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

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