Two SNPs in the promoter region of Toll-like receptor 4 gene are not associated with smoking in Saudi Arabia

Figures & data

Table 1 Clinical characteristics of study subjects

Variable	Nonsmokers (n=126)	Smokers (n=177)
Age (years), median ± average	20±21	24±27
BMI
Obese (≥30 kg/m^2)	20/100 (20%)	27/163 (17%)
Nonobese (<30 kg/m^2)	80/100 (80%)	136/163 (83%)
Years of smoking
>5	–	104/165 (63%)
≤5	–	61/165 (37%)
Cigarettes per day
≥20	–	99/159 (62.3%)
<20	–	60/159 (37.7%)

Abbreviation: BMI, body mass index.

Table 2 Description of the selected SNPs

Gene	SNP ID	SNP location SNP type	Ancestral allele
TLR4	rs2770150	NC_000009.11:g.120463139 Promoter	T>C
	rs10759931	NC_000009.11:g.120464147 Promoter	G>A

Abbreviations: SNP, single-nucleotide polymorphism; TLR, Toll-like receptor.

Table 3 Genotype frequencies of TLR4 gene polymorphism in smoker and control patients

Gene	SNP	Allele	Nonsmokers, n (%)	Smokers, n (%)	OR	95% CI	χ^2	P-value
TLR4	rs2770150	Total	112	156
		TT	55 (0.49)	85 (0.54)	Ref
		TC	43 (0.38)	54 (0.35)	0.81	0.4807–1.3735	0.6012	0.4381
		CC	14 (0.13)	17 (0.11)	0.79	0.3586–1.7217	0.3640	0.5463
		TC + CC	57 (0.51)	71 (0.46)	0.81	0.4956–1.3108	0.7563	0.3845
		T	153 (0.68)	224 (0.72)	Ref
		C	71 (0.32)	88 (0.28)	0.85	0.5823–1.2308	0.7617	0.3828
	rs10759931	Total	118	168
		AA	14 (0.12)	13 (0.08)	Ref
		AG	38 (0.32)	62 (0.37)	1.76	0.7464–4.1362	1.6870	0.1940
		GG	66 (0.56)	93 (0.55)	1.52	0.6696–3.4392	1.0072	0.3156
		AG + GG	104 (0.88)	155 (0.92)	1.61	0.7250–3.5534	1.3804	0.2400
		A	66 (0.28)	88 (0.26)	Ref
		G	170 (0.72)	248 (0.74)	1.09	0.7527–1.5905	0.2222	0.6374

Abbreviations: TLR, Toll-like receptor; SNP, single-nucleotide polymorphism; OR, odds ratio; CI, confidence interval.

Table 4 Comparison of genotype frequencies of TLR4 gene SNPs with overall controls depending on smoking duration

