Rheumatoid Arthritis Susceptibility Loci Research Articles

Exome sequencing of Singapore Chinese anti-citrullinated-protein-antibody-positive rheumatoid arthritis patients.

More than 130 susceptibility loci for rheumatoid arthritis (RA) have been identified with genome-wide association studies (GWAS). To investigate the genetic predisposition of Chinese anti-cyclic-citrullinated-peptides-antibody-positive RA, we carried out an exome sequencing study. Patients were recruited from three major public hospitals in Singapore, Tan Tock Seng Hospital (TTSH), Singapore General Hospital and National University Health System. Controls came from an established exome collection and from the TTSH Health Control Biobank. All the participants were of Chinese descent. We performed whole-exome sequencing (WES) in 595 ACPA-positive RA patients and 1281 controls and validated the candidate variants by genotyping 795 RA cases and 600 controls. The discovery cohort yielded 73 susceptibility SNVs that reached statistical significance. In the validation study with an independent cohort, two SNVs remained significant: PCNXL4 (p-value 1.50x10-5) and DHRS7 (p-value 6.02x10 -5). The majority of known susceptibility foci are not captured by exome sequencing. In this WES study of ACPA-positive RA in Chinese patients, we discovered two new variants in PCNXL4 and DHRS7 associated with risk of the disease.

Missense variant in interleukin-6 signal transducer identified as susceptibility locus for rheumatoid arthritis in Chinese patients.

Objectives This study aims to uncover variants of large effect size and allele frequency below 5% by sequencing all extant genes associated with rheumatoid arthritis (RA) in a homogeneous patient cohort.Patients and methods This retrospective study was conducted between January 2001 and December 2017. We selected Chinese RA patients positive for anti-citrullinated peptide antibody (ACPA). All the 128 known candidate genes identified through genome-wide association studies were sequenced in 48 RA patients (15 males, 33 females; mean age 53.32±8.98 years; range, 32 to 75 years) and 45 controls (11 males, 34 females; mean age 32.18±9.54; range, 21 to 57 years). The exonic regions of these genes were sequenced. The resultant data were analyzed for association using single variant association and pathway-based association enrichment tests. The genetic burden due to low-frequency variants was assessed with the C-alpha test. The candidate variants that showed significant association were validated in a larger cohort of 500 RA cases (71 males, 429 females; mean age 48.6±12.2 years; range, 24 to 92 years) and 500 controls (66 males, 434 females; mean age 32.3±10.1 years; range, 21 to 73 years).Results Thirty-nine variants in 21 genes were identified using single variant association analysis and C-alpha test, with stepwise filtering. Among these, the missense variant in interleukin-6 signal transducer (IL-6ST) 5:55260065 (p.Cys47Phe) was significantly associated with RA in Chinese patients in Singapore.Conclusion Our results suggest that a mutation in IL-6ST (5:55260065) confers risk of RA in Chinese patients in Singapore.

Large-scale meta-analysis across East Asian and European populations updated genetic architecture and variant-driven biology of rheumatoid arthritis, identifying 11 novel susceptibility loci

ObjectivesNearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly...

Investigating the GWAS-Implicated Loci for Rheumatoid Arthritis in the Pakistani Population.

Rheumatoid arthritis (RA) is a complex and multifactorial autoimmune disorder with the involvement of multiple genetic and environmental factors. Genome-wide association studies (GWAS) have identified more than 50 RA genetic loci in European populations. Given the anticipated overlap of RA-relevant genes and pathways across different ethnic groups, we sought to replicate 58 GWAS-implicated SNPs reported in Europeans in Pakistani subjects. 1,959 unrelated subjects comprising 1,222 RA cases and 737 controls were collected from three rheumatology facilities in Pakistan. Genotyping was performed using iPLEX or TaqMan® methods. A total of 50 SNPs were included in the final association analysis after excluding those that failed assay design/run or postrun QC analysis. Fourteen SNPs (LINC00824/rs1516971, PADI4/rs2240336, CEP57/rs4409785, CTLA4/rs3087243, STAT4/rs13426947, HLA-B/MICA/rs2596565, C5orf30/rs26232, CCL21/rs951005, GATA3/rs2275806, VPS37C/rs595158, HLA-DRB1/rs660895, EOMES/rs3806624, SPRED2/rs934734, and RUNX1/rs9979383) were replicated in our Pakistani sample at false discovery rate (FDR) of <0.20 with nominal p values ranging from 4.73E-06 to 3.48E-02. Our results indicate that several RA susceptibility loci are shared between Pakistani and European populations, supporting the role of common genes/pathways.

Genome-wide association study in a Korean population identifies six novel susceptibility loci for rheumatoid arthritis

ObjectiveGenome-wide association studies (GWAS) in rheumatoid arthritis (RA) have discovered over 100 RA loci, explaining patient-relevant RA pathogenesis but showing a large fraction of missing heritability. As a continuous effort,...

Integrative analysis highlighted susceptibility genes for rheumatoid arthritis

Genetic factors underlying susceptibility to rheumatoid arthritis (RA) are largely unknown. The aim of this study was to identify potential genes for RA. We conducted summary statistic data-based Mendelian randomization (SMR) analysis to detect potential causal genes for RA. Further, we performed additional bioinformatics analysis to show the potential relevance of the identified genes to RA. We identified 140 genes that showed causal association with RA. Among these genes, 24 have not been reported to be associated with RA (e.g., IFNAR2, FLOT1, ITPR3, PPP2R3C and SLC35B2). The unreported genes were highly connected with some well-known RA-related genes (e.g., HLA-DQB1, CD226, PTPN22, CD40, IFNGR2, BLK, TRAF1, SYNGR1 and CCR6) that were also found to be causally associated with RA. The identified genes were involved in the significant enriched RA-related biological pathways. We found integrative evidence in support of IFNAR2 as a potential causal gene of RA in SMR, differential expression, weighted gene co-expression network, protein–protein interaction and functional enrichment analyses. The present study highlights a list of potential causal genes for RA. The findings provide new insights into the mechanism underlying known genome-wide associated RA susceptibility loci.

Exploring the overlap between rheumatoid arthritis susceptibility loci and long non-coding RNA annotations.

Whilst susceptibility variants for many complex diseases, such as rheumatoid arthritis (RA), have been well characterised, the mechanism by which risk is mediated is still unclear for many loci. This is especially true for the majority of variants that do not affect protein-coding regions. lncRNA represent a group of molecules that have been shown to be enriched amongst variants associated with RA and other complex diseases, compared to random variants. In order to establish to what degree direct disruption of lncRNA may represent a potential mechanism for mediating RA susceptibility, we chose to further explore this overlap. By testing the ability of annotated features to improve a model of disease susceptibility, we were able to demonstrate a local enrichment of enhancers from immune-relevant cell types amongst RA susceptibility variants (log2 enrichment 3.40). This was not possible for lncRNA annotations in general, however a small, but significant enrichment was observed for immune-enriched lncRNA (log2 enrichment 0.867002). This enrichment was no longer apparent when the model was conditioned on immune-relevant enhancers (log2 enrichment -0.372734), suggesting that direct disruption of lncRNA sequence, independent of enhancer disruption, does not represent a major mechanism by which susceptibility to complex diseases is mediated. Furthermore, we demonstrated that, in keeping with general lncRNA characteristics, immune-enriched lncRNA are expressed at low levels that may not be amenable to functional characterisation.

Influence of the TNFSF4 rs1234315 polymorphism in the susceptibility to systemic lupus erythematosus and rheumatoid arthritis

ObjectivesThe tumour necrosis factor superfamily 4 (TNFSF4) is a candidate gene for autoimmune diseases. We investigated the relationship of this gene with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in a Chinese Guangxi population. MethodsA total of 294 patients with SLE, 210 with RA, and 282 healthy controls were genotyped for single nucleotide polymorphism (SNP) rs1234315 using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP). The potential functional effects of the SNP were predicted by in silico analysis. ResultsStatistically significant associations with SLE and RA were detected at rs1234315, both by allele analysis (odds ratio 1.47, 95% confidence interval 1.17–1.86, p = 0.001; odds ratio 1.49, 95% confidence interval 1.15–1.92, p = 0.002; respectively), and genotype analysis (p = 0.003 and p = 7.000 × 10−5, respectively). The Akaike’s information criterion (AIC) values indicated that the recessive model may serve as the best-fit model for the SNP for SLE and RA. ConclusionOur results provided support for TNFSF4 rsl234315 as a SLE and RA susceptibility locus in a Chinese Guangxi population.

Genome-Wide Identification of N6-Methyladenosine (m6A) SNPs Associated With Rheumatoid Arthritis.

Previous large scale genome-wide association studies (GWAS) have identified more than one hundred susceptibility loci for rheumatoid arthritis (RA) (Stahl et al., 2010; Eyre et al., 2012; Okada et al., 2012, 2014b). One major issue in the post GWAS era is to identify functional (causal) variants in the disease-associated loci. Recently, whole-exome sequencing studies have identified several missense mutations for RA (Mitsunaga et al., 2013; Okada et al., 2014a). Nevertheless, few studies have focused on potentially functional variants which could affect N6-methyladenosine (m6A) methylation. N6-methyladenosine (m6A) has been discovered as the first example of reversible RNA methylation and is a pervasive modification in the mRNA of all eukaryotes. It plays critical roles in regulating many fundamental biological processes such as gene expression control (Meyer and Jaffrey, 2014) and regulation of mRNA stability (Wang et al., 2014) and homeostasis (Edupuganti et al., 2017). Evidence has increasingly shown that m6A modification modulates almost all aspects of RNA processing such as nuclear export, translatability, splicing, and miRNA processing (Visvanathan and Somasundaram, 2018). Thus, m6A modification adds a new layer of gene expression regulation, and it has been implicated in T cell differentiation, homeostasis, and response to HIV infection (Li et al., 2018). Moreover, it was found to be involved in the etiology of various diseases (Visvanathan and Somasundaram, 2018). Given the vital function of m6A modification in gene expression regulation and immune response, it is possible that m6A is involved in the etiology of RA. Recent studies have suggested that SNPs would affect m6A by altering the RNA sequences of the target sites or key flanking nucleotides (Zheng et al., 2018). It means that m6A-associated SNPs (m6A-SNPs) may have regulatory potential to affect gene expression and mRNA stability and homeostasis, which may consequently affect disease such as RA. However, what is the relationship between m6A-SNPs and RA is still unclear. Thus, we examined the effect of the m6A-SNPs on RA in a large scale GWAS. Then, to test whether the RA-associated m6A-SNPs have potential regulatory effects on gene expression and whether these disruptions may contribute to RA, we performed eQTL and differential expression analyses using whole genome data of about 10.5 million SNPs and 21,323 mRNAs from 26 RA cases and 17 controls, as well as public data.

An Extensive Study of the Functional Polymorphisms of Kinin-Kallikrein System in Rheumatoid Arthritis Susceptibility.

This study aims to examine the following functional polymorphisms in rheumatoid arthritis (RA) susceptibility: (i) the 587C>T of kininogen gene, (ii) the 287 bp Alu repeat insertion of angiotensin converting enzyme gene, (iii) the 9 bp insertion of bradykinin receptor 2 gene, (iv) the -58T>C of bradykinin receptor 2 gene, and (v) the -699G>C of bradykinin receptor 1 gene. The study included 136 RA patients (27 males; 109 females; mean age 60.8 years; range 39 to 75 years) and 149 ethnic matching controls (30 males, 119 females; mean age 56.2 years; range 35 to 78 years). Polymerase chain reaction coupled with restriction assay was performed for 587C>T, -58T>C, and -699G>C. Rheumatoid arthritis patients and controls carried the wild type allele of 587C>T; therefore, produced the high molecular weight kininogen. No significant difference was observed in genotype or allele distribution of the studied functional polymorphisms between RA patients and controls. Kinin-kallikrein system related genes might not be major RA susceptibility loci.

Brief Report: IRF4 Newly Identified as a Common Susceptibility Locus for Systemic Sclerosis and Rheumatoid Arthritis in a Cross-Disease Meta-Analysis of Genome-Wide Association Studies.

Systemic sclerosis (SSc) and rheumatoid arthritis (RA) are autoimmune diseases that have similar clinical and immunologic characteristics. To date, several shared SSc-RA genetic loci have been identified independently. The aim of the current study was to systematically search for new common SSc-RA loci through an interdisease meta-genome-wide association (meta-GWAS) strategy. The study was designed as a meta-analysis combining GWAS data sets of patients with SSc and patients with RA, using a strategy that allowed identification of loci with both same-direction and opposite-direction allelic effects. The top single-nucleotide polymorphisms were followed up in independent SSc and RA case-control cohorts. This allowed an increase in the sample size to a total of 8,830 patients with SSc, 16,870 patients with RA, and 43,393 healthy controls. This cross-disease meta-analysis of the GWAS data sets identified several loci with nominal association signals (P < 5 × 10(-6) ) that also showed evidence of association in the disease-specific GWAS scans. These loci included several genomic regions not previously reported as shared loci, as well as several risk factors that were previously found to be associated with both diseases. Follow-up analyses of the putatively new SSc-RA loci identified IRF4 as a shared risk factor for these 2 diseases (Pcombined = 3.29 × 10(-12) ). Analysis of the biologic relevance of the known SSc-RA shared loci identified the type I interferon and interleukin-12 signaling pathways as the main common etiologic factors. This study identified a novel shared locus, IRF4, for the risk of SSc and RA, and highlighted the usefulness of a cross-disease GWAS meta-analysis strategy in the identification of common risk loci.

