What does POSTGAP do?

POSTGAP works in 5 stages:

1. Extracting significant GWAS peaks

If provided a diseases description(s), it attempts to map it to the Experimental Factor Ontology (EFO) using EMBL-EBI's Zooma service.

It then uses whatever diseases descriptions and ontology terms available and queries a number of public GWAS databases, in particular:

• GWAS Catalog
• GRASP
• GWAS DB
• Phewas Catalog

All SNPs with a p-value association below 1e-5 are retained as GWAS SNPs.

2. Computing SNP clusters of interest

Using the 1000 Genomes genotypes it creates a cluster around each GWAS SNP, by selecting all SNPs with LD r^2 > 0.7.

3. Extracting regulatory information

It queries a few databases for any evidence of regulatory activity on all of the SNPs:

• Ensembl for ExAC variant frequencies
• Regulome DB for evidence of epigenomic activity

4. Extracting cis-regulatory information

It queries a few databases for any evidence of cis-regulatory interactions on all of the SNPs:

• GTEx eQTLs
• VEP for transcript overlaps
• Fantom5 for CAGE-tag activity correlation
• ENCODE for DNAse Hypersensitivity Correlation
• CHiCAGO for Promoter Capture Hi-C links

5. Synthesising results