Index Top Overview RXR homodimer-binding sites in the human genoeme. rSNPs in the identified RXR homodimer-binding sites.

rSNPs in the identified RXR homodimer-binding sites. rSNPs in transcription factor-binding sites, which alter the ability of a transcription factor to interact with DNA, may lead to predictable differences in gene expression and may be associated with disease susceptibility. Therefore, we tried to identify rSNPs in each of the RXR homodimer-binding sequences using the NCBI SNP database. Fifteeen rSNPs were identified and the effect on the binding affinity was examined by EMSA. As a result, 12 rSNPs were identified based on differences in the DNA-binding affinities.

No.	Chr.	Gene	GeneID	OMIM ID	dbSNP	DR-1 Motif	EMSA competition (%)
							x12.5	x100
65	3	LOC100129848	100129848	not match	rs12679361	gaaAGGTCAgGGGTCAaag	56.6±1.2	79.7±1.8
122						gaaAGGTCAtGGGTCAaag	Not detected	52.4±1.5
66	17	LOC645754	645754	not match	rs192176628	cagAGGTCAaAGGGCAtcc	37.9±3.0	63.1±2.3
123						cagAGGTCAaAGGACAtcc	Not detected	Not detected
67	2	hCG_1795065	727919	not match	rs77565285	cagAGGTGAgAGGTCAgaa	Not detected	25.2±2.1
124						cagAAGTGAgAGGTCAgaa	Not detected	Not detected
68	4	SULT1E1	6783	600043	rs191482803	gttAGTTCAaAGTTCAaag	Not detected	49.8±0.9
125						gttACTTCAaAGTTCAaag	Not detected	Not detected
69	22	RPL35P8	643653	not match	rs190830415	actCGGTCAaAGGTGAttt	Not detected	25.2±1.2
126						actCAGTCAaAGGTGAttt	Not detected	Not detected
70	19	BCAM	4059	612773	rs28399616	ggcGGGTCAaAGGTTAcgg	70.8±0.4	99.3±1.3
127						ggcGGGTTAaAGGTTAcgg	39.2±3.3	71.7±10.9
71	6	CFB	629	138470	rs113359665	tacAGGTCAaAGGTCAcct	95.7±1.5	103.5±0.9
128						tacAGGTCAaAGGTCTcct	Not detected	38.2±0.3
129						tacAGGTCAaAGGTCGcct	65.9±1.6	82.6±1.1
72	13	MBNL2	10150	607327	rs1318048	caaAGGTTAcAGGACAtgc	Not detected	Not detected
130						caaAGGTTAcAGAACAtgc	Not detected	Not detected
73	12	RPS27P22	100131418	not match	rs139616437	ctcAGGTCCaACGTCAgtg	Not detected	Not detected
131						ctcAGGTCCaATGTCAgtg	Not detected	Not detected
74	19	ACPT	93650	606362	rs191582950	ttgGGGTCAaATGTCAgag	Not detected	45.2±1.5
132						ttgGGGTCAaATATCAgag	Not detected	29.6±1.5
75	12	HNF1A	6927	142410	rs35126805	tgaAGTTCAaAGTTCAgtc	30.5±3.5	49.4±1.6
133						tgaAGTCCAaAGTTCAgtc	Not detected	Not detected
76	9	FBXO10	26267	609092	rs113505634	ctaAGGTCGgAGTTCAtgt	Not detected	Not detected
134						ctaAGGTTGgAGTTCAtgt	Not detected	Not detected
135	1	TNFRSF8	943	153243	rs11569928	gaaAGGTGAgAGGGCAtcc	Not detected	Not detected
136						gaaAGGTGAgAGGTCAtcc	Not detected	29.2±1.7
137	6	OR4A6P	390131	not match	rs190270606	ttgAGGTCAaAGGTGAgaa	37.5±2.0	60.8±1.1
138						ttgAGGTCAaAGTTGAgaa	Not detected	30.8±1.0
139	6	RPS3AP24	100271253	not match	rs192458666	gagAGGTCAaAGGTTAatt	86.8±1.4	97.6±1.2
140						gagAGGTCAaAGGCTAatt	Not detected	Not detected

Index Top Overview RXR homodimer-binding sites in the human genoeme. rSNPs in the identified RXR homodimer-binding sites.

Kazuyuki Yanai Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan