Data description

File naming pattern and file structure

Summary association statistics

GWAS summary statistics (tab-delimited, bgzipped, genome build 38, tabix index files included) are named as {endpoint}.gz. For example, endpoint I9_CHD has I9_CHD.gz and I9_CHD.gz.tbi. Note that the results are based on imputed genotype data and produced using SAIGE and that is why the data is not presented as integers but might contain digits.

To learn more about the methods used, see section GWAS.

The {endpoint}.gz have the following structure:

Column name	Description
#chrom	chromosome on build GRCh38 (1-22, X)
pos	position in base pairs on build GRCh38
ref	reference allele
alt	alternative allele (effect allele)
rsids	variant identifier
nearest_genes	nearest gene name from variant
pval	p-value from SAIGE
beta	effect size estimated with SAIGE for the alternative allele
sebeta	standard deviation of effect size estimated with SAIGE
maf	alternative (effect) allele frequency
maf_cases	alternative (effect) allele frequency among cases
maf_controls	alternative (effect) allele frequency among controls
n_hom_cases	number of homozygous cases*
n_het_cases	number of heterozygous cases*
n_hom_controls	number of homozygous controls*
n_het_controls	number of heterozygous cases*

*)Note that the results are based on imputed genotype dosages and produced using SAIGE and that is why the data is not presented as integers but might contain digits.

Fine-mapping results

Two fine-mapping methods were used:

• SuSiE

• FINEMAP

Fine-mapping results are tab-delimited and bgzipped.

SuSiE results have the following filename pattern:

• {endpoint}.SUSIE.cred.bgz

• {endpoint}.SUSIE.snp.bgz

FINEMAP results have the following filename pattern:

• {endpoint}.FINEMAP.region.bgz

• {endpoint}.FINEMAP.snp.bgz

• {endpoint}.FINEMAP.config.bgz

To learn more about the methods used, see section Fine-mapping.

SuSiE output files {endpoint}.SUSIE.snp.bgz have the following structure:

Column name	Description
trait	endpoint name
region	chr:start-end
v	variant identifier
rsid	rs variant identifier
chromosome	chromosome on build GRCh38 (1-22, X)
position	position in base pairs on build GRCh38
allele1	reference allele
allele2	alternative allele (effect allele)
maf	minor allele frequency
beta	effect size GWAS
se	standard error GWAS
p	p-value GWAS
mean	posterior expectation of true effect size
sd	posterior standard deviation of true effect size
prob	posterior probability of association
cs	identifier of 95% credible set (-1 = variant is not part of credible set)

LD estimation

Linkage disequilibrium (LD) was estimated from SISU v3 for each chromosome. Use the tool LDstore (v1.1) for further usage of the bcor files.

ldstore --bcor FG_LD_chr1.bcor --incl-range 20000000-50000000 --table output_file_name.table

To learn more about the methods used, see section LD estimation.

Variant annotation

The variant annotation has measures (HWE, INFO, ...) listed per batch.