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.

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

Fine-mapping results

Two fine-mapping methods were used:

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.cred.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.