Haplotype Blocks and Linkage Disequilibrium

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About This MicroSim

Chapter 5: Genetic Variation and Genome Diversity

Library: p5.js

Type: Interactive diagram sim-id: haplotype-blocks-ld
Library: p5.js
Status: Specified

An interactive visualization showing a linear genomic region with multiple SNP positions. The top panel shows individual haplotypes as rows of colored alleles. The bottom panel shows an LD heatmap (triangle plot) where cell color intensity represents \(r^2\) values between SNP pairs (dark red = high LD, white = low LD). Haplotype block boundaries are outlined on the heatmap. Tag SNPs are highlighted with a star icon. Users can adjust a "generations of recombination" slider to watch LD decay over time as haplotype blocks shrink and the heatmap becomes lighter. Population dropdown (African, European, Asian) shows different LD block sizes.