Ernst et al. report an enrichment among the lupus GWAS SNPs from Han et al. In the first tab, "Build Query", select "Systemic lupus erythematosus (Han et al., 2009), 18 SNPs" from the GWAS drop-down menu. In the second tab, "Set Options", select an LD threshold of 0.6 and set the 1000G population to ASN (the study's subjects were Han Chinese). Now click "Submit Query." Note that the SNPs appear in separate tables with their LD blocks (the second is at the HLA locus.) Also note that the enhancer enrichment analysis reports a 9-fold enrichment for all enhancers in GM12878 lymphoblasts. (This enrichment is based on the query SNPs and is indepenedent of the population or LD threshold.) Find rs9271055 on the LD block with tag SNP rs9271100; note that it has r² = 0.76 and D' = 0.98 with the GWAS-reported SNP. Also note that, like the lead SNP, it is reported as an eQTL by Montgomery et al.
Then click on the rsid rs9271055 to reach its detail page. Note at the bottom of the detail page that, as illustrated in Ernst et al. Figure 5d, the alternate allele of the SNP strengthens a match to a literature Ets-family PWM. Hover over "Ets_known9" to obtain its TRANSFAC accession number.
Now, return to the main page and select "Systemic lupus erythematosus (8 studies combined), 62 SNPs" in the first tab and select an LD threshold of "NA" in the second tab, and click "Submit Query." Note that all variants appear in the same table.