A user may submit queries in two formats: a comma-delimited list of rsids, or a one of the GWAS or traits from the NHGRI catalog. To illustrate (Figure 1), we select the lupus study by Han et al. (35). Since the study was conducted in Han Chinese, we select ASN (CHB + JPT) as the population for LD calculation, and we select all SNPs in the ASN population as the background for enhancer enrichment analysis. As was reported by Ernst et al. (6), there is a strong enrichment for GM12878 (lymphoblastoid) enhancers. To demonstrate LD blocks, we select an LD threshold of r2 = 0.95. In the LD block with lead SNP rs9271100, there is a SNP rs9271055 which affects an Ets-family binding site. Clicking on rs9271055 leads to a detail view (Figure 2) in which the complete chromatin state data are available. The positions in two literature motifs for Ets-family proteins can be seen, where the alternate T allele strengthens the predicted affinity relative to the reference G allele. In addition, links to NCBI RefSeq and ENSEMBL pages detailing the neighboring HLA-DRB1 gene are provided.
