Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples
Related Experiment Video
Updated: Jul 13, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data
Published on: December 13, 2024
Amanda F Marvelle1, Leslie A Lange1, Li Qin1
1Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Abstract:
Patterns of linkage disequilibrium (LD) act as the framework for designing efficient association studies; these patterns are being studied and catalogued by The International HapMap Project. The current study assessed the transferability of tag SNPs chosen from HapMap panels to a cohort of 80 individuals from metro Cebu, Philippines, who participated in the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The analyses focused on 627 single nucleotide polymorphisms (SNPs) in the central 40 kb within each of the 10 HapMap ENCODE regions. The similarity between the genetic variants in Cebu Filipino samples and HapMap panels was examined using allele frequency estimates, measures of pairwise linkage disequilibrium (LD), and haplotype frequency estimates. For these measures, strong correlations were observed between the Cebu Filipino samples and the Asian panels from HapMap, with the strongest correlations observed with the Han Chinese from Beijing (CHB) panel. Tag SNPs selected using the HapMap CHB panel were particularly effective at representing the genetic variation in Cebu Filipino samples. These results suggest that the HapMap data will be an effective resource for future studies in Cebu Filipino samples.
Related Concept Videos
Comparing Copy Number Variations and SNPs
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%...
Single Nucleotide Polymorphisms-SNPs
Evolutionary Relationships through Genome Comparisons
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Cis-regulatory Sequences
Histone Variants at the Centromere
