hr at 16 °C. The ligated samples were decrosslinked at 65 °C with proteinase K for overnight and were Phenol/Chloroform extracted, EtOH precipitated and desalted. Target primers were designed against HindIII digested fragments within or close to DHS around SNPs in the region of risk loci and, anchor primers were designed against the fragments cut by HindIII in the TF promoters (primers available upon request). PCR was performed using Taq polymerase (Qiagen), 3C library and the oligonucleotides listed in Table S3. PCR conditions; 5 min at 94°C, (20 s at 94°C, 20 s at 57, and 30 s at 72°C) ×42 cycles, and 10 min at 72°C for extension. 7ul of PCR samples were loaded on the 1.7% agarose gel. The PCR products were then gel purified and sequenced. Since spurious interactions are typically undetectable beyond 150 kilobases, the ESR1 and KLF4 ligation fragments represent bona fide interactions.
