Permutation test - (Jan/25/2006 )

Hi all,

I'm working on association study. Recently, I genotyped many SNPs in a gene and found a significant association from one of the SNPs. I reported my supervisor and he asked me to do the permutation test. I then used Haploview to do that without any knowledge about it.

Please help, what exactly is permutation ?
I tried 1,000 permutations and my SNP still gave significant association, is that enough?.

Isn't a permutation having an equal number of options and items? For instance, 4 pots, 4 plants to put them in? We just did this in math class, I'm not sure if it's exactly what you're asking. So I could be completely wrong...