Detailed steps:

1. Select or enter a GWAS SNP rsID.
   
   
   
   
   
   • We gathered a total of 21 low-grade glioma GWAS SNPs.
   • A GWAS annotation table on the right updates based on the selected GWAS SNP.
   
   
   
   
   
2. Select or enter a high linkage disequilibrium (LD) SNP rsID and click the submit button.
   
   
   
   
   
   • For the selected GWAS SNP, select one of the SNPs in high LD (r² >= 0.8) with the GWAS SNP. The LD calculations are based on the 1000 Genomes Phase 3 (EUR) data.
   • By clicking the submit button, the various modules organized as tabs below show the detailed analyis results of the selected GWAS and high LD SNPs.
   
   
   
   
   
3. Genome browser
   
   
   
   
   • For the selected LD SNP, the genome browser shows various tracks at the SNP's locus.
4. ENCODE data
   
   
   
   
   • For the selected LD SNP, this tab shows all the ChIP-seq datasets from ENCODE which contain peaks overlapping the LD SNP.
   • The table can be filtered based on brain tissue/cell lines.
5. Motif disruption
   
   
   
   
   • For the selected LD SNP, motif analysis as described in the paper is performed to show all the potential transcription factors whose binding affinity is disrupted by the LD SNP.
   • For each potential disruption, permutation test p-value and other information is tabulated.