Genotype association help

[Altair]

Dear All,

Please forgive my ignorance I am new to association studies. Please provide me with some comments and insight on what I would like to achieve.

Maim goal:
I have genotyped 100+ individuals for 40 SNP makers and would like to associate a genotype with particular phenotypic trait etc.

Phenotypes:
1. I have several phenotype traits I would like to associate a genotype with.
2. The individuals are also group into different class based on several phenotype observations.
What I have read so far is that I can add phenotypic trait to a phenotype file to be used with plink. With regards to the groups do I treat each group as a "phenotype" and also add these to the phenotype file I will be using with plink.

Results
What I would like to achieve in the end is for each group a representative genotype. Would this be possible any help would be appreciated, if possible examples of ped,map and pheno files would also be appreciated as this is what I am aslo unsure of as to how to represent this is the different files.

Thanks

[Altair]

Any insight help would be appreciated.

Have I posted in the wrong section?

[gringer]

A genome-wide association study using 40 SNPs is almost completely useless, and very likely to net useless false positive associations when testing against a large array of phenotypes.

[Altair]

Thanks for the response.
I do believe I am not expressing myself clearly I apologies.
The 40SNPs that have been chosen have been associated with the phenotypes/traits in previous studies (published) so the association to the phenotype/trait does indeed exist. I would like to determine if a specific SNP call ( A/G or A/C ) has a effect on the trait/phenotype.

Example:
These are just to explain what I would like to achieve and not real cases.
Using on 2 markers for this example and 8 plants (same species).

Marker 1 : associated with flower colour
Marker 2 : associated with plant height
Plant 1 Flower colour : Red
Plant 2 Flower colour : Yellow
Plant 3 Flower colour: Red
Plant 4 Flower colour : Yellow
Plant 1 height : 60cm (classified as tall)
Plant 2 height : 45cm (classified as average)
Plant 3 height : 52cm (classified as average)
Plant 4 height : 62cm (classified as tall )
So results for
Plant Marker 1 Maker 2
1 A/A C/A
2 A/T C/T
3 A/A C/T
4 A/T C/A
Given the example results if a seedling of a plant is test for bother markers and Marker 1 is A/A is could be hypothesized that it will have red flowers and Marker 2 is C/T it would be of average height.

I do hope this helps.

Thanks