Why would a single causal SNP in a large haplotype block result in a greater effect size than a causal SNP in a small haplotype block?
Replying to “Why would a single causal SNP in a large haplotype…”:
It would have a “bigger effect” because the correlated SNPs in the haplotype block would also appear to have that effect — but they don’t actually have a bigger effect, they’re just correlated with the SNP that does. (They’re just friends with that SNP)
Replying to “Why would a single causal SNP in a large haplotype…”:
Okay thank you! Would the bivariate LD score regression using the product of a trait A causal SNP and different trait B causal SNP both in high LD result in a deceptively high chi squared for that LD bin?
Replying to “Why would a single causal SNP in a large haplotype…”:
The number would be high but not deceptively high! Comparing within the LD bin, you could meaningfully say it’s a larger effect (you just couldn’t compare to snps in ld blocks of different sizes)
Replying to “Why would a single causal SNP in a large haplotype…”:
Thanks so much!