All polymorphisms studied in this paper [PMID: 12509789] , total : 44 polymorphisms

Title : Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis.
Abstract : Rheumatoid arthritis (RA) is a chronic inflammatory joint disease with a complex etiology in which environmental factors within a genetically susceptible host maneuver the innate and adaptive arms of the immune system toward recognition of autoantigens. This ultimately leads to joint destruction and clinical symptomatology. Despite the identification of a number of disease-susceptibility regions across the genome, RA's major genetic linkage remains with the major histocompatibility complex (MHC), which contains not only the key immune-response class I and class II genes but also a host of other loci, some with potential immunological relevance. Inside the MHC itself, the sole consistent RA association is that with HLA-DRB1, although this does not encode all MHC-related susceptibility. Indeed, in a set of Japanese patients with RA and a control group, we previously reported the presence of a second RA-susceptibility gene within the telomeric human leukocyte antigen (HLA) class III region. Using microsatellites, we narrowed the susceptibility region to 70 kb telomeric of the TNF cluster, known to harbor four expressed genes (I kappa BL, ATP6G, BAT1, and MICB). Here, using numerous single-nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms, we identify the second RA-susceptibility locus within the HLA region, as the T allele of SNP 96452 (T/A), in the promoter region (position -62) of the I kappa BL gene (P=.0062). This -62T/A SNP disrupts the putative binding motif for the transcriptional repressor, delta EF1, and hence may influence the transcription of I kappa BL, homologous to I kappa B alpha, the latter being a known inhibitor of NF kappa B, which is central to innate immunity. Therefore, the MHC may harbor RA genetic determinants affecting the innate and adaptive arms of the immune system.
Author : Okamoto K,Makino S,Yoshikawa Y,Takaki A,Nagatsuka Y,Ota M,Tamiya G,Kimura A,Bahram S,Inoko H,
Source : Am J Hum Genet. 2003 Feb;72(2):303-12. Epub 2002 Dec 31.
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No.Polymorphism nameGene SymbolEntrez Gene ID
31 rs2523511 DDX39B 7921
32 rs2523512 DDX39B 7922
33 rs2516393 DDX39B 7919
34 rs2071596 DDX39B 7919
35 rs933208 DDX39B 7919
36 rs1129640 ATP6V1G2-DDX39B 100532737
37 rs2075580 DDX39B 3118
38 rs929138 DDX39B 7919
39 rs2516478 DDX39B 7919
40 ss4480602 NA NA
41 rs3219189 MCCD1 401250
42 rs3219190 MCCD1 401250
43 NA TNF 7124
44 NA MICB 4277
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