This repository has been archived by the owner on Feb 28, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 21
How do I use POSTGAP output?
Daniel Zerbino edited this page Feb 21, 2019
·
5 revisions
The POSTGAP output is a tab-delimited file with many columns:
- ld_snp_rsID rsID of putative causal SNP (LD SNP) being tested
- chrom chromosome name of LD SNP
- pos position of LD SNP on chromosome
- GRCh38_chrom chromosome name of LD SNP on GRCh38
- GRCh38_pos position of LD SNP on chromosome in GRCh38
- afr 1000 Genomes MAF for AFR
- amr 1000 Genomes MAF for AMR
- eas 1000 Genomes MAF for EAS
- eur 1000 Genomes MAF for EUR
- sas 1000 Genomes MAF for SAS
- gnomad Overall gnomaD MAF
- gnomad_sas gnomaD MAF for SAS
- gnomad_oth gnomaD MAF for OTH
- gnomad_asj gnomaD MAF for ASJ
- gnomad_nfe gnomaD MAF for NFE
- gnomad_afr gnomaD MAF for AFR
- gnomad_amr gnomaD MAF for AMR
- gnomad_fin gnomaD MAF for FIN
- gnomad_eas gnomaD MAF for EAS
- gene_symbol HGNC symbol of gene being tested
- gene_id Ensembl ID of gene being tested
- gene_chrom Chromosome name of gene being tested
- gene_tss Position on the chromosome of TSS of gene being tested
- GRCh38_gene_chrom Chromosome name of gene being tested in GRCh38
- GRCh38_gene_pos Position on the chromosome of TSS of gene being tested on GRCh38
- disease_name Normalised name of disease or trait being tested
- disease_efo_id Ontology ID of disease or trait being tested
- score Stopgap V2G score tying LD SNP to gene
- rank Rank of gene's V2G score among other genes tied to LD SNP
- r2 Pearson correlation of LD SNP to the GWAS SNP with lowest p-value
- cluster_id Internal ID to LD SNP cluster
- gwas_source Source database of GWAS SNPs
- gwas_snp SNPs associated to disease by GWAS
- gwas_pvalue P-values of reported associations
- gwas_pvalue_description Description of study associated to p-value
- gwas_odds_ratio Odds ratio
- gwas_odds_ratio_ci_start Lower limit of OR confidence interval
- gwas_odds_ratio_ci_end Upper limit of OR confidence interval
- gwas_beta GWAS Beta coefficient
- gwas_size Sample sizes of reported associations
- gwas_pmid Source publication PubmedID of reported associations
- gwas_study Study identifier
- gwas_reported_trait Disease or trait of reported association
- ld_snp_is_gwas_snp 1 if LD SNP is one of the GWAS SNPs, 0 otherwise
- vep_terms VEP consequence terms associated to LD_SNP
- vep_sum Sum of consequence impacts of LD SNP across all transcripts of gene:
- 'HIGH': 4,
- 'MEDIUM': 3,
- 'LOW': 2,
- 'MODIFIER': 1,
- 'MODERATE': 1
- vep_mean Mean of consequence impacts of LD SNP across all transcripts of gene:
- 'HIGH': 4,
- 'MEDIUM': 3,
- 'LOW': 2,
- 'MODIFIER': 1,
- 'MODERATE': 1
- GTEx_Thyroid 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Testis 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Artery_Tibial 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Nerve_Tibial 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Frontal_Cortex_BA9 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Artery_Aorta 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Vagina 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Hypothalamus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Whole_Blood 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Breast_Mammary_Tissue 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Pituitary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Small_Intestine_Terminal_Ileum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Adrenal_Gland 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Heart_Atrial_Appendage 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Stomach 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Caudate_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Colon_Transverse 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Cerebellum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Esophagus_Muscularis 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Liver 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Muscle_Skeletal 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Prostate 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Pancreas 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Adipose_Subcutaneous 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Spleen 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Colon_Sigmoid 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Anterior_cingulate_cortex_BA24 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Esophagus_Gastroesophageal_Junction 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Hippocampus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Cortex 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Heart_Left_Ventricle 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Cells_Transformed_fibroblasts 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Uterus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Ovary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Cells_EBV-transformed_lymphocytes 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Artery_Coronary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Adipose_Visceral_Omentum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Nucleus_accumbens_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Cerebellar_Hemisphere 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Esophagus_Mucosa 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Skin_Not_Sun_Exposed_Suprapubic 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Brain_Putamen_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Lung 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx_Skin_Sun_Exposed_Lower_leg 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
- GTEx Maximum of all the above GTEx scores
- VEP Max of consequence impacts of LD SNP across all transcripts of gene:
- 'HIGH': 4,
- 'MEDIUM': 3,
- 'LOW': 2,
- 'MODIFIER': 1,
- 'MODERATE': 1
- Fantom5 Maximum score of FANTOM5 link between LD SNP and gene, normalised for FDR
- DHS Maximum score of ENCODE DHS link between LD SNP and gene, normalised for FDR
- PCHiC Maximum score of CHiCAGO links between LD SNP and gene across tissues, normalised for FDR
- Nearest 1 if gene has the nearest protein-coding TSS to LD SNP, 0 otherwise
- Regulome 1 if LD SNP is of Category 1 or 2, 0.5 if LD SNP in Category 3
- GERP GERP conservation score across mammalian species