The system accepts four formats for variants including either GWAS format such as Plink-like format and single dbSNP ID, or NGS format such as VCF-like format and single variant chromosome position resulting from high-throughput sequencing. LD information of different populations for both HapMap and 1000 Genomes Project is well supported by GWAS3D, which also allows users to define the cutoffs of association P-value and LD. More stringent settings will reduce the running time but some truely associated variants with moderate effect size might be lost. Also, GWAS3D provides information for 16 different cell types, which have been extensively investigated on chromatin states by recent ENCODE project, especially for long-range chromosome interactions. We recommend users to select the cell type that is relevant to the observed disease/trait in their GWAS/NGS study. Furthermore, GWAS3D allows users to choose relevant TF families and related known/novel motifs, which benefit capturing the binding affinity changes for a set of specific TFs. User can define a specific P-value cut off for putative TF-binding site scanning. Other settings, such as user-defined genomic regions and visualization options, including promoter definition, allowed number of variants and distal intentions for plotting, are also adjustable by the users.
