Fig. 3

The co-occurrence of VDR and NF-κB1 binding at sites of significant genetic variation. a The wordcloud characterizes the transcription factors binding at the location of significantly associated Lead SNPs (and not linked to a DR3 motif) were identified by RegulomeDB; 95 different transcription factors, representing eight unique subgroups, overlapped with, and their function was altered by, these SNPs. The font size of transcription factor related to the number of times it was identified to associate with a significant SNP site. b The intersection of VDR and NF-κB ChIP-Seq from CEPH cell lines. The VDR ChIP-seq in the unstimulated and ligand-stimulated states in the CEPH cell lines GM10855 and GM10861 were intersected to generate a consensus cistrome for VDR binding sites in the unstimulated and stimulated states. Similarly, a consensus NF-κB cistrome was generated by intersecting the ChIP-Seq from the cell lines GM12878, GM12891, GM12892, GM15510, GM18505, GM18526, GM18951, GM19099, GM19193. These consensus cistromes were then intersected to reveal the unique and shared binding sites, and the overlap with the identified SNPs. c The effect of rs10174949 genotype on NF-κB binding in ChIP-seq from HapMap cell lines. The altered allele of rs10174949 was predicted to decrease the strength of predicted affinity of NF-κB1 by HaploReg. The ENCODE ChIP-seq data sets of NF-κB for HapMap cell lines for which genotype data was available were downloaded into Integrative Genomics Viewer (IGV). Population ID and the genotype for each cell lines is shown. Cell lines with homozygous reference allele are shown in blue, heterozygous samples are shown in green and sample with homozygous altered allele is shown in red. Samples with the homozygous altered allele (AA) completely lost NF-κB binding compared to the homozygous (GG) or heterozygous (AG) reference alleles