Oxidative stress in susceptibility to breast cancer: study in Spanish population

Rodrigues, Patricia; de Marco, Griselda; Furriol, Jessica; Mansego, Maria Luisa; Pineda-Alonso, Mónica; Gonzalez-Neira, Anna; Martin-Escudero, Juan Carlos; Benitez, Javier; Lluch, Ana; Chaves, Felipe J; Eroles, Pilar

doi:10.1186/1471-2407-14-861

BMC Cancer

Table 1 Summary of the 76 selected SNPs in 27 genes

From: Oxidative stress in susceptibility to breast cancer: study in Spanish population

Gene	Chr	SNP id	Alleles^a	Chr position	Location	MAF controls^b	HWE controls^c
*CAT*	11	rs1049982	C/T	34417117	5´UTR	0.355	0.66
		rs475043	A/G	34450377	downstream	0.334	0.73
		rs511895	A/G	34444305	intronic	0.332	0.73
		rs7104301	A/G	34450214	downstream	0.308	0.18
		rs769214	A/G	34416293	promoter	0.349	0.61
*CYBB*	X	rs5964125	A/G	37543395	intronic	0.150	0.37
*CYBB*	X	rs5964151	G/T	37555673	3´UTR	0.149	0.45
*GCLC*	6	rs1014852	A/T	53478711	intronic	0.057	0.27
		rs11415624	-/A	53470407	3´UTR	0.315	0.08
		rs3736729	A/C	53487364	intronic	0.462	0.36
		rs4140528	C/T	53469648	downstream	0.265	0.62
*GCLM*	1	rs7515191	A/G	94139685	intronic	0.368	0.57
*GCLM*	1	rs7549683	G/T	94126037	3´UTR	0.367	0.46
*GNAS*	20	rs4812042	A/G	56895310	intronic	0.340	0.20
		rs7121	C/T	56912202	coding (synonymous)	0.449	0.70
		rs919196	C/T	56917480	intronic	0.195	0.63
*GPX6*	6	rs406113	A/C	28591461	coding (missense)	0.310	0.08
*GPX6*	6	rs974334	C/G	28582197	intronic	0.157	0.31
*GSR*	8	rs1002149	G/T	30705280	promoter	0.152	0.65
		rs2551715	A/G	30666178	intronic	0.375	1.00
		rs2911678	A/T	30659513	intronic	0.189	0.53
		rs8190996	C/T	30673548	intronic	0.437	0.81
*GSS*	20	rs13041792	A/G	33008716	promoter	0.202	0.63
		rs2273684	G/T	32993427	intronic	0.438	0.07
		rs725521	C/T	32979732	downstream	0.456	0.02
*M6PR*	12	rs1805754	A/C	8994515	promoter	0.236	0.16
*M6PR*	12	rs933462	G/T	8994932	promoter	0.419	0.94
*MSRB2*	10	rs11013291	C/T	23440197	intronic	0.394	0.69
*NCF2*	1	rs2274064	C/T	181809010	coding (missense)	0.444	0.27
		rs2274065	A/C	181826327	5´UTR	0.067	0.22
		rs2296164	C/T	181801558	intronic	0.452	0.24
*NCF4*	22	rs2072712	C/T	35601748	coding (synonymous)	0.089	0.05
*NOS1*	12	rs570234	A/C	116255365	intronic	0.385	0.80
		rs576881	A/G	116257218	intronic	0.372	0.62
		rs816296	A/C	116255127	intronic	0.189	0.17
*NOS2A*	17	rs2779248	C/T	23151959	upstream	0.362	0.11
*NOS2A*	17	rs3729508	A/G	23133157	intronic	0.447	0.58
*NOX1*	X	rs4827881	A/C	100016329	upstream	0.223	0.05
*NOX1*	X	rs5921682	A/G	100017093	upstream	0.459	0.88
*NOX3*	6	rs231954	C/T	155791727	coding (synonymous)	0.442	0.02
*NOX3*	6	rs3749930	G/T	155802938	coding (missense)	0.037	0.24
*NOX4*	11	rs490934	C/G	88863264	intronic	0.056	1.00
*NOX5*	15	rs2036343	A/C	67092815	promoter	0.048	0.19
*NOX5*	15	rs34990910	A/G	67118435	intronic	0.027	0.38
*OGG1*	3	rs1052133	C/G	9773773	coding (missense)	0.213	0.87
*SOD1*	21	rs17881274	C/T	31953051	upstream	0.039	0.07
*SOD2*	6	rs2842980	A/T	160020106	downstream	0.219	0.50
*SOD2*	6	rs2855116	G/T	160026115	intronic	0.454	0.12
		rs8031	A/T	160020630	intronic	0.459	0.35
*SOD3*	4	rs2284659	G/T	24403895	promoter	0.371	0.25
*TXN*	9	rs2301241	C/T	112059329	promoter	0.514	0.25
		rs4135168	A/G	112056706	intronic	0.222	0.82
		rs4135179	A/G	112055821	intronic	0.156	0.24
		rs4135225	C/T	112046512	intronic	0.390	0.29
*TXN2*	22	rs2281082	G/T	35202696	intronic	0.170	0.41
*TXN2*	22	rs5756208	A/T	35207988	promoter	0.179	0.51
*TXNRD1*	12	rs10861201	A/C	103243089	intronic	0.259	0.31
		rs4077561	C/T	103204498	promoter	0.387	0.46
		rs4964287	C/T	103233689	coding (synonymous)	0.320	0.93
		rs4964778	C/G	103210194	intronic	0.184	0.61
		rs4964779	C/T	103218991	intronic	0.062	0.31
		rs5018287	A/G	103231281	intronic	0.419	0.88
*TXNRD2*	22	rs737866	A/G	18310109	intronic	0.293	0.77
*XDH*	2	rs10175754	C/T	31475102	intronic	0.153	0.65
		rs10187719	C/T	31453650	intronic	0.311	0.78
		rs1346644	C/G	31479549	intronic	0.150	0.55
		rs1429374	A/G	31425902	intronic	0.338	0.10
		rs17011353	C/T	31441941	intronic	0.028	0.01
		rs17011368	C/T	31444421	coding (missense)	0.044	0.54
		rs17323225	C/T	31446769	coding (missense)	0.029	1.00
		rs1884725	A/G	31425290	coding (synonymous)	0.234	0.20
		rs206801	C/T	31482250	intronic	0.050	1.00
		rs206812	A/G	31491373	promoter	0.486	0.54
		rs2073316	A/G	31464533	intronic	0.427	0.69
		rs207454	A/C	31421136	intronic	0.087	0.81
		rs761926	C/G	31444289	intronic	0.300	0.72

