rs7453920

plus

Geno	Mag	Summary
(A;A)
(G;G)	1	Slight increase in risk for chronic hepatitis B infection

Make rs7453920(A;G)

Reference

GRCh38 38.1/141

Chromosome

6

Position

32762235

Gene

HLA-DQB2

is a	snp
is	mentioned by
dbSNP	rs7453920
dbSNP (classic)	rs7453920
ClinGen	rs7453920
ebi	rs7453920
HLI	rs7453920
Exac	rs7453920
Gnomad	rs7453920
Varsome	rs7453920
LitVar	rs7453920
Map	rs7453920
PheGenI	rs7453920
Biobank	rs7453920
1000 genomes	rs7453920
hgdp	rs7453920
ensembl	rs7453920
geneview	rs7453920
scholar	rs7453920
google	rs7453920
pharmgkb	rs7453920
gwascentral	rs7453920
openSNP	rs7453920
23andMe	rs7453920
SNPshot	rs7453920
SNPdbe	rs7453920
MSV3d	rs7453920
GWAS Ctlg	rs7453920

GMAF

0.2975

Max Magnitude

1

?

(A;A) (A;G) (G;G)

28

rs7453920 adds an additional polymorphism to the growing body of literature supporting a genetic component to HBV infection and clearance. It is located in intron 1 of the HLA-DQB2 gene at the 6p21.32 locus. Therefore, the SNP does not affect the structure of the protein by any direct means. The A allele of this SNP has been associated with increased HLA-DQB2 mRNA levels in circulating monocytes (which are critical for mounting immune responses), increased HBV clearance, and CHB infection. [PMID 24162738]

Alleles 1 and 2 at this location are A and G with G being the risk allele (p = 5.98E-28; OR = 1.81). [PMID 21750111]

The HLA-DQB1 (Human Leukocyte Antigen) and HLA-DQB2 genes belongs to the HLA class II beta chain class paralogues. Class II molecules are heterodimers comprised of alpha (DQA) and beta (DQB) chains that are both anchored in the membrane. They play an integral role in the immune system and more specifically HBV clearance by presenting peptide sequences from extracellular proteins and are predominantly expressed in antigen-presenting cells such as B lymphocytes, dendritic cells, and macrophages. Polymorphisms in the protein-coding portions of the genes for these heterodimers will result in the display of different kinds of peptides. The beta chain contains six exons and is approximately 26-28 kDa long. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. rs7453920 is a mutation in the first intron of the gene and therefore does not directly affect the structure and function of the protein.

Hepatitis B virus (HBV) is the most common cause of infectious liver disease, afflicting more than 400 million people worldwide. This chronic viral condition can be transmitted vertically during the neonatal period; horizontally during childhood via bites, lesions or sanitary habits; or during adulthood via sexual contact, drug use, or medical exposure. Though there are many factors that influence the expression of the disease including viral, host immunological, and environmental, there increasingly appears to be a strong genetic component to the body’s response to HBV.

Genes are impact five different pathways that affect the infection and clearance of HBV. These include (1) viral entry into the cells, (2) the immune response to HBV infection, (3) pathological alterations in liver tissue, (4) liver cirrhosis and subsequent hepatocellular carcinoma, and (5) resistance to antiviral therapies. [PMID 12679901 ] Mutations in HLA class I and II alleles, cytokine and chemokines, as well as mannose binding protein (MBP) have all demonstrated strong associations with HBV clearance. Specifically, mutations in the DRB1 gene are associated with self-limiting courses of acute HBV while DQA1 and DQB1 are linked to viral persistence. [PMID 10068598]

The varying release of cytokines and chemokines impacts the host’s immunological response to HBV as well as viral persistence. Tumor necrosis factor a (TNF-a) is associated with non-cytotoxic antiviral mechanisms. [PMID 9528902 ] Polymorphisms in the promotor region of TNF-a are associated with HBV and HCV persistence. [PMID 9515764] Finally, mannose binding protein (MBP) is an opsonin that activates the classical complement pathway of innate immunity and phagocytosis. Mutations in several codons including 52, 54, and 57 have impaired the functionality of MBP and therefore the phagocytotic defenses against HBV. [PMID 8965590]

