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. 2019 Aug 13;10:696. doi: 10.3389/fgene.2019.00696

Table 2.

Host genetic factors associated with chronic HBV infection.

Category Gene ontology Gene Genetic determinants (SNP/Hap/CNVs) Main reference
I HLA HLA-B *07, *58 Seshasubramanian et al., 2018
HLA-DPA1 rs3077 Kamatani et al., 2009; Mbarek et al., 2011; Yan et al., 2012b; Jiang et al., 2015
HLA-DPB1 rs2281388, rs9277535, rs9277542 Kamatani et al., 2009; Mbarek et al., 2011; Nishida et al., 2012; Yan et al., 2012b; Zhang et al., 2013b; Jiang et al., 2015; Trinks et al., 2017
HLA-DQ rs9275319, rs9275572 Al-Qahtani et al., 2014; Zhang et al., 2014b; Kim et al., 2015; Xu et al., 2018
HLA-DQB1 *0201, *0301, *0303, *0502, *0604, rs2856718 Mbarek et al., 2011; Jiang et al., 2015; Huang et al., 2016; Xu et al., 2017b; Xu et al., 2018
HLA-DQB2 rs7453920 Hu et al., 2013; Jiang et al., 2015; Xu et al., 2017b; Xu et al., 2018
HLA-DRB1 *13 Zhu et al., 2016b
Cytokines IL-10 −592 Cheong et al., 2006; Chen et al., 2010
IL-18 −137 Karra et al., 2015
IFN-γ +874 Sun et al., 2015
TNF-α −238, −308, −857, −863 Kim et al., 2003; Cheong et al., 2006; Shi et al., 2012; Zheng et al., 2012
Chemokines CCR5 Δ32 Suneetha et al., 2006
TLRs TLR-3 rs3775291 Geng et al., 2016
MicroRNAs MiR-106b-25 rs999885 Liu et al., 2012b; Zhou et al., 2015
miR-122 rs3783553 Zhou et al., 2015
miR-196a-2 rs11614913 Zhou et al., 2015; Al-Qahtani et al., 2017
miR-let-7c rs6147150 Zhou et al., 2015
Others CTLA-4 rs231775, rs5742909 Schott et al., 2007; Huang et al., 2013; Xu et al., 2013
NTCP rs2296651 Hu et al., 2016; Wang et al., 2017a; Nfor et al., 2018
STAT4 rs7574865 Kim et al., 2015; Jiang et al., 2016b
TCF19 rs1419881 Kim et al., 2013; Jiang et al., 2015
VDR FokI He et al., 2018
II HLA HLA-A *33:03:01 Miao et al., 2013
HLA-B *13:01:01 Miao et al., 2013
HLA-C Leu-15, rs2853953, rs3130542 Hu et al., 2013; Jiang et al., 2015; Zhu et al., 2016b
HLA-DOA rs378352 Jiang et al., 2015
HLA-DP rs9366816 Chang et al., 2014
HLA-DPA1 rs2301220, rs2395309, rs9277341 Guo et al., 2011; Li et al., 2011a
HLA-DPB1 rs9277534, *0201, *0401, *0901, positions 84–87, *0402, *0501, *0201-*0401, *0201-*0402, *0201-*0501, *0401-*0402, *0401-*0501, *0402-*0402, *0402-*0501, *0501-*0501, *0501-*0901, *0501*others, rs9277378, rs10484569, rs3117222, rs9380343, rs3135021, G-A-G-A-T-T1, G-G-G-G-T-C2 Guo et al., 2011; Thomas et al., 2012; Wong et al., 2013; Zhang et al., 2013e; Hu et al., 2014; Nishida et al., 2014; Nishida et al., 2015; Zhu et al., 2016b
HLA-DQ A1*0101-B1*0501, A1*0102-B1*0303, A1*0102-B1*0604, A1*0301-B1*0601, A1*0102-B1*0602, A1*0301-B1*0302, A1*0301-B1*0303, A1*0301-B1*0401, A1*0501-B1*0301 Mbarek et al., 2011
HLA-DQA2 rs9276370 Chang et al., 2014
HLA-DQB2 rs7756516 Chang et al., 2014