Chr – chromosome; MAF – Minor Allele Frequency; HWE – Hardy Weinberg Equilibrium. ^amajority allele are in bold; ^bpolymorphisms with MAF <5% are excluded for further analysis; ^cpolymorphisms with p-values <0.05 are not in HWE and they are excluded for further analysis. The information about MAF and HWE are referent to the Set 1.
CAT: catalase; CYBB: cytochrome b-245, beta polypeptide; GCLC: glutamate-cysteine ligase, catalytic subunit; GCLM: glutamate-cysteine ligase, modifier subunit; GNAS: GNAS complex locus; GPX6: glutathione peroxidase 6; GSR: glutathione reductase; GSS: glutathione synthetase; M6PR: mannose-6-phosphate receptor; MSRB2: methionine sulfoxide reductase B2; NCF2: neutrophil cytosolic factor 2; NCF4: neutrophil cytosolic factor 4; NOS1: nitric oxide synthase 1; NOS2A: nitric oxide synthase 2; NOX1: NADPH oxidase 1; NOX3: NADPH oxidase 3; NOX4: NADPH oxidase 4; NOX5: NADPH oxidase 5; OGG1: 8-oxoguanine DNA glycosylase; SOD1: superoxide dismutase 1; SOD2: superoxide dismutase 2; SOD3: superoxide dismutase 3; TXN: thioredoxin; TXN2: thioredoxin 2; TXNRD1: thioredoxin reductase 1; TXNRD2: thioredoxin reductase 2; XDH: xanthine dehydrogenase.

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ISSN: 1471-2407

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