Additionally, several studies have demonstrated genetically variable outcomes to HBV vaccine-induced immunity. Peak vaccine-induced anti-HBs level is directly related to antibody decay, risk of infection, and persistent carriage. Variation in the IFNG, MAPK8, AND IL10RA genes affect peak anti-HBs levels (p ≤ 0.001). [PMID 18365030 ]

[PMID 21750111] Significant association between SNP and chronic hepatitis B in a Japanese population. DQA1*0102-DQB1*0604 and DQA1*0101-DQB1*0501 [odds ratios (OR) =0.16, and 0.39, respectively] as protective haplotypes and DQA1*0102-DQB1*0303 and DQA1*0301-DQB1*0601 (OR = 19.03 and 5.02, respectively) as risk haplotypes.

[PMID 24162738] This study found an association with rs7453920 and CHB with an odds ratio of 0.53 and a Pmeta value of P = 4.93e-37.

[PMID 20502693 ] A transcriptome study demonstrated that the A allele of rs7453920 was associated with higher HLA-DQ mRNA levels in circulating monocytes, which are critical for mounting immune responses.

[PMID 24465366 ] The rs7453920 allele frequency is found more often in chronically infected patients than with clearance group infections, but did not reach significance when the association was examined between HBV infections in Saudi Arabian patients.

[PMID 22105689] Rs7453920 is associated with HBV clearance in Japanese populations. There is an association between rs7453920, two other SNPs and HBV clearance in Han Chinese populations (P = 7.61e-7). }}

[PMID 21750111] A Genome-Wide Association Study of Chronic Hepatitis B Identified Novel Risk Locus in a Japanese Population

[PMID 17660530] Risk alleles for multiple sclerosis identified by a genomewide study.

[PMID 18204098] Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.

[PMID 20017995 ] A principal-components-based clustering method to identify multiple variants associated with rheumatoid arthritis and arthritis-related autoantibodies.

[PMID 22105689] Genetic variants in human leukocyte antigen/DP-DQ influence both hepatitis B virus clearance and hepatocellular carcinoma development.

GWAS snp
PMID	[PMID 23349640 ]
Trait	Lymphoma
Title	Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies.
Risk Allele
P-val	5E-6
Odds Ratio	1.19 [1.11-1.3]

GWAS snp
PMID	[PMID 23760081]
Trait	Chronic hepatitis B infection
Title	A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
Risk Allele
P-val	7E-26
Odds Ratio	2.00 [1.72-2.27]

[PMID 23428460] Genetic variants in HLA-DP/DQ contribute to risk of cervical cancer: a two-stage study in Chinese women.

GWAS snp
PMID	[PMID 24162738]
Trait	Hepatitis B
Title	New loci associated with chronic hepatitis B virus infection in Han Chinese.
Risk Allele	G
P-val	5E-37
Odds Ratio	1.89 [1.69-2.08]

GWAS snp
PMID	[PMID 24940741 ]
Trait	Chronic hepatitis B infection
Title	A genome-wide association study on chronic HBV infection and its clinical progression in male Han-Taiwanese.
Risk Allele	G
P-val	7E-15
Odds Ratio	2.31 [1.87-2.85]

[PMID 25802187] Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B

[PMID 25376093 ] Association between single-nucleotide polymorphisms and early spontaneous hepatitis B virus e antigen seroconversion in children

[PMID 27394003] Association of HLA-DP/DQ and STAT4 polymorphisms with ankylosing spondylitis in Southwest China.

[PMID 28267888] Role of HLA-DP and HLA-DQ on the clearance of hepatitis B virus and the risk of chronic infection in a multiethnic population.

[PMID 28231665] [Prognosis and related risk factors for 465 subjects infected with hepatitis C virus in Danyang, Jiangsu province].

[PMID 29467950 ] Genetic polymorphisms in HLA-DP and STAT4 are associated with IgA nephropathy in a Southwest Chinese population.