The system accepts inputs either from an association study or a SNP list. Many formats are supported, including the Plink-like (32) format, VCF-like format, single dbSNP ID and variant chromosome position. The input of association P-value is compulsory when the GWAS effect size is considered for prioritization. A user-defined P-value cut off is applied to filter out the less significant SNPs and to reduce data volume. SNPs or Indels will be checked and mapped to dbSNP137 or 1000 Genomes Project variants. Variants not using VCF-like format will be assigned respective alleles according to dbSNP137 then 1000 Genomes Project. The web server will filter the variant not mapped onto either dbSNP137 or 1000 Genomes Project unless VCF-like format is used. Then, it would fetch all variants in LD of each aforementioned leading variants by user-defined LD standard (HapMap or 1000 Genomes Project), population and r-square (r2) cut off.
