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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Related Experiment Video

Updated: Jul 4, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

SNP ID-info: SNP ID searching and visualization platform.

Cheng-Hong Yang¹, Li-Yeh Chuang, Yu-Huei Cheng

¹Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Taiwan, ROC.

Omics : a Journal of Integrative Biology

|June 28, 2008

Summary

This study introduces SNP ID-info, a freeware tool that identifies single nucleotide polymorphism (SNP) IDs using genomic data. It aids researchers in systematic SNP association studies by providing visualized SNP information.

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Published on: June 23, 2012

Area of Science:

Genomics
Bioinformatics

Background:

Association studies often identify relationships between genetic variations like single nucleotide polymorphisms (SNPs) and diseases or cancers without providing specific SNP IDs.
This lack of direct SNP identification hinders systematic analysis and replication of genetic association findings.

Purpose of the Study:

To develop a user-friendly freeware tool, SNP ID-info, for efficiently retrieving SNP IDs from genomic and physical information.
To provide a visualized environment for SNP identification, aiding in complex genetic association studies.

Main Methods:

The SNP ID-info freeware incorporates functions such as "SNP-ePCR" for sequence generation, "SNPosition" for matching sequences to SNP IDs, and "SNP search" and "SNP fasta" for querying SNPs by cytogenetic band, contig position, or keywords.
The tool visualizes the SNP neighboring environment, ordered by contig position, and marks flanking hits, overcoming limitations of existing tools like NCBI SNP BLAST.

Main Results:

Successful development of SNP ID-info freeware, enabling the retrieval of SNP IDs from various genomic inputs.
The tool provides a comprehensive and visualized SNP identification environment, improving upon existing methods.

Conclusions:

SNP ID-info offers a valuable resource for researchers conducting systematic SNP association studies by simplifying SNP identification and visualization.
The freeware assists in overcoming challenges in SNP identification, thereby supporting advancements in understanding the genetic basis of diseases and cancers.