All polymorphisms studied in this paper [PMID: 19300490] , total : 12 polymorphisms

Title : An African ancestry-specific allele of CTLA4 confers protection against rheumatoid arthritis in African Americans.

Abstract : Cytotoxic T-lymphocyte associated protein 4 (CTLA4) is a negative regulator of T-cell proliferation. Polymorphisms in CTLA4 have been inconsistently associated with susceptibility to rheumatoid arthritis (RA) in populations of European ancestry but have not been examined in African Americans. The prevalence of RA in most populations of European and Asian ancestry is approximately 1.0%; RA is purportedly less common in black Africans, with little known about its prevalence in African Americans. We sought to determine if CTLA4 polymorphisms are associated with RA in African Americans. We performed a 2-stage analysis of 12 haplotype tagging single nucleotide polymorphisms (SNPs) across CTLA4 in a total of 505 African American RA patients and 712 African American controls using Illumina and TaqMan platforms. The minor allele (G) of the rs231778 SNP was 0.054 in RA patients, compared to 0.209 in controls (4.462 x 10(-26), Fisher's exact). The presence of the G allele was associated with a substantially reduced odds ratio (OR) of having RA (AG+GG genotypes vs. AA genotype, OR 0.19, 95% CI: 0.13-0.26, p = 2.4 x 10(-28), Fisher's exact), suggesting a protective effect. This SNP is polymorphic in the African population (minor allele frequency [MAF] 0.09 in the Yoruba population), but is very rare in other groups (MAF = 0.002 in 530 Caucasians genotyped for this study). Markers associated with RA in populations of European ancestry (rs3087243 [+60C/T] and rs231775 [+49A/G]) were not replicated in African Americans. We found no confounding of association for rs231778 after stratifying for the HLA-DRB1 shared epitope, presence of anti-cyclic citrullinated peptide antibody, or degree of admixture from the European population. An African ancestry-specific genetic variant of CTLA4 appears to be associated with protection from RA in African Americans. This finding may explain, in part, the relatively low prevalence of RA in black African populations.

Author : Kelley JM,Hughes LB,Faggard JD,Danila MI,Crawford MH,Edberg Y,Padilla MA,Tiwari HK,Westfall AO,Alarcon GS,Conn DL,Jonas BL,Callahan LF,Smith EA,Brasington RD,Allison DB,Kimberly RP,Moreland LW,Edberg JC,Bridges SL Jr,

Source : PLoS Genet. 2009 Mar;5(3):e1000424. doi: 10.1371/journal.pgen.1000424. Epub 2009 Mar 20.

No.	Polymorphism name	Gene Symbol	Entrez Gene ID
1	rs231778	CTLA4	1493
2	rs733168	C1orf177	163747
3	rs231772	CTLA4	1493
4	rs231775	CTLA4	1493
5	rs231776	CTLA4	1493
6	rs231777	CTLA4	1493
7	rs231779	CTLA4	1493
8	NA	CTLA4	1493
9	rs231780	CTLA4	1493
10	rs34031880	CTLA4	1493
11	rs3087243	CTLA4	1493
12	rs11571319	CTLA4	1493