How do I use POSTGAP output?

The POSTGAP output is a tab-delimited file with many columns:

1. ld_snp_rsID rsID of putative causal SNP (LD SNP) being tested
2. chrom chromosome name of LD SNP
3. pos position of LD SNP on chromosome
4. GRCh38_chrom chromosome name of LD SNP on GRCh38
5. GRCh38_pos position of LD SNP on chromosome in GRCh38
6. afr 1000 Genomes MAF for AFR
7. amr 1000 Genomes MAF for AMR
8. eas 1000 Genomes MAF for EAS
9. eur 1000 Genomes MAF for EUR
10. sas 1000 Genomes MAF for SAS
11. gnomad Overall gnomaD MAF
12. gnomad_sas gnomaD MAF for SAS
13. gnomad_oth gnomaD MAF for OTH
14. gnomad_asj gnomaD MAF for ASJ
15. gnomad_nfe gnomaD MAF for NFE
16. gnomad_afr gnomaD MAF for AFR
17. gnomad_amr gnomaD MAF for AMR
18. gnomad_fin gnomaD MAF for FIN
19. gnomad_eas gnomaD MAF for EAS
20. gene_symbol HGNC symbol of gene being tested
21. gene_id Ensembl ID of gene being tested
22. gene_chrom Chromosome name of gene being tested
23. gene_tss Position on the chromosome of TSS of gene being tested
24. GRCh38_gene_chrom Chromosome name of gene being tested in GRCh38
25. GRCh38_gene_pos Position on the chromosome of TSS of gene being tested on GRCh38
26. disease_name Normalised name of disease or trait being tested
27. disease_efo_id Ontology ID of disease or trait being tested
28. score Stopgap V2G score tying LD SNP to gene
29. rank Rank of gene's V2G score among other genes tied to LD SNP
30. r2 Pearson correlation of LD SNP to the GWAS SNP with lowest p-value
31. cluster_id Internal ID to LD SNP cluster
32. gwas_source Source database of GWAS SNPs
33. gwas_snp SNPs associated to disease by GWAS
34. gwas_pvalue P-values of reported associations
35. gwas_pvalue_description Description of study associated to p-value
36. gwas_odds_ratio Odds ratio
37. gwas_odds_ratio_ci_start Lower limit of OR confidence interval
38. gwas_odds_ratio_ci_end Upper limit of OR confidence interval
39. gwas_beta GWAS Beta coefficient
40. gwas_size Sample sizes of reported associations
41. gwas_pmid Source publication PubmedID of reported associations
42. gwas_study Study identifier
43. gwas_reported_trait Disease or trait of reported association
44. ld_snp_is_gwas_snp 1 if LD SNP is one of the GWAS SNPs, 0 otherwise
45. vep_terms VEP consequence terms associated to LD_SNP
46. vep_sum Sum of consequence impacts of LD SNP across all transcripts of gene:
    • 'HIGH': 4,
    • 'MEDIUM': 3,
    • 'LOW': 2,
    • 'MODIFIER': 1,
    • 'MODERATE': 1
47. vep_mean Mean of consequence impacts of LD SNP across all transcripts of gene:
    • 'HIGH': 4,
    • 'MEDIUM': 3,
    • 'LOW': 2,
    • 'MODIFIER': 1,
    • 'MODERATE': 1
48. GTEx_Thyroid 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
49. GTEx_Testis 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
50. GTEx_Artery_Tibial 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
51. GTEx_Nerve_Tibial 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
52. GTEx_Brain_Frontal_Cortex_BA9 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
53. GTEx_Artery_Aorta 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
54. GTEx_Vagina 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
55. GTEx_Brain_Hypothalamus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
56. GTEx_Whole_Blood 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
57. GTEx_Breast_Mammary_Tissue 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
58. GTEx_Pituitary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
59. GTEx_Small_Intestine_Terminal_Ileum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
60. GTEx_Adrenal_Gland 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
61. GTEx_Heart_Atrial_Appendage 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
62. GTEx_Stomach 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
63. GTEx_Brain_Caudate_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
64. GTEx_Colon_Transverse 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
65. GTEx_Brain_Cerebellum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
66. GTEx_Esophagus_Muscularis 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
67. GTEx_Liver 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
68. GTEx_Muscle_Skeletal 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
69. GTEx_Prostate 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
70. GTEx_Pancreas 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
71. GTEx_Adipose_Subcutaneous 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
72. GTEx_Spleen 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
73. GTEx_Colon_Sigmoid 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
74. GTEx_Brain_Anterior_cingulate_cortex_BA24 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
75. GTEx_Esophagus_Gastroesophageal_Junction 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
76. GTEx_Brain_Hippocampus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
77. GTEx_Brain_Cortex 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
78. GTEx_Heart_Left_Ventricle 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
79. GTEx_Cells_Transformed_fibroblasts 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
80. GTEx_Uterus 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
81. GTEx_Ovary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
82. GTEx_Cells_EBV-transformed_lymphocytes 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
83. GTEx_Artery_Coronary 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
84. GTEx_Adipose_Visceral_Omentum 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
85. GTEx_Brain_Nucleus_accumbens_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
86. GTEx_Brain_Cerebellar_Hemisphere 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
87. GTEx_Esophagus_Mucosa 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
88. GTEx_Skin_Not_Sun_Exposed_Suprapubic 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
89. GTEx_Brain_Putamen_basal_ganglia 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
90. GTEx_Lung 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
91. GTEx_Skin_Sun_Exposed_Lower_leg 1 - pvalue of association between the LD SNP and the Gene in GTEx for that tissue
92. GTEx Maximum of all the above GTEx scores
93. VEP Max of consequence impacts of LD SNP across all transcripts of gene:
    • 'HIGH': 4,
    • 'MEDIUM': 3,
    • 'LOW': 2,
    • 'MODIFIER': 1,
    • 'MODERATE': 1
94. Fantom5 Maximum score of FANTOM5 link between LD SNP and gene, normalised for FDR
95. DHS Maximum score of ENCODE DHS link between LD SNP and gene, normalised for FDR
96. PCHiC Maximum score of CHiCAGO links between LD SNP and gene across tissues, normalised for FDR
97. Nearest 1 if gene has the nearest protein-coding TSS to LD SNP, 0 otherwise
98. Regulome 1 if LD SNP is of Category 1 or 2, 0.5 if LD SNP in Category 3
99. GERP GERP conservation score across mammalian species