Investigation of the genetic overlap between rheumatoid arthritis and psoriatic arthritis in a Greek population

Objectives: Several rheumatoid arthritis (RA) susceptibility loci have also been found to be associated with psoriatic arthritis (PsA), demonstrating that there is a degree of genetic overlap between various autoimmune diseases. We sought to investigate whether single nucleotide polymorphisms (SNPs) mapping to previously reported RA and/or PsA susceptibility loci, including PLCL2, CCL21, REL, STAT4, CD226, PTPN22, and TYK2, are associated with risk for the two diseases in a genetically homogeneous Greek population.Method: This study included 392 RA patients, 126 PsA patients, and 521 healthy age- and sex-matched controls from Greece. Genotyping of the SNPs was performed with Taqman primer/probe sets. Bioinformatic analysis was performed using BlastP, PyMOL, and Maestro and Desmond.Results: A significant association was detected between the GC genotype of rs34536443 (TYK2) in both the PsA and RA cohorts. The C allele of this SNP was associated with PsA only. Evidence for association with PsA was also found for the GG genotype and G allele of the rs10181656 SNP of STAT4. The TC genotype of the rs763361 SNP of CD226 was associated with PsA only.Conclusions: Genetic overlap between PsA and RA was detected for the rs34536443 SNP of the TYK2 gene within a Greek population. An association of STAT4 (rs10181656) with PsA was confirmed whereas CD226 (rs763361) was associated with PsA but not with RA, in contrast to previous reports. The different findings of this study compared to previous ones highlights the importance of comparative studies that include various ethnic or racial populations.

A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus

ObjectivesDuring the last years, genome-wide association studies (GWASs) have identified a number of common genetic risk factors for rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). However, the genetic overlap...

Genome-wide pathway analysis identifies oxidative stress related gene MSRA as rheumatoid arthritis susceptibility locus

Objective: Genome-wide association studies (GWASs) carried out in rheumatoid arthritis (RA) have led to the discovery of several genetic associations with this disease. Still, the current associated genetic variations can explain only part of the genetic risk involved in RA, and it is well recognised that these GWASs are likely underpowered to detect all common disease variants. Therefore, we explored the genomic regions showing low-significance associations in previous GWASs of RA. Methods: To reduce the false-positive signal fraction, we exploited pathway analysis to prioritise regions containing genes most likely to be implicated in RA. We hypothesised that true disease genes would be in a similar pathway. Therefore, genes from similar pathways but located in different regions were prioritised for replication using Prioritizer software. 384 genetic variants selected from previous RA GWASs were tested in a Spanish case/control discovery cohort comprising 376 RA patients and 478 healthy controls for replication. Statistically significant associations were further validated in replication cohorts from Spain and Netherlands, up to a total of 1,818 RA patients and 2,498 controls. Results: We detected a novel genetic association between RA and the MSRA gene (rs10903323, P = 2.91×10-5, OR = 1.51) in the Spanish combined population. This association was further tested in our independent Dutch replication cohort. Combined analysis showed an overall association of MSRA with RA (P = 2.19×10-4, OR = 1.28). Conclusion: Novel association in the MSRA gene related to oxidative stress is described herein and support a major role for this process in RA.

Atopic dermatitis is associated with an increased risk for rheumatoid arthritis and inflammatory bowel disease, and a decreased risk for type 1 diabetes

Atopic dermatitis (AD) is characterized by epidermal barrier failure and immune-mediated inflammation. Evidence on AD as a potential risk factor for inflammatory comorbidities is scarce. We sought to test the hypothesis that prevalent AD is a risk factor for incident rheumatoid arthritis (RA) and inflammatory bowel disease (IBD; Crohn disease [CD], ulcerative colitis [UC]) and is inversely related to type 1 diabetes (T1D) and to investigate established RA, IBD, