Colocalization results format
Last updated
Last updated
vas1_info
The colocalization data contains data that was acquired by running a colocalization analysis between FinnGen data and other datasets.
The colocalization results are tab-separated files. The results contain one source1-phenotype1-locus1 source2-phenotype2-locus2-pair per line. More information about data sources, phenotypes and loci can be found in the Colocalization in FinnGen page.
The results contains the following columns:
Column name | Column description |
---|---|
More information about the methods can be found in th Colocalization in FinnGen page, as well as the methods document:
/finngen/library-green/finngen_R12_analysis_data/colocalization/methods.pdf
More documentation about the data, including the columns and their descriptions, can be found in the release notes.
Read more about Colocalization and Colocalization in FinnGen
source1
Data source 1, always FinnGen
source2
Data source 2
pheno1
Phenotype 1
pheno2
Phenotype 2
pheno1_description
Description of phenotype 1
pheno2_description
Description of phenotype 2
quant1
Data quantification for phenotype 1. For eQTL Catalog data, this can be exon counts, gene counts, transcript usage, txrevise event usage. For other sources blank.
quant2
Data quantification for phenotype 1. For eQTL Catalog data, this can be exon counts, gene counts, transcript usage, txrevise event usage. For other sources blank.
tissue1
Tissue for phenotype 1 if applicable
tissue2
Tissue for phenotype 1 if applicable
locus_id1
Locus identifier of credible set of pheno1, locus_id = top SNP (max PIP). Formatted as CHROM_POS_REF_ALT
locus_id2
Locus identifier of credible set of pheno2, locus_id = top SNP (max PIP). Formatted as CHROM_POS_REF_ALT
chrom
Chromosome where the loci are
start
Start position of intersecting credible sets (in bp, on build hg38)
stop
End position of intersecting credible sets (in bp, on build hg38)
clpp
Colocalization posterior probability: sum_i(PIP1_i*PIP2_i). See Colocalization in FinnGen for more information
clpa
Colocalization posterior agreement: sum_i(min(PIP1_i,PIP2_i)). See Colocalization in FinnGen for more information
vars
Intersecting variants
len_cs1
Amount of variants in pheno1 credible set
len_cs2
Amount of variants in pheno2 credible set
len_inter
Amount of variants shared between credible set 1 and credible set 2
vars1_info
Information about variants in the credible set of phenotype 1. Each variant has its variant identifier, PIP, beta, and p-value. Variant fields are separated by comma, and variants are separated by semicolon.
vars2_info
Information about variants in the credible set of phenotype 2. Each variant has its variant identifier, PIP, beta, and p-value. Variant fields are separated by comma, and variants are separated by semicolon.
beta1
effect size of lead SNP in locus 1
beta2
effect size of lead SNP in locus 2
pval1
p-value of lead SNP in locus 1
pval2
p-value of lead SNP in locus 2