4.4 Are these SNPs in LD?
If we run table
on each SNP column, we can see which alleles exist at SNP1 and SNP2.
- SNP1 can be
A
orG
- SNP2 can be
C
orT
##
## A G
## 3456 1552
##
## C T
## 2825 2183
If these two SNPs were in perfect LD, we’d expect to see only two haplotypes in our data (Fig. 4A).
A
C
: If someone carries anA
at SNP1, they will always carry aC
at SNP2.G
T
: If they carry aG
at SNP1, they will always carry aT
at SNP2.
If these two SNPs were in linkage equilibrium, the allele at SNP1 would give us no information about SNP2. We would expect to see all four possible haplotypes, in amounts proportional to the component allele frequencies (Fig. 4B).
A
C
A
T
G
C
G
T