UKBB-FinnGen meta-analysis file formats

The meta-analysis result files are TSV tabix-indexed files compressed with bgzip, which contain the summary statistics from the FinnGen and UKBB analyses and the summary statistics of the meta-analysis. The columns of the table are described below.

Read more about the UKBB-FinnGen meta-analysis.

Column name	Description
#CHR	Chromosome
POS	Position
REF	Reference base
ALT	Alternative allele(s)
SNP	Variant in format #CHR:POS:REF:ALT
FINNGEN_beta	FinnGen summary beta
FINNGEN_sebeta	FinnGen summary standard deviation
FINNGEN_pval	FinnGen summary p-value
FINNGEN_af_alt	FinnGen alternative allele frequency
FINNGEN_af_alt_cases	FinnGen alternative allele frequency in cases
FINNGEN_af_alt_controls	FinnGen alternative allele frequency in controls
UKBB_beta	UKBB summary beta
UKBB_sebeta	UKBB summary standard deviation
UKBB_pval	UKBB summary p-value
UKBB_af_alt	UKBB alternative allele frequency
all_meta_N	Number of studies used for meta-analysis
all_inv_var_meta_beta	Inverse-variance weighted meta-analysis beta
all_inv_var_meta_sebeta	Inverse-variance weighted meta-analysis standard deviation
all_inv_var_meta_p	Inverse-variance weighted meta-analysis p-value
all_inv_var_meta_mlogp	Inverse-variance weighted meta-analysis -log10(p-value)
all_inv_var_het_p	Inverse-variance weighted meta-analysis Cochran's Q test p-value
rsid	Reference SNP ID assigned by dbSNP