Identification of phenotype associated regulatory SNPs from publically available VDR ChIP-SEQ and encode data
Vreugdenhil, Ing. A. Angie
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The interest for vitamin D has been integrated in many studies; osteoporosis, the immune response, and various cancer types. A common factor in cancer research is of great interest, considering that cancer is an extremely heterogeneous disease. However, the mechanism through which vitamin D acts out its beneficial affect are poorly understood. Data from ENCODE, HapMap, and the 1,000 Genomes Project are used to examine genome wide association study findings in the context of vitamin D receptor (VDR signaling. Starting with an overlap of significant (FDR < 0.01) ChIP-seq and (CEPH lymphoblastoid, THP1 acute monocytic leukemia, and LS180 colon adenocarcinoma) GWAS data, including all SNPs in LD taken from 1,000 Genomes Project. Next the SNP position within DR3 motifs and motifs from JASPER and TRANSFAC Public was determined to get the overall phenotype associated genetic variation. This project shows that VDR binding sites within DR3 response elements are significantly lower than expected and VDR summit regions bind at a higher than expected rate with other transcription factors (TFs). With respect to phenotype association, we found that genetic variation impacts VDR binding in phenotypes most closely related to immune disorders, and by contrast binding regions contain few genetic variation associated with cancer.