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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
Epigenetic Regulation01:37

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Comparing Copy Number Variations and SNPs02:26

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%...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Related Experiment Video

Updated: May 10, 2026

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
14:56

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

SNPs located at CpG sites modulate genome-epigenome interaction.

Degui Zhi1, Stella Aslibekyan, Marguerite R Irvin

  • 1Department of Biostatistics; University of Alabama; Birmingham, AL USA.

Epigenetics
|July 2, 2013
PubMed
Summary

Genetic variants at CpG sites, known as meSNPs, explain most DNA methylation differences (meQTLs). These meSNPs directly impact methylation and influence nearby sites, revealing key mechanisms linking genetics to epigenetics.

Keywords:
DNA methylationInfinium Human Methylation 450K BeadChipepigenome-wide studymeQTLmeSNP

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Area of Science:

  • Epigenetics
  • Genetics
  • Genomics

Background:

  • DNA methylation is a key molecular phenotype connecting genotypes to complex diseases.
  • Previous studies identified local correlations between genetic variants and DNA methylation (cis-meQTLs).
  • The underlying mechanisms of cis-meQTLs remain largely unclear.

Purpose of the Study:

  • To investigate the general mechanisms underlying cis-meQTLs.
  • To analyze the role of genetic variants at CpG sites (meSNPs) in DNA methylation patterns.

Main Methods:

  • Conducted a cis-meQTL analysis using the Genetics of Lipid Lowering Drugs and Diet Network data (n=593).
  • Identified meQTL loci and analyzed the impact of meSNPs on methylation levels.

Main Results:

  • Over 80% of genetic variants at CpG sites (meSNPs) were identified as meQTL loci (P<10^-9).
  • meSNPs accounted for over two-thirds of the strongest meQTL signals (P<10^-200).
  • meSNPs not only affected methylation at their own site but also lowered methylation at nearby CpG sites (<45 bp) and influenced methylation up to 10 kb away.

Conclusions:

  • meSNPs are responsible for a significant portion of observed meQTL signals.
  • These meSNPs play a critical role in the biological processes linking genetic variation to epigenetic modifications.
  • The findings provide insights into the mechanisms connecting genotype to phenotype through DNA methylation.