About dbSNP (Updated March 11, 2025)

Introduction

The Single Nucleotide Polymorphism Database (dbSNP) is a freely accessible public database that catalogs small genetic variations, including single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and other minor genomic variations. Launched in 1998 by the National Center for Biotechnology Information (NCBI), dbSNP has played a crucial role in genomic research, disease association studies, pharmacogenomics, and population genetics.

Over the past 25 years, dbSNP has grown significantly, integrating data from large-scale sequencing projects such as 1000 Genomes, gnomAD, TOPMed, and ALFA. It currently hosts 5.0 billion submitted SNPs (ss) and 1.2 billion unique reference SNPs (rs), making it one of the most comprehensive resources for human genetic variation.

dbSNP continues to evolve with advancements in next-generation sequencing (NGS), cloud computing, and artificial intelligence (AI)-driven variant annotation, ensuring its relevance for precision medicine, clinical genetics, and evolutionary biology.

Key Features of dbSNP

• Comprehensive Variant Catalog: Includes SNPs, short indels, microsatellites, and small structural variations.
• Integration with Major Genomic Projects: Data sourced from 1000 Genomes, ExAC, gnomAD, ALFA, and more.
• Support for Population Genetics: Provides allele frequency data across global populations.
• Standardized Reference SNP IDs (rsIDs): Enables consistent tracking of genetic variations.
• Clinical and Functional Annotations: Links variants to GWAS, ClinVar, and other biomedical datasets.
• Multiple Access Methods: Users can access dbSNP through the NCBI website, API (eUtils), and FTP downloads.

Accessing dbSNP Data

1. Web Interface

The dbSNP web portal allows researchers to search for SNPs using rsIDs, gene names, genomic coordinates, and functional classifications. Visit:
👉 NCBI dbSNP Portal

2. Entrez Search and Advanced Queries

dbSNP is integrated with NCBI Entrez, enabling Boolean searches and field-specific queries. Advanced users can filter SNPs by:

• Chromosome location (e.g., 8[CHR] AND 19956018[POSITION])
• Gene association (e.g., BRCA1[GENE])
• Clinical significance (e.g., pathogenic[CLIN])

🔗 Learn more about dbSNP search syntax.

3. NCBI API & eUtils

For automated queries, dbSNP provides API access via NCBI eUtils, supporting:

• Batch SNP retrieval
• Functional annotation lookups
• Filtering based on population genetics data

🔗 API documentation: dbSNP eUtils Guide

🔗 Tutorials: GitHub

4. Variation Services API

The Variation Services API offers programmatic access for variant annotation and conversion (HGVS, SPDI, and VCF formats). It supports:

• Cross-referencing variants across datasets
• Genomic region-based filtering
• Population allele frequency analysis

🔗 API documentation: Variation Services API

🔗 Tutorials: GitHub

5. FTP Downloads (Bulk Data)

For large-scale analysis, dbSNP offers JSON and VCF data downloads via FTP:

• Latest SNP release: dbSNP FTP

Clinical and Research Applications

dbSNP plays a critical role in multiple fields of genomic research:

• Genome-Wide Association Studies (GWAS)
  Helps identify genetic risk factors for complex diseases.

• Pharmacogenomics
  Guides drug response predictions based on genetic variations.

• Cancer Genomics
  Supports the discovery of tumor-specific mutations and driver variants.

• Forensic Genetics
  Used in ancestry classification and human identification.

• Personalized Medicine
  dbSNP aids in precision medicine efforts, linking variants to FDA-approved genetic tests.

Future Directions

As genomic research advances, dbSNP is expanding in several key areas:

• Integration with NIH "All of Us" Research Program
  Enriching the database with diverse genetic data from over 1 million individuals.

• Support for Telomere-to-Telomere (T2T) Genome Assembly
  Enhancing SNP cataloging in previously unsequenced genome regions.

• Expanded Cloud-Based Infrastructure
  Enabling scalable access and analysis for global researchers.

Conclusion

For 25 years, dbSNP has remained a cornerstone of genetic research, supporting discoveries in human genetics, precision medicine, and evolutionary biology. As next-generation sequencing and AI-driven genomics continue to evolve, dbSNP will play an even greater role in advancing clinical diagnostics and population genetics. To learn more about the history, evolution, and impact of dbSNP, read the dbSNP 25th Anniversary Publication, which highlights its critical contributions to genomics research and its vision for the future.

📌 Additional Resources

• dbSNP Home: https://www.ncbi.nlm.nih.gov/snp/
• NCBI SNP FAQ: https://www.ncbi.nlm.nih.gov/snp/docs/faq/
• NCBI Entrez Help: https://www.ncbi.nlm.nih.gov/snp/docs/entrez_help/
• Allele Frequency Aggregator (ALFA): https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/
• Citing dbSNP: The evolution of dbSNP: 25 years of impact in genomic research