See these posts:

A: GWAS dataset: SNPs with association p-value

A: Gwas Stepwise Tutorial

Gwas Vs. Qtl Mapping?

A: I'm a new guy on GWAS data, what should I do?

and several papers below:

Effects of normalization on quantitative traits in association test

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-415

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930510/

Genome-wide association analysis

http://www.stat-gen.org/tut/tut_analysis.html

Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain

http://www.sciencedirect.com/science/article/pii/S0969996112000915

Rank-Based Inverse Normal Transformations are Increasingly Used, But are They Merited?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921808/

[ Inverse Normal Transformation Of A Quantitative Trait In Gwas

this post discussed the same paper ]

For microarrays:

https://www.researchgate.net/publication/11014612_Microarray_Data_Normalization_and_Transformation

Disease case:

Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes

http://hmg.oxfordjournals.org/content/early/2013/10/08/hmg.ddt461.full