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

Table 2 SNPs present in DR3-type motifs contained within VDR peaks and associated with traits

Chr	Chr Start	Chr End	Strand	Reference Allele	Observed Alleles	SNP under VDR peak (Lead in bold)	Derived From (Lead SNP ID)	Trait	DR3 HOMER score	DR3 motif sequence (Homer)	SNP position in the motif
chr2	8442247	8442248	+	G	A/G	*rs10174949* ^a	*rs10174949*	*Self-reported allergy*	4	AGATCATCGGGGTTT	11
chr15	50946814	50946815	+	A	A/G	rs11070802	rs2414059	QT interval	7	AGTGCACATGGTGCA	7
chr3	119278467	119278468	+	A	A/G	rs16829980 ^a	rs59374417	Vitiligo	6	AGTTCACTCAGTACT	5
chr19	49867015	49867016	+	C	C/G	rs2288480	rs2303759	Multiple sclerosis	4	GTGTCACCAAGGGCG	7
chr4	95088557	95088558	+	C	C/T	rs28613890	rs11097407	Bipolar disorder and schizophrenia	8	GTGGTCATTGAGTTC	14
chr6	109704441	109704442	+	T	C/T	rs3757230	rs1046943	Height	7	AGGTCATTGGGGAGG	3
chr6	109704450	109704451	+	A	A/C	rs3757231	rs1046943	Height	7	AGGTCATTGGGGAGG	12
chr5	95265555	95265556	+	G	A/G	rs4563648	rs7700895	IgG glycosylation	5	GGGTGAGAAAGTTTC	2
chr1	205641342	205641343	+	C	C/G	rs55915134	rs16856186	Pulmonary function decline	6	TGGGTGAGGGGGGGG	6
chr11	118575418	118575419	-	G	C/T	rs625735	rs494459	Height	9.18	GTGTCAAAGGGTTCA	10
chr11	128206409	128206410	+	C	C/T	rs6590322	rs6590322	Hippocampal atrophy	8	AAAGTCAGAGAGGAC	7
chr15	49167995	49167996	+	G	A/G	rs73402209	rs8023445	Major depressive disorder	9.18	AGGTCAAAGAGGTCG	14
chr21	35348499	35348500	-	C	A/G	rs743418	rs2032314	Red blood cell traits	4	AGGCTGCTGGGTCCA	12
chr5	150169882	150169883	+	A	A/T	rs74973123	rs13361189	Crohn’s disease	5	ATGTTAAAGGGTTTA	7
chr9	123664122	123664123	+	A	A/G	rs7859805	rs881375	Rheumatoid arthritis	6	GGGGCAAAAGGTGTG	5

All the 574 disease- or phenotype-associated SNPs were overlapped with 8,884 VDR ChIP-seq loci containing DR3 motifs to identify SNPs present in DR3 motif. This analysis identified 15 SNPs to be present in DR3-type motifs. Table shows the details of 15 SNPs including homer score, associated Lead SNPs and traits/phenotypes. SNPs in bold survive multiple test correction
SNPs in bold are LEAD SNPs
^aSNPs common with 42 significant trait SNPs, bases in red in motif sequence show the position of the SNP in the motif

ISSN: 1471-2164