Understanding how genetic variation translates into phenotypic variation, and how this translation depends on the environment, is fundamental to many fields of biology. We have been attempting to tackle this problem using A. thaliana as a model for many years. Because it naturally exists as inbred lines, A. thaliana can be brought into the laboratory and grown, in replicate, under different environmental conditions. As part of the 1,001 Genomes Project, we have sequenced 200 Swedish lines, and are generating multiple phenotypes, in the field as well as in the lab. We are also generating “in-between-ome” data, such as genome-wide transcription and DNA methylation data, in order to gain insight into the mechanism whereby particular polymorphisms lead to phenotypic variation. The sequencing has revealed massive variation in genome-size, mostly due to variation in 45S rDNA clusters, and evidence for strong selective sweeps. GWAS results vary greatly between phenotypes due to difference in the underlying genetic architecture. Compared to efforts in other organisms, we find much greater effects of individual loci. At the transcriptome level, a very high proportion of genes show evidence of strong cis-regulation in GWAS, with effects peaking close to transcription start sites, while trans-effects appear to be smaller, and typically interact with the environment. In terms of DNA methylation, most of the genome is unmethylated, with methylation concentrated in repetitive parts of the genome. Methylation patterns vary between genotypes, but are largely conserved across environments, although differences in overall level are seen and appear to have a genetic basis. We are now attempting to connect all layers of data to create a genotype-phenotype map.