HLA-DPA1/DPB1 A-A3, A-A4, T-A-T5,C-A-T6,A1*0103-B1*0401, A1*0103-B1*0402, A1*0202-B1*0301, A1*0202-B1*0501, A-A-C-T7, A-A-C-C//A-G-T-G-C-C8, A-A-C-T//A-G-T-G-C-C9, G-G-T-C//A-G-T-G-C-C10 Kamatani et al., 2009; Guo et al., 2011; Li et al., 2011a; Wang et al., 2011; Wong et al., 2013
HLA-DP/DQ T-T-G-A-T11, T-T-G-G-T12, carrying 4–6 variant alleles, G-A13, A-G14, A-A15 Hu et al., 2012; Chang et al., 2014; Al-Qahtani et al., 2014
HLA-J rs400488 Zhu et al., 2016b
Cytokines IL-10RB rs2834167 Romporn et al., 2013; Ma et al., 2014
IL-12B rs3212227 He et al., 2015
IL-16 rs11556218 Li et al., 2011b
IL-21 rs2221903 Li et al., 2013a
IFN-α2 p.Ala120Thr Zhao et al., 2012
IFN-αR2 rs1051393, rs12233338 Ma et al., 2018a
IFNLR1 rs4649203, rs7525481 Ma et al., 2018a
IFN-γR1 rs3799488 He et al., 2015
IFN-γR2 rs1059293 He et al., 2015
TNF-α T-C-C-G-G-G16, C-A-C-G-G-G17 Kim et al., 2003
TGF-α +106151, +103461, A-T-G-T-T-T-T-C-T18 Kim et al., 2009
TLRs TLR-3 rs1879026 Al-Qahtani et al., 2012a
TLR-9 rs352140 He et al., 2015
MicroRNAs miR-30a rs1358379 Al-Qahtani et al., 2017
miR-101-2 rs12375841, T-C19 Bae et al., 2012
miR-122 rs4309483 Liu et al., 2014b
miR-219-1 rs107822, rs213210, rs421446, C-A-C20, T-G-T21 Cheong et al., 2013
miR-323b rs56103835 Yu et al., 2014
miR-423 rs6505162 Al-Qahtani et al., 2017
miR-492 rs2289030 Al-Qahtani et al., 2017
Others C2 p.Glu318Asp, rs7746553, rs9267673, rs9267665, rs9267677, rs9279450, rs10947223 Zhao et al., 2012; Namgoong et al., 2018
CD40 rs1883832 Jiang et al., 2015
CFB rs12614 Jiang et al., 2015
CTLA-4 rs3087243, C-A-C-C-G22, T/C-A-C-C-G23, T-A-C-C-A24 Thio et al., 2004; Chen et al., 2010
EHMT2 rs7887, rs652888, rs35875104, rs41267090 Jiang et al., 2015; Shin et al., 2017
ESR1 +29 Deng et al., 2004
IFN4/HLA-DQ rs12971396-rs9275319, rs12971396-rs12979860-rs9275319 Fan et al., 2016a
INST10 rs7000921 Li et al., 2016
KIF1B A-T-A25 Al-Qahtani et al., 2012b
MCP1 −2518, −2518/−2076(−/ht2), −2518/−2076(ht2/ht2) Park et al., 2006; Chen et al., 2010
MIF rs755622 Moudi et al., 2016
MxA −123 Cao et al., 2009; Rebbani et al., 2017
MX1 rs467960 He et al., 2015
NF-κB rs2233406, rs3138053 Zhang et al., 2014a
NLRX1 p.Arg707Cys Zhao et al., 2012
NOTCH4 rs422951 Jiang et al., 2015
NTCP rs943277, rs4646285 Wang et al., 2017a; Wu et al., 2018a
OCT4 rs13409, rs885952, rs879882, rs1265163, rs2394882, rs3094193, rs3130501, rs3130503, rs3130931, rs3132526, rs3757349, rs9263800, rs117265349 Shin et al., 2017
PAPL rs423058 Ma et al., 2014
SOCS3 rs111033850, rs12953258, C-C 26 Hoan et al., 2017
SPP1 −1800, T-T-C-T-A27 Shin et al., 2007
STAT4 rs8179673, rs10168266, rs11889341, C-T-C-T-T28 Jiang et al., 2016b, Lu et al., 2015b
TMEM2 p.Ser1254Asn Zhao et al., 2012
TMEM2/IFNA2/NLRX1/C2 p.Ser1254-Asn/p.Ala120Thr/p.Arg707Cys/p.Glu318Asp Zhao et al., 2012
UBE2L3 rs2266959, rs4821116 Liu et al., 2018d, Hu et al., 2013
VARS2 rs1043483, rs1264295, rs2249464, rs2517459, rs2532932, rs9394021, Cheong et al., 2015
ZNRD1 rs3757328, G-G-A29 Wen et al., 2015

