Study of Single Nucleotide Polymorphisms Associated with Breast Cancer Patients among Arab Ancestries

Table 2

The most significant SNPs associated with breast cancer in Saudi Arabians.

S. no	CHR	SNP ID	BP	MA	MAF	value	OR(L95-U95)	Gene	AA	CCF
1	3	rs202018563	43389699	A	0.482	6.97E-10	18.9 (6.49-55.01)	SNRK and SNRK-AS1	G	0.875, 0.270
2	13	rs2227943	32911278	T	0.415	4.89E-09	0.05 (0.01-0.17)	BRCA2	C	0.806, 0.214
3	2	rs199826847	239049921	T	0.473	4.91E-09	10.17 (3.95-26.11)	ZNF484	C	0.868, 0.347
4	11	rs1695739	126196175	A	0.383	9.14E-09	25.67 (6.74-97.79)	DCPS	G	0.875, 0.214
5	2	rs189581518	136111018	A	0.394	5.17E-08	11.07 (4.09-29.92)	ZRANB3	C	0.808, 0.235
6	16	rs7206703	57091977	T	0.4	6.83E-08	0.04 (0.01-0.19)	NLRC5	C	0.947, 0.439
7	21	rs112011493	44840296	C	0.474	9.63E-08	0.09 (0.03-0.24)	SIK1	T	0.841, 0.329
8	16	rs762349227	682670	T	0.382	1.24E-07	0.04 (0.01-0.20)	WFIKKN1	C	0.767, 0.222
9	12	rs200582033	6031943	C	0.311	1.56E-07	18.91 (5.20-68.72)	ANO2	T	0.978, 0.535
10	15	rs114516513	51758447	T	0.397	1.61E-07	0.05 (0.01-0.22)	DMXL2	C	0.889, 0.220
11	3	rs192044702	81698005	A	0.185	1.70E-07	12.43 (4.41-35.01)	GBE1	G	0.542, 0.059
12	17	rs139171143	4802111	C	0.3	2.10E-07	19.69 (5.38-72.1)	CHRNE and C17orf107	G	0.600, 0.129
13	6	rs140709825	111697900	A	0.357	2.28E-07	12.2 (4.35-34.24)	REV3L	G	0.719, 0.182
14	9	rs142712699	95610753	A	0.256	2.46E-07	14.17 (4.39-45.65)	ZNF484	C	0.722, 0.117
15	16	rs11552432	1823054	C	0.186	2.53E-07	44 (7.28-266.1)	MRPS34, EME2 and NME3	G	0.800, 0.083
16	7	rs141963459	2691854	G	0.02	2.64E-07	21.64 (4.56-102.7)	TTYH3	A	1.000, 0.972
17	14	rs35064097	57700585	T	0.207	2.71E-07	10.81 (4.06-28.79)	EXOC5	G	0.455, 0.056
18	6	rs200026839	66204932	T	0.385	2.94E-07	11.5 (4.18-31.64)	EYS	G	0.767, 0.212
19	16	rs16957552	75269124	T	0.365	2.94E-07	0.05 (0.01-0.22)	BCAR1	C	0.950, 0.488
20	6	rs57738384	129763368	A	0.286	2.96E-07	10.13 (3.73-27.52)	LAMA2	G	0.700, 0.156
21	2	rs140626972	160602359	A	0.211	3.03E-07	20 (5.68-70.42)	7-mar	G	0.577, 0.062
22	23	rs145970300	107819173	A	0.151	3.43E-07	10.36 (3.81-28.17)	COL4A5	C	0.389, 0.029
23	19	rs114544630	1481787	G	0.429	3.72E-07	11.67 (4.08-33.29)	PCSK4	C	0.900, 0.419
24	8	rs187011732	144992465	C	0.449	3.99E-07	0.08 (0.02-0.24)	PLEC	T	0.875, 0.385
25	6	rs562092150	170115902	A	0.118	4.03E-07	39.5 (4.88-319.5)	PHF10	C	0.367, 0.014
26	18	rs201319761	19997762	A	0.145	4.28E-07	42 (6.55-269.3)	CTAGE1	G	0.406, 0.038
27	14	rs146398509	92470845	T	0.282	4.85E-07	12.71 (4.15-38.87)	TRIP11	C	0.579, 0.125
28	2	rs115282281	26534041	T	0.219	4.89E-07	0.06 (0.02-0.23)	ADGRF3 and LOC105374334	C	0.500, 0.079
29	1	rs202005618	226411686	G	0.349	5.13E-07	9.62 (3.72-24.89)	MIXL1	C	0.952, 0.500
30	9	rs56170708	96010036	G	0.351	5.51E-07	0.07 (0.02-0.24)	WNK2	A	0.935, 0.500
31	7	rs41273999	23821123	A	0.351	5.68E-07	0.025 (0.003-0.19)	STK31	G	0.769, 0.191
32	15	rs11574476	73994778	G	0.337	6.01E-07	17.11 (4.42-66.15)	CD276	A	0.731, 0.194
33	12	rs7302017	63004583	A	0.214	6.34E-07	10.96 (3.96-30.32)	None	G	0.800, 0.087
34	15	rs55799438	40544493	A	0.415	6.58E-07	11.48 (3.99-33.03)	C15orf56, PAK6 and BUB1B-PAK6	G	0.938, 0.432
35	18	rs138472116	9124917	T	0.196	6.72E-07	0.08 (0.03-0.25)	NDUFV2 and NDUFV2-AS1	C	0.472, 0.066
36	2	rs150343979	25384086	A	0.45	6.95E-07	15.19 (5.56-41.44)	POMC	G	0.909, 0.342
37	4	rs75428449	175224971	A	0.337	7.05E-07	28.36 (5.64-142.6)	CEP44	C	0.731, 0.194
38	5	rs199715117	130517944	A	0.255	7.29E-07	11.24 (3.96-31.97)	LYRM7	C	0.559, 0.111
39	7	rs34850251	94164820	A	0.337	7.87E-07	12.42 (4.16-37.12)	CASD1 and LOC105375404	C	0.731, 0.182
40	5	rs147680491	61779069	A	0.29	7.89E-07	0.10 (0.03-0.27)	IPO11	G	0.633, 0.143
41	23	rs146662506	11207098	A	0.365	9.23E-07	14.93 (4.71-47.38)	ARHGAP6	G	0.719, 0.188

CHR: Chromosome; SNP ID: Single nucleotide polymorphism ID; BP: Base pair position at the respective chromosome as per GRCh37.p13; MA: Minor allele name; MAF: Frequency of minor allele in controls; OR: Odd ratio; SE: Standard error; L95: Lower bound of 95% confidence interval for odds ratio; U95: Upper bound of 95% confidence interval for odds ratio. AA: Associated Allele; CCF: Case, Control Frequencies.