How to analyze co-occurrence of multiple SNPs? I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?

I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.

Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.
I found the LDheatmap package in R very helpful at calculating linkage disequilibrium. You can make plots such as this: