7.4 LD and GWAS

LD is both a blessing and a curse for GWAS. On one hand, LD means that we need not genotype every SNP to discover associations. We merely need to genotype “tag SNPs”, which are in LD with variants that causally influence the phenotype.

On the other hand, this also means that even when we find a signficant association, it is often challenging to disentangle the causal gene and/or variant that drives the association from all the other variants on the same haplotype.

Fig. 3 (source). Even without finding the causal variant, we can still discover the causal haplotype through genotyping variants in LD .
Fig. 3 (source). Even without finding the causal variant, we can still discover the causal haplotype through genotyping variants in LD .
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