Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes

Singh, Prashant K.; van den Berg, Patrick R.; Long, Mark D.; Vreugdenhil, Angie; Grieshober, Laurie; Ochs-Balcom, Heather M.; Wang, Jianmin; Delcambre, Sylvie; Heikkinen, Sami; Carlberg, Carsten; Campbell, Moray J.; Sucheston-Campbell, Lara E.

doi:10.1186/s12864-017-3481-4

Table 1 List of trait SNPs showing significant enrichment for associated traits

From: Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes

Trait	(A) Trait SNPs (No of SNPs associated with the trait (GWAS + LD)	(B) No. of Trait SNPs under VDR peaks	LD SNP/Lead SNP	Total No. of SNPs under VDR peaks	Corrected p-value	VDR peak set
Esophageal cancer (squamous cell)	160	7	rs4686848/rs2239612 rs2097461/rs2239815 rs2239815/rs2239815 rs2269577/rs2239815 rs5752809/rs2239815 rs5752812/rs2239815 rs763073/rs2239815	574	0.0001	Combined
Esophageal cancer (squamous cell)	160	4	rs2097461/rs2239815 rs2269577/rs2239815 rs5752809/rs2239815 rs5752812/rs2239815	149	0.002	GM10855.D3
Leprosy	187	4	rs11231770/rs538147 rs11231771/rs538147 rs10897487/rs538147 rs475032/rs538147	78	0.0003	LS180.D3
Mean corpuscular hemoglobin	148	5	rs4366668/rs6494537 rs2974750/rs11085824 rs131807/rs470119 rs131806/rs470119 rs131804/rs470119	574	0.02	Combined
	148	4	rs4366668/rs6494537 rs2974750/rs11085824 rs131806/rs470119 rs131804/rs470119	121	0.0006	GM10861.Veh
	148	3	rs4366668/rs6494537 rs2974750/rs11085824 rs131806/rs470119	81	0.008	GM10855.Veh
Helicobacter pylori serologic status	22	3	rs10012017/rs10004195 rs10034903/rs10004195 rs10004195/rs10004195	574	0.008	Combined
Helicobacter pylori serologic status	22	3	rs10012017/rs10004195 rs10034903/rs10004195 rs10004195/rs10004195	316	0.001	GM10861.D3
Vitiligo	463	8	rs10824732/rs11593576 rs10876864/rs10876864 rs4807000/rs6510827 rs41271391/rs59374417 rs16829980/rs59374417 rs885654/rs59374417 rs867234/rs59374417 rs7628982/rs9851967	574	0.02	Combined
	463	7	rs10824732/rs11593576 rs10876864/rs10876864 rs4807000/rs6510827 rs41271391/rs59374417 rs16829980/rs59374417 rs885654/rs59374417 rs867234/rs59374417	316	0.003	GM10861.D3
	463	5	rs10876864/rs10876864 rs41271391/rs59374417 rs16829980/rs59374417 rs885654/rs59374417 rs867234/rs59374417	149	0.007	GM10855.D3
Self-reported allergy	400	6	rs10174949/rs10174949 rs10178845/rs10174949 rs5743566/rs2101521 rs5743565/rs2101521 rs45588337/rs2101521 rs55830619/rs2101521	316	0.012	GM10861.D3
Celiac disease	576	9	rs1250567/rs1250552 rs1250568/rs1250552 rs12924957/rs12928822 rs12928822/rs12928822 rs34289272/rs13098911 rs71327040/rs13098911 rs17035355/rs17035378 rs2984920/rs2816316 rs4310388/rs3748816	574	0.016	Combined

For each trait, the number of SNPs (GWAS + LD; (B)) under VDR peaks was compared to the total number of SNPs (GWAS + LD; (A)) associated with the trait. The significance of enrichment was tested by a hypergeometric test and the p-values were corrected using Bonferroni (corrected p-value). LD SNP/Lead SNP shows the SNPs under VDR peaks (Lead SNP and/or LD SNPs). The lead SNPs which are also present under VDR peaks are shown in bold. VDR peak set is the the number of data sets in which the VDR peak and SNP relationship was found; Combined = all the peaks from six studies considered together, or cell line and treatment specific data set (D3 = treated with VDR ligand_, Veh = vehicle control). Peaks represent the data sets in which the traits showed significant enrichment. This analysis revealed 42 unique SNPs associated with VDR binding and enrichment of a trait

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ISSN: 1471-2164

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