Linkage Disequilibrium (LD) refers to the non-random association of alleles at different loci (positions on a chromosome).

❖In GWAS, LD is critical because when a SNP is found to be associated with a trait (e.g., a disease), that SNP might not be the causal variant itself. Instead, it could be in LD with a nearby causal variant.

LDlinkR package and 1000 Genomes reference data were employed to calculate LD metrics (r²) for obesity-associated SNPs. Annotated SNPs displaying strong LD were cross-referenced with candidate enhancers to reveal potential regulatory variants.

❖379,127 SNP in LD with the Human Obesity GWAS

❖10,748 SNP has strong linkage (R2>0.8)

❖Overlaps with our data converted human enhancers: 1028 SNP

➢Top ones with large R2 value

Reference:

Harris TJ, Machiela MJ, Chanock SJ (2019). “LDlinkR: An R Package for Rapidly Calculating and Visualizing Linkage Disequilibrium.” PLOS ONE, 14(2): e0210563. doi:10.1371/journal.pone.0210563.