Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma

Jiang, Deke; Deng, Jiaen; Dong, Changzheng; Ma, Xiaopin; Xiao, Qianyi; Zhou, Bin; Yang, Chou; Wei, Lin; Conran, Carly; Zheng, S. Lilly; Ng, Irene Oi-lin; Yu, Long; Xu, Jianfeng; Sham, Pak C.; Qi, Xiaolong; Hou, Jinlin; Ji, Yuan; Cao, Guangwen; Li, Miaoxin

doi:10.1186/s12885-020-06842-0

Table 3 Summary of genetic association results in the replication

From: Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma

CHR	SNP	BP	CADD.CScore	SuRFR	FunSeq2	HCCCell_Prob	RegulomeDB	A1	A2	Additive^a		Dominant^a		Recessive^a
CHR	SNP	BP	CADD.CScore	SuRFR	FunSeq2	HCCCell_Prob	RegulomeDB	A1	A2	OR (95% CI)	p	OR (95% CI)	p	OR (95% CI)	p
1	rs3813948	207,269,858	−0.039	14.356	0.7635	0.796	5	C	T	1.04 (0.87–1.24)	0.668	1.02 (0.83–1.25)	0.845	1.27 (0.72–2.23)	0.412
2	rs60325402	16,077,873	0.144	17.3	0.1852	0.370	5	A	T	0.85 (0.59–1.21)	0.360	0.83 (0.58–1.19)	0.319	- ^b	0.999
3	rs7612684	178,984,575	−0.163	19.334	0.8109	0.370	4	G	A	0.79 (0.59–1.05)	0.105	0.76 (0.56–1.03)	0.080	1.53 (0.23–10.01)	0.657
3	rs76863563	178,987,536	−0.498	15.493	0.1881	0.370	5	C	T	0.91 (0.66–1.26)	0.567	0.89 (0.64–1.24)	0.506	2.00 (0.17–24.06)	0.587
5	rs116966235	57,794,613	−0.636	.	0.1852	0.370	3a	G	A	1.07 (0.79–1.46)	0.670	1.06 (0.78–1.45)	0.705	- ^b	0.999
5	rs12514619	1,783,655	1.741	7.556	2.705	0.370	2b	C	T	1.10 (0.94–1.28)	0.252	1.06 (0.87–1.28)	0.563	1.45 (0.96–2.20)	0.078
6	rs389883	31,947,460	0.142	14.213	1.623	0.370	1f	G	T	0.86 (0.75–0.98)	0.026	0.86 (0.71–1.03)	0.108	0.73 (0.55–0.97)	0.032
6	rs615672	32,574,171	−0.162	4.627	0.7972	0.370	6	G	C	0.93 (0.81–1.07)	0.293	0.98 (0.81–1.17)	0.795	0.74 (0.54–1.01)	0.056
7	rs17343667	6,065,194	0.392	15.543	0.8898	0.370	1f	A	G	1.11 (0.96–1.27)	0.151	1.27 (1.04–1.55)	0.020	0.97 (0.76–1.24)	0.792
7	rs55744175	18,332,396	2.275	17.195	0.6909	0.370	5	A	G	1.05 (0.90–1.24)	0.524	1.07 (0.89–1.30)	0.474	1.02 (0.65–1.62)	0.924
8	rs16898013	124,138,891	0.780	17.314	0	0.370	3a	A	G	0.85 (0.63–1.16)	0.306	0.85 (0.61–1.16)	0.304	0.82 (0.11–6.23)	0.847
8	rs2275959	37,455,059	0.245	6.377	0.3114	0.863	4	A	G	0.98 (0.86–1.12)	0.791	1.02 (0.83–1.25)	0.854	0.93 (0.74–1.16)	0.503
8	rs2736020	15,714,529	−0.002	3.977	9.418E-161	0.370	7	C	T	1.09 (0.94–1.25)	0.255	1.13 (0.93–1.36)	0.209	1.06 (0.79–1.44)	0.687
10	rs3001719	10,409,365	−0.113	3.277	0.1852	0.370	5	G	T	1.08 (0.94–1.25)	0.288	1.11 (0.92–1.34)	0.261	1.08 (0.76–1.52)	0.674
11	rs10897243	62,043,174	−0.497	15.511	4.535E-33	0.370	6	G	C	0.92 (0.79–1.08)	0.311	0.93 (0.77–1.13)	0.468	0.81 (0.55–1.20)	0.296
12	rs79475045	39,083,557	−0.264	15.822	0.1881	0.370	5	T	G	0.88 (0.73–1.06)	0.189	0.91 (0.74–1.12)	0.377	0.55 (0.29–1.06)	0.072
12	rs979722	118,217,304	0.014	15.899	0.4365	0.370	7	C	T	1.05 (0.91–1.20)	0.512	1.05 (0.87–1.27)	0.597	1.09 (0.81–1.46)	0.577
16	rs12918376	56,558,181	−0.025	12.043	4.562E-74	0.370	6	T	G	1.11 (0.96–1.27)	0.153	1.11 (0.91–1.35)	0.303	1.19 (0.92–1.54)	0.182
20	rs2425046	33,871,661	0.090	17.787	1.78	0.918	2b	C	T	0.98 (0.77–1.24)	0.848	0.92 (0.72–1.19)	0.540	2.20 (0.79–6.14)	0.134

Note. CHR chromosome, BP base pairs, OR odd ratio, CI confidence interval, A1 minor allele, A2 major allele, CADD.CScore, SuRFR and FunSeq2 scores are annotated by KGGSeq (V1.0). HCCCell_Prob: Probability of cell type-specific regulation in GENCODE liver cancer cells (HepG2)
^a This model was tested under Logistic regression model with adjustment for age and sex
^b The value is not available

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ISSN: 1471-2407

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