Gene	SNP	Allele	Nonsmokers, n (%)	Smokers, n (%)	OR	95% CI	χ^2	P-value
TLR4	rs2770150	Patients smoking for >5 years
		Total	112	91
		TT	55 (0.49)	52 (0.57)	Ref
		TC	43 (0.38)	31 (0.34)	0.76	0.4195–1.3859	0.7924	0.3734
		CC	14 (0.13)	8 (0.09)	0.60	0.2343–1.5594	1.0979	0.2947
		TC + CC	57 (0.51)	39 (0.43)	0.72	0.4149–1.2624	1.3006	0.2541
		T	153 (0.68)	135 (0.74)	Ref
		C	71 (0.32)	47 (0.26)	0.75	0.4855–1.1593	1.6795	0.1950
	rs2770150	Patients smoking for ≤5 years
		Total	112	55
		TT	55 (0.49)	29 (0.53)	Ref
		TC	43 (0.38)	18 (0.33)	0.79	0.3901–1.6159	0.4058	0.5241
		CC	14 (0.13)	8 (0.15)	1.08	0.4075–2.8825	0.0260	0.8720
		TC + CC	57 (0.51)	26 (0.47)	0.87	0.4534–1.6507	0.1934	0.6601
		T	153 (0.68)	76 (0.69)	Ref
		A	170 (0.72)	146 (0.74)	1.09	0.7123–1.6680	0.1578	0.6912
TLR4	rs10759931	Patients smoking for >5 years
		Total	118	99
		AA	14 (0.12)	8 (0.08)	Ref
		AG	38 (0.32)	36 (0.36)	1.66	0.6216–4.4219	1.0309	0.3099
		GG	66 (0.56)	55 (0.56)	1.46	0.5700–3.7314	0.6242	0.4295
		AG + GG	104 (0.88)	91 (0.92)	1.53	0.6145–3.8159	0.8459	0.3577
		A	66 (0.28)	52 (0.26)	Ref
		G	170 (0.72)	146 (0.74)	1.09	0.7123–1.6680	0.1578	0.6912
	rs10759931	Patients smoking for ≤5 years
		Total	118	59
		AA	14 (0.12)	5 (0.08)	Ref
		AG	38 (0.32)	19 (0.32)	1.40	0.4388–4.4667	0.3248	0.5687
		GG	66 (0.56)	35 (0.59)	1.48	0.4941–4.4621	0.5003	0.4794
		AG + GG	104 (0.88)	54 (0.92)	1.45	0.4973–4.2502	0.4717	0.4922
		A	66 (0.28)	29 (0.25)	Ref
		G	170 (0.72)	89 (0.75)	1.19	0.7181–1.9770	0.4604	0.4974

Abbreviations: TLR, Toll-like receptor; SNP, single-nucleotide polymorphism; OR, odds ratio; CI, confidence interval.

Table 5 Genotype frequencies of TLR4 gene SNPs with overall controls according to the daily quantity of cigarettes

Gene	SNP	Allele	Nonsmokers, n (%)	Smokers, n (%)	OR	95% CI	χ^2	P-value
TLR4	rs2770150	Patients smoking ≥20 cigarettes/day
		Total	112	87
		TT	55 (0.49)	53 (0.61)	Ref
		TC	43 (0.38)	25 (0.29)	0.60	0.3243–1.1224	2.5621	0.1095
		CC	14 (0.13)	9 (0.10)	0.67	0.2663–1.6714	0.7521	0.3858
		TC + CC	57 (0.51)	34 (0.39)	0.62	0.3507–1.0925	2.7530	0.0971
		T	153 (0.68)	131 (0.75)	Ref
		C	71 (0.32)	43 (0.25)	0.71	0.4534–1.1036	2.3369	0.1263
	rs2770150	Patients smoking <20 cigarettes/day
		Total	112	53
		TT	55 (0.49)	24 (0.45)	Ref
		TC	43 (0.38)	22 (0.42)	1.17	0.5806–2.3676	0.1971	0.6571
		CC	14 (0.13)	7 (0.13)	1.15	0.4106–3.1974	0.0677	0.7948
		TC + CC	57 (0.51)	29 (0.55)	1.17	0.6053–2.2459	0.2108	0.6461
		T	153 (0.68)	70 (0.66)	Ref
		C	71 (0.32)	36 (0.34)	1.11	0.6785–1.8103	0.1686	0.6814
TLR4	rs10759931	Patients smoking ≥20 cigarettes/day
		Total	118	95
		AA	14 (0.12)	9 (0.09)	Ref
		AG	38 (0.32)	35 (0.37)	1.43	0.5513–3.7234	0.5474	0.4594
		GG	66 (0.56)	51 (0.54)	1.20	0.4821–2.9972	0.1561	0.6928
		AG + GG	104 (0.88)	86 (0.91)	1.29	0.5310–3.1161	0.3123	0.5763
		A	66 (0.28)	53 (0.28)	Ref
		G	170 (0.72)	137 (0.72)	1.00	0.6556–1.5363	0.0003	0.9870
	rs10759931	Patients smoking <20 cigarettes/day
		Total	118	57
		AA	14 (0.12)	4 (0.07)	Ref
		AG	38 (0.32)	19 (0.33)	1.75	0.5063–6.0485	0.7943	0.3728
		GG	66 (0.56)	34 (0.60)	1.80	0.5509–5.9016	0.9692	0.3249
		AG + GG	104 (0.88)	53 (0.93)	1.78	0.5595–5.6864	0.9785	0.3226
		A	66 (0.28)	27 (0.24)	Ref
		G	170 (0.72)	87 (0.76)	1.25	0.7460–2.0978	0.7223	0.3954

