Identifying changes in punitive transcriptional factor binding sites from regulatory single nucleotide polymorphisms that are significantly associated with disease or sickness

Table 2 Genes whose single nucleotide polymorphisms are significantly associated with human disease or sickness

Gene symbol
ADRBK1	Ethnic group	B		B
	disease or sickness	12		12
	SNP	rs948988 (G/A)		rs4370946 (C/T)
	alleles (MAF)	G	A (0.29)	C	T (0.2)
	potential unique TFBS	KLF1, 4	BATF:JUN	E2F1,3,4,6	ARNT:AHR
			ESR2	EGR1	ATOH1
			FOS	INSM1	ELF1
			FOSL2	KLF4	ESR2
			JUND	NFKB1	NR3C1
			JUN:FOS	NRF1
			MYB	SP1, 2
			NFE2L1:MAF
			NR3C1
			SOX17
AKT3	Ethnic group	G		C		C
	disease or sickness	1		14		14
	SNP	rs4590656 (C/T)		rs10157763 (C/T)		rs2125230 (G/A)
	alleles (MAF)	C	T (0.41)	C	T (0.33)	G	A (0.2)
	potential unique TFBS	ARNT:AHR	GFI	ELF5	CTCF	ARNT:AHR	GATA1
		HIF1a:ARNT	HNF4A	ELK1	NFATC2	FEV	HNF4a
			PAX2	MYCN	SOX17	HIF1a:ARNT	HOXA5
			SPIB	SPIB	ZNF354C	SPI1	IRF1
				SPI1			NR2F1
				TFAP2A			SOX17
ATF3	Ethnic group	C		C
	disease or sickness	15		15
	SNP	rs3125289 (C/T)		rs11119982 (C/T)
	alleles (MAF)	C	T (0.10)	C	T (0.36)
	potential unique TFBS	ARNT	FOXA1, 2	HLTF	ARID3A
		ARNT:AHR	FOXL1		MAX
		GABPa	FOXO3		MYB
		MYC	HLTF		USF1
		MYCN	SOX10		ZEB1
		MZF1	SOX17
		SPIB	SRY
		USF1
DIO2	Ethnic group	F		F		C
	disease or sickness	2		2		17
	SNP	rs225015 (G/A)		rs225011 (C/T)		rs12885300 (C/T)
	alleles (MAF)	G	A (0.4)	C	T (0.42)	C	T (0.23)
	potential unique TFBS	EBF1	ELF1	CRX	FOXL1		ARID3A
		ESRRA	ELK1	RXRa	MEF2A		BATF:JUN
		PPARg:RXRa	ERG		PDX1		IRF1
		RFX5	ETS1				JUN:FOS
		THAP1	FLI1				PAX2
			RUNX1				SOX6
			SOX9
			SPI1
			TCF7L2
EPAS1	Ethnic group	G		G
	disease or sickness	1		1
	SNP	rs6756667 (A/G)		rs1868093 (A/G)
	alleles (MAF)	A	G (0.20)	A	G (0.25)
	potential unique TFBS	CEBPa	ATF7	NR2C2	HIC2
		NFIA	GMEB2	NFIA	KLF5
		NRL	JDP2	YY1	MGA
					TEAD1
					USF1
LIPA	Ethnic group	C, D, E
	disease or sickness	20, 21
	SNP	rs1412444 (C/T)
	alleles (MAF)	C	T (0.32)
	potential unique TFBS	ELF1	FOXA1
		ETS1	FOXL1
		GABPa	FOXO3
		HOXA5	HNF1B
		SPI1	MEF2A
			NFKB1
			NFIC
			PAX2
			SOX6
			SOX9
			SRY
			THAP1
STAT4	Ethnic group	A, C		A, C
	disease or sickness	2,6,10		2,10
	SNP	rs8179673 (T/C)		rs10181656 (C/G)
	alleles (MAF)	T	C (0.26)	C	G (0.26)
	potential unique TFBS	EN1	FOXA2	AR	HNF4g
		NFIL3	FOXH1	E2F6	STAT3
			FOXO1	NR1H3:RXRa
			FOXP1	ZNF263
			FOXQ1
			HNF1a
			HNF4g
TBXA2R	Ethnic group	A		A		A
	disease or sickness	22		22		22
	SNP	rs2238631 (G/A)		rs2238632 (C/T)		rs2238634 (G/T)
	alleles (MAF)	G	A (0.2)	C	T (0.21)	G	T (0.22)
	potential unique TFBS	FOXC1	ELK1		ARNT		HLTF
		TFAP2a	ELK4		CREB1		HNF4a
			ETS1		HIF1a:ARNT		NR2F1
			GATA2		MAX		NR2E3
			HAND1:TCFE2a		USF1		NR4A2
			SPZ1
VEGFA	Ethnic group	G		G		G
	disease or sickness	1		1		1
	SNP	rs34357231 (I/D)		rs1570360 (G/A)		rs3025039 (C/T)
	alleles (MAF)	D	I (0.28)	G	A (0.13)	C	T (0.09)
	potential unique TFBS	HNF4a	AR	EGR1	EGR2	BRCA1	NFE2::MAF
		HNF4g	EGR1,2	MZF1	EHF	ESR2	RFX5
		JUN	KLF5	SP2	FOXH1	HIF1A:ARNT	YY1
		MYB	MZF1_1-4		MAFK	NFE2L1:MAFG
		NFIC	NFYB		SPIB
		NR2C2	NFATC2		THAP1
		NR4A2	NKX2-5
		PAX2	NKX3-2
		RFX5	SP1, 2
			STAT5A:STAT5B
Ethnic Group	Disease		Disease			Disease
A. Asian	1. Chronic mountain sickness		8. Juvenile idiopathic arthritis			15. Hypospadias
B. Black	2. Diabetes		9. Primary biliary cirrhosis and Crohn's disease			16. Mental retardation
C. Caucasian	3. Hepatitis B virus- related hepatocellular		10. Lupus			17. Osteoarthritis
D. Chinese	4. Hepatitis B virus infection		11. Ulcerative colitis			18. Insulin resistance
E. Hispanic	5. HBV viral clearance		12. Cardiovascular disease			19. Hepatic glucose output
F. Pima Indians	6. Hepatocellular carcinoma		13. Renal cell carcinoma risk			20. Coronary artery disease
G. Tibetan	7. Inflammatory bowel disease		14. Aggressive prostate cancer			21. Myocardial infarction
						22. Asthma

Also listed are the SNP alleles and frequencies within the ethnic group as well as the potential unique transcriptional factor binding site created with each SNP allele. For a complete list of significant gene SNPs see references (Table 1). SNP: Single nucleotide polymorphisms; ADRBK1: Adrenergic, beta, receptor kinase 1; AKT3: V-akt murine thymoma viral oncogene homolog 3; ATF3: Activating transcription factor 3; DIO2: Type 2 demodkinase gene; EPAS1: Endothetal Per-Arnt-Sim domain protein 1; STAT4: Signal transducer and activator of transcription 4; TBXA2R: Thromboxane A2 receptor; VEGFA: Vascular endothelial growth factor A; LIPA: Lysosomal acid lipase A.