All polymorphisms studied in this paper [PMID: 19116923] , total : 18 polymorphisms

Title : Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci.

Abstract : OBJECTIVE: The HLA-DRB1 locus within the major histocompatibility complex (MHC) at 6p21.3 has been identified as a susceptibility gene for rheumatoid arthritis (RA); however, there is increasing evidence of additional susceptibility genes in the MHC region. The aim of this study was to estimate their number and location. METHODS: A case-control study was performed involving 977 control subjects and 855 RA patients. The HLA-DRB1 locus was genotyped together with 2,360 single-nucleotide polymorphisms in the MHC region. Logistic regression was used to detect DRB1-independent effects. RESULTS: After adjusting for the effect of HLA-DRB1, 18 markers in 14 genes were strongly associated with RA (P<10(-4)). Multivariate logistic regression analysis of these markers and DRB1 led to a model containing DRB1 plus the following 3 markers: rs4678, a nonsynonymous change in the VARS2L locus, approximately 1.7 Mb telomeric of DRB1; rs2442728, upstream of HLA-B, approximately 1.2 Mb telomeric of DRB1; and rs17499655, located in the 5'-untranslated region of DQA2, only 0.1 Mb centromeric of DRB1. In-depth investigation of the DQA2 association, however, suggested that it arose through cryptic linkage disequilibrium with an allele of DRB1. Two non-shared epitope alleles were also strongly associated with RA (P<10(-4)): *0301 with anti- cyclic citrullinated peptide-negative RA and *0701 independently of autoantibody status. CONCLUSION: These results confirm the polygenic contribution of the MHC to RA and implicate 2 additional non-DRB1 susceptibility loci. The role of the HLA-DQ locus in RA has been a subject of controversy, but in our data, it appears to be spurious.

Author : Vignal C,Bansal AT,Balding DJ,Binks MH,Dickson MC,Montgomery DS,Wilson AG,

Source : Arthritis Rheum. 2009 Jan;60(1):53-62. doi: 10.1002/art.24138.

No.	Polymorphism name	Gene Symbol	Entrez Gene ID
1	rs1264341	NA	NA
2	rs2844657	NA	NA
3	rs886422	DDR1	780
4	rs1264308	VARS2	57176
5	rs4678	VARS2	57176
6	rs3132571	NA	NA
7	rs3132580	DPCR1	135656
8	rs3131934	NA	NA
9	rs3130955	NA	NA
10	rs3130557	PSORS1C1	170679
11	rs7750641	TCF19	6941
12	rs2442728	NA	NA
13	rs3132472	NA	NA
14	rs423023	NOTCH4	4855
15	rs415929	NOTCH4	4855
16	rs4248166	BTNL2	56244
17	rs3763313	BTNL2	56244
18	rs17499655	PADI4	23569