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Lu et al. Hepatoma Res 2018;4:21 I http://dx.doi.org/10.20517/2394-5079.2018.44 Page 5 of 10

Table 2. Significant genes and SNPs within the KEGG antigen processing and presentation pathway
Gene symbol Gene name SNP (rs id)
CANX Calnexin rs7734102
CD4 CD4 molecule rs1075835
CD74 CD74 molecule, major histocompatibility complex, class II invariant chain rs2748249
CIITA Class II, major histocompatibility complex, transactivator rs6498122
CIITA Class II, major histocompatibility complex, transactivator rs7203275
CIITA Class II, major histocompatibility complex, transactivator rs11074934
CIITA Class II, major histocompatibility complex, transactivator rs6498119
CTSS Cathepsin S rs11204722
HLA-A Major histocompatibility complex, class I, A rs12202296
HLA-DMA Major histocompatibility complex, class II, DM alpha rs11539216
HLA-DMA Major histocompatibility complex, class II, DM alpha rs17617515
HLA-DMB Major histocompatibility complex, class II, DM beta rs3132132
HLA-DMB Major histocompatibility complex, class II, DM beta rs714289
HLA-DOA Major histocompatibility complex, class II, DO alpha rs3129304
HLA-DOA Major histocompatibility complex, class II, DO alpha rs3129303
HLA-DOA Major histocompatibility complex, class II, DO alpha rs3130602
HLA-DOA Major histocompatibility complex, class II, DO alpha rs3129302
HLA-DPB1 Major histocompatibility complex, class II, DP beta 1 rs9277378
HLA-DQA2 Major histocompatibility complex, class II, DQ alpha 2 rs9275356
HLA-DQA2 Major histocompatibility complex, class II, DQ alpha 2 rs9276427
HLA-DQA2 Major histocompatibility complex, class II, DQ alpha 2 rs9469266
HLA-DRA Major histocompatibility complex, class II, DR alpha rs7194
HLA-G Major histocompatibility complex, class I, G rs2517898
HSP90AB1 Heat shock protein 90kDa alpha (cytosolic), class B member 1 rs504697
HSPA2 Heat shock 70kDa protein 2 rs4313734
HSPA4 Heat shock 70kDa protein 4 rs7702889
HSPA5 Heat shock 70kDa protein 5 rs12009
HSPA8 Heat shock 70kDa protein 8 rs4936770
KIR2DL3 Killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3 rs9797797
KIR2DL3 Killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3 rs13344915
KIR2DL4 Killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 rs10500318
KIR2DL4 Killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 rs3865509
KIR2DS4 Killer cell immunoglobulin-like receptor, two domains, short cytoplasmic tail, 4 rs11673276
KLRD1 Killer cell lectin-like receptor subfamily D, member 1 rs17206564
LGMN Legumain rs8177528
LGMN Legumain rs2250672
LGMN Legumain rs716097
LGMN Legumain rs12885208
LGMN Legumain rs9791
LOC100509457 HLA class II histocompatibility antigen, DQ alpha 1 chain-like rs2647015
LOC100509457 HLA class II histocompatibility antigen, DQ alpha 1 chain-like rs2859090
LOC100509457 HLA class II histocompatibility antigen, DQ alpha 1 chain-like rs9272219
RFXAP Regulatory factor X-associated protein rs6563500
TAP1 Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) rs4148882
TAP2 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) rs3819720
TAP2 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) rs2228396
TAP2 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) rs241428
TAP2 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) rs9784758
TAP2 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) rs241431

controls. This confirms that the pathway utilizes information (interactions between loci) that would not be
observed in simple single locus GWAS assessments.

“ANTIGEN PROCESSING AND PRESENTATION” TRANSCRIPTIONAL ACTIVITY
It is possible to assess whether the germline variation in “antigen processing and presentation” translates
into functionally significant difference in normal liver when contrasted to tumor adjacent liver and HCC.