COMSATS University Islamabad, Sahiwal Campus

Assignment # 4
Submitted To:
Sir Saad
Submitted By:
Sara Fatima
FA20-BSI-006
Course Title:
Structural and Functional
Bioinformatics
Department:
Biosciences
 A Human Genetic Variant RS12730935
LD LINK:
 To calculate linkage disequilibrium (LD) using LDlink, a web-based LD analysis tool,
you can follow these steps:
 Select LDlink tool: On the LDlink homepage, you will find a list of tools and resources.
Choose the tool called "LDpair" to calculate LD between two genetic variants.
 Input variant information: In the LDpair tool, enter the variant information for the two
genetic variants you want to analyze. You can enter the variant IDs (e.g., rs numbers) or
genomic coordinates (chromosome and position) for the variants.
 Choose reference population: Select the reference population for LD calculation. LDlink
offers multiple population options, including different global populations and specific
ethnic groups. Choose the population that is most relevant to your study or analysis.
 Run the analysis: After entering the variant information and selecting the reference
population, initiate the analysis by clicking on the "Calculate LD" or similar button.
LDlink will perform the LD calculation using the selected variants and reference
population.
 Review the results: Once the analysis is complete, LDlink will display the results. This
typically includes LD statistics such as the correlation coefficient (r^2) or D' between the
two variants. The results may also include LD plots or visualizations to help interpret the
LD patterns.
 Interpret the LD results: Review and interpret the LD results. Assess the strength and
significance of LD between the two variants. High LD values indicate strong correlation
or association, while low LD values suggest weaker or no association.

Variants:
1. rs11265613
2. rs61812598

Results:
1) LDexpress
2) LDhap
3) LDmatrix
4) LDpair
5) LDtrait

LDexpress:
  It calculate allelic freq
 Effect size
 P value

LDtrait:
LD traits can encompass a wide range of phenotypes, including physical traits (such as height,
eye color), disease susceptibility (such as diabetes, cardiovascular disease), behavioral
characteristics (such as intelligence, personality traits), and response to medications or therapies.
LDhap:

LDhap is designed to estimate haplotype frequencies and LD statistics using

genotype data from population samples. It is commonly used in population
genetics and genetic association studies.

Ensemble: