SNP variants associated with non-Hodgkin lymphoma (NHL) correlate with human leukocyte antigen (HLA) class II expression

Sci Rep. 2017 Jan 31;7:41400. doi: 10.1038/srep41400.


Large consortia efforts and genome-wide association studies (GWASs) have linked a number of genetic variants within the 6p21 chromosomal region to non-Hodgkin lymphoma (NHL). Complementing these efforts, we genotyped previously reported SNPs in the human leukocyte antigen (HLA) class I (rs6457327) and class II (rs9271100, rs2647012 and rs10484561) regions in a total of 1,145 subjects (567 NHL cases and 578 healthy controls) from two major ethnic groups in Malaysia, the Malays and the Chinese. We identified a NHL-associated (PNHL_add = 0.0008; ORNHL_add = 0.54; 95% CI = 0.37-0.77) and B-cell associated (PBcell_add = 0.0007; ORBcell_add = 0.51; 95% CI = 0.35-0.76) SNP rs2647012 in the Malaysian Malays. In silico cis-eQTL analysis of rs2647012 suggests potential regulatory function of nearby HLA class II molecules. Minor allele rs2647012-T is linked to higher expression of HLA-DQB1, rendering a protective effect to NHL risk. Our findings suggest that the HLA class II region plays an important role in NHL etiology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Demography
  • Female
  • Gene Expression Regulation*
  • Genetic Predisposition to Disease*
  • Herpesvirus 4, Human / physiology
  • Histocompatibility Antigens Class II / genetics*
  • Humans
  • Lymphocytes / virology
  • Lymphoma, Non-Hodgkin / genetics*
  • Malaysia
  • Male
  • Middle Aged
  • Polymorphism, Single Nucleotide / genetics*
  • Quantitative Trait Loci / genetics


  • Histocompatibility Antigens Class II