOR if endpoint is binary)
female_se	standard error of the female-only effect of the ALT allele
female_pval	p-value of the female-only effect
female_af_alt	allele frequency of the ALT allele in all females
female_af_alt_cases	allele frequency of the ALT allele in female cases only
female_af_alt_controls	allele frequency of the ALT allele in female controls only
male_beta	male-only per-allele effect of the ALT allele on endpoint (units are SDs if endpoint is continuous or logOR if endpoint is binary)
male_se	standard error of the male-only effect of the ALT allele
male_pval	p-value of the male-only effect
male_af_alt	allele frequency of the ALT allele in all males
male_af_alt_cases	allele frequency of the ALT allele in male cases only
male_af_alt_controls	allele frequency of the ALT allele in male controls only
all_meta_N	number of sexes contributing to meta-analysis statistics. Values of 1 indicate that the variant does not have statistics in one sex
all_inv_var_meta_beta	meta-analysed female-male per-allele effect of the ALT allele on the endpoint - units are SDs if endpoint is continuous or logOR if endpoint is binary
all_inv_var_meta_sebeta	standard error of the meta-analysed female-male per-allele effect of ALT
all_inv_var_meta_p	p-value of the meta-analysed female-male per-allele effect
all_inv_var_meta_mlogp	-log10(p-value) of the meta-analysed female-male per-allele effect
all_inv_var_het_p	Cochran's Q heterogeneity p-value denoting significance of the difference of effect between females and males
rsid	rsID of variant (if applicable)