How to Identify set of associated SNPs with single SNP using 1001 genomes

Question

[ES.67]

Dear all,

In the check up of aligned sequences from 1000 Arabidopsis GP for a gene of interest, one particular SNP was found in a subset of population (about 5%).

While there are other SNPs too in this gene within 1000 genomes population (at different densities),

1. How can I identify more SNPs (in a nearby region or in far away other genes) associated or correlated (at least statistically) with this one SNP within this subset of population ? Would this be called a Haplotype mapping ?

2. Can I correlate phenotype data of this population with the set of SNPs ?

Any literature suggestions are also most welcome.

Many thanks in advance.

[Matthias Zepper]

Not my area of research, but the latter task is called Quantitative Trait Mapping as far as I know. You might find helpful tutorials and tools like that.