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),
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 ?
Can I correlate phenotype data of this population with the set of SNPs ?
Any literature suggestions are also most welcome.
Many thanks in advance.