Abbreviations: TLR, Toll-like receptor; SNP, single-nucleotide polymorphism; OR, odds ratio; CI, confidence interval.

Figure 1 Regional LD plot for the TLR4 rs2770150 SNP.

Abbreviations: LD, linkage disequilibrium; TLR, Toll-like receptor; SNP, single-nucleotide polymorphism; CEU, Utah residents with Northern and Western European ancestry from the CEPH collection; CEPH, Centre d”Etude du Polymorphisme Humain.

Figure 2 Regional LD plot for rs10759931 SNP in TLR4.

Abbreviations: LD, linkage disequilibrium; SNP, single-nucleotide polymorphism; TLR, Toll-like receptor; CEU, Utah residents with Northern and Western European ancestry from the CEPH collection; CEPH, Centre d”Etude du Polymorphisme Humain.

Table 6 Allele and genotype frequencies of TLR4 gene polymorphisms in the Riyadh region compared to other populations

Population	Genotype frequency (n)			Allele frequency		χ^2	P-value
	TT	TC	CC	T	C
(A) TLR4 rs2770150
CRS (n=112)	0.491 (55)	0.384 (43)	0.125 (14)	0.683	0.317	–	–
CEU (n=226)	0.522 (118)	0.381 (86)	0.097 (22)	0.712	0.288	0.3006	0.5835
HCB (n=86)	0.977 (84)	0.023 (2)	–	0.988	0.012	30.0691	<0.005
JPT (n=88)	1.000 (88)	–	–	1.000	–	33.9123	<0.005
YRI (n=226)	0.796 (180)	0.204 (46)	–	0.898	0.102	24.1620	<0.005
MEX (n=100)	0.640 (64)	0.260 (26)	0.100 (10)	0.770	0.230	1.9997	0.1573
MKK (n=286)	0.720 (206)	0.231 (66)	0.049 (14)	0.836	0.164	11.4701	<0.005
TSI (n=176)	0.625 (110)	0.330 (58)	0.045 (8)	0.790	0.210	4.1589	0.0414
	AA	AG	GG	A	G	χ^2	P-value
(B) TLR4 rs10759931
CRS (n=118)	0.119 (14)	0.322 (38)	0.559 (66)	0.280	0.720	–	–
D-0 (n=48)	–	0.167 (8)	0.833 (40)	0.083	0.917	7.6210	0.0058
E-0 (n=38)	0.105 (4)	0.526 (20)	0.368 (14)	0.368	0.632	1.0657	0.3019
CABG (n=2,156)	0.141 (304)	0.458 (987)	0.401 (865)	0.370	0.630	3.9379	0.0472

Abbreviations: TLR, Toll-like receptor; CABG, coronary artery bypass graft; CEU, Utah residents with Northern and Western European ancestry from the CEPH collection; CEPH, Centre d”Etude du Polymorphisme Humain; HCB, Han Chinese in Beijing, China; JPT, Japanese in Tokyo, Japan; YRI, Yoruba in Ibadan, Nigeria; MEX, Mexican ancestry in Los Angeles, CA, USA; MKK, Maasai in Kinyawa, Kenya; TSI, Toscans in Italy; CRS, Saudi population residing in the Riyadh region of central Saudi Arabia; D-0, from Coriell Human Variation Panel – African American; E-0, from Coriell CEPH/Utah Pedigree – Caucasian; CABG, North American.