gwas-database

GWAS Catalog Database

Overview

The GWAS Catalog is a comprehensive repository of published genome-wide association studies maintained by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EBI). The catalog contains curated SNP-trait associations from thousands of GWAS publications, including genetic variants, associated traits and diseases, p-values, effect sizes, and full summary statistics for many studies.

When to Use This Skill

This skill should be used when queries involve:

• Genetic variant associations: Finding SNPs associated with diseases or traits
• SNP lookups: Retrieving information about specific genetic variants (rs IDs)
• Trait/disease searches: Discovering genetic associations for phenotypes
• Gene associations: Finding variants in or near specific genes
• GWAS summary statistics: Accessing complete genome-wide association data
• Study metadata: Retrieving publication and cohort information
• Population genetics: Exploring ancestry-specific associations
• Polygenic risk scores: Identifying variants for risk prediction models
• Functional genomics: Understanding variant effects and genomic context
• Systematic reviews: Comprehensive literature synthesis of genetic associations

Core Capabilities

1. Understanding GWAS Catalog Data Structure

The GWAS Catalog is organized around four core entities:

• Studies: GWAS publications with metadata (PMID, author, cohort details)
• Associations: SNP-trait associations with statistical evidence (p ≤ 5×10⁻⁸)
• Variants: Genetic markers (SNPs) with genomic coordinates and alleles
• Traits: Phenotypes and diseases (mapped to EFO ontology terms)

Key Identifiers:

• Study accessions: GCST IDs (e.g., GCST001234)
• Variant IDs: rs numbers (e.g., rs7903146) or variant_id format
• Trait IDs: EFO terms (e.g., EFO_0001360 for type 2 diabetes)
• Gene symbols: HGNC approved names (e.g., TCF7L2)

2. Web Interface Searches

The web interface at https://www.ebi.ac.uk/gwas/ supports multiple search modes:

By Variant (rs ID):

rs7903146

Returns all trait associations for this SNP.

By Disease/Trait:

type 2 diabetes
Parkinson disease
body mass index

Returns all associated genetic variants.

By Gene:

APOE
TCF7L2

Returns variants in or near the gene region.

By Chromosomal Region:

10:114000000-115000000

Returns variants in the specified genomic interval.

By Publication:

PMID:20581827
Author: McCarthy MI
GCST001234

Returns study details and all reported associations.

3. REST API Access

The GWAS Catalog provides two REST APIs for programmatic access:

Base URLs:

• GWAS Catalog API: https://www.ebi.ac.uk/gwas/rest/api
• Summary Statistics API: https://www.ebi.ac.uk/gwas/summary-statistics/api

API Documentation:

• Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api
• Summary stats docs: https://www.ebi.ac.uk/gwas/summary-statistics/docs/

Core Endpoints:

1. Studies endpoint - /studies/{accessionID}

```python import requests

# Get a specific study url = "https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795" response = requests.get(url, headers={"Content-Type": "application/json"}) study = response.json() ```

1. Associations endpoint - /associations

``python # Find associations for a variant variant = "rs7903146" url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) associations = response.json() ``

1. Variants endpoint - /singleNucleotidePolymorphisms/{rsID}

``python # Get variant details url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7903146" response = requests.get(url, headers={"Content-Type": "application/json"}) variant_info = response.json() ``

1. Traits endpoint - /efoTraits/{efoID}

``python # Get trait information url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360" response = requests.get(url, headers={"Content-Type": "application/json"}) trait_info = response.json() ``

4. Query Examples and Patterns

Example 1: Find all associations for a disease

import requests

trait = "EFO_0001360"  # Type 2 diabetes
base_url = "https://www.ebi.ac.uk/gwas/rest/api"

# Query associations for this trait
url = f"{base_url}/efoTraits/{trait}/associations"
response = requests.get(url, headers={"Content-Type": "application/json"})
associations = response.json()

# Process results
for assoc in associations.get('_embedded', {}).get('associations', []):
    variant = assoc.get('rsId')
    pvalue = assoc.get('pvalue')
    risk_allele = assoc.get('strongestAllele')
    print(f"{variant}: p={pvalue}, risk allele={risk_allele}")

Example 2: Get variant information and all trait associations

import requests

variant = "rs7903146"
base_url = "https://www.ebi.ac.uk/gwas/rest/api"

# Get variant details
url = f"{base_url}/singleNucleotidePolymorphisms/{variant}"
response = requests.get(url, headers={"Content-Type": "application/json"})
variant_data = response.json()

# Get all associations for this variant
url = f"{base_url}/singleNucleotidePolymorphisms/{variant}/associations"
params = {"projection": "associationBySnp"}
response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
associations = response.json()

# Extract trait names and p-values
for assoc in associations.get('_embedded', {}).get('associations', []):
    trait = assoc.get('efoTrait')
    pvalue = assoc.get('pvalue')
    print(f"Trait: {trait}, p-value: {pvalue}")

Example 3: Access summary statistics

import requests

# Query summary statistics API
base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"

# Find associations by trait with p-value threshold
trait = "EFO_0001360"  # Type 2 diabetes
p_upper = "0.000000001"  # p < 1e-9
url = f"{base_url}/traits/{trait}/associations"
params = {
    "p_upper": p_upper,
    "size": 100  # Number of results
}
response = requests.get(url, params=params)
results = response.json()

# Process genome-wide significant hits
for hit in results.get('_embedded', {}).get('associations', []):
    variant_id = hit.get('variant_id')
    chromosome = hit.get('chromosome')
    position = hit.get('base_pair_location')
    pvalue = hit.get('p_value')
    print(f"{chromosome}:{position} ({variant_id}): p={pvalue}")

Example 4: Query by chromosomal region

import requests

# Find variants in a specific genomic region
chromosome = "10"
start_pos = 114000000
end_pos = 115000000

base_url = "https://www.ebi.ac.uk/gwas/rest/api"
url = f"{base_url}/singleNucleotidePolymorphisms/search/findByChromBpLocationRange"
params = {
    "chrom": chromosome,
    "bpStart": start_pos,
    "bpEnd": end_pos
}
response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
variants_in_region = response.json()

5. Working with Summary Statistics

The GWAS Catalog hosts full summary statistics for many studies, providing access to all tested variants (not just genome-wide significant hits).

Access Methods:

1. FTP download: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
2. REST API: Query-based access to summary statistics
3. Web interface: Browse and download via the website

Summary Statistics API Features:

• Filter by chromosome, position, p-value
• Query specific variants across studies
• Retrieve effect sizes and allele frequencies
• Access harmonized and standardized data

Example: Download summary statistics for a study

import requests
import gzip

# Get available summary statistics
base_url = "https://www.ebi.ac.uk/gwas/summary-sta