Haplotypes

1G-A-G-A-T-T, rs9277535-rs10484569-rs3128917-rs2281388-rs3117222-rs9380343; 2G-G-G-G-T-C, rs9277535-rs10484569-rs3128917-rs2281388-rs3117222-rs9380343; 3A-A, rs3077-rs9277535; 4A-A, rs2395309-rs9277535; 5T-A-T, rs3077-rs9277378-rs3128917; 6C-A-T, rs3077-rs9277378-rs3128917; 7A-A-C-T, rs2395309-rs3077-rs2301220-rs9277341; 8A-A-C-C//A-G-T-G-C-C, rs2395309-rs3077-rs2301220-rs9277341//rs9277535-rs10484569-rs3128917 -rs2281388-rs3117222-rs9380343; 9A-A-C-T//A-G-T-G-C-C, rs2395309-rs3077-rs2301220-rs9277341//rs9277535-rs10484569-rs3128917 -rs2281388-rs3117222-rs9380343; 10G-G-T-C//A-G-T-G-C-C, rs2395309-rs3077-rs2301220-rs9277341//rs9277535-rs10484569-rs3128917 -rs2281388-rs3117222-rs9380343; 11T-T-G-A-T, rs9276370-rs7756516-rs7453920-rs9277535-rs9366816; 12T-T-G-G-T, rs9276370-rs7756516-rs7453920-rs9277535-rs9366816; 13G-A, rs2856718- rs9275572; 14A-G, rs2856718- rs9275572; 15A-A, rs2856718- rs9275572; 16T-C-C-G-G-G, -1031/-863/-857/-308/-238/-163; 17C-A-C-G-G-G, -1031/-863/-857/-308/-238/-163; 18A-T-G-T-T-T-T-C-T, +88344/+102906/+103432/+103437/+103461/+104261/+104802/+106151/+106318; 19T-C, rs12375841-rs17803780; 20C-A-C, rs421446-rs107822-rs213210; 21T-G-T, rs421446-rs107822-rs213210; 22C-A-C-C-G, -1722/-1661/-658/-319/+49; 23T/C-A-C-C-G, -1722/-1661/-658/-319/+49; 24T-A-C-C-A, -1722/-1661/-658/-319/+49; 25A-T-A, rs17401966-rs12734551-rs3748578; 26C-C, rs111033850-rs12953258; 27T-T-C-T-A, -1800/-1627/+4645/+5806/+6139; 28C-T-C-T-T, rs8179673-rs7574865-rs4274624-rs11889341-rs10168266; 29G-G-A, rs3757328-rs6940552-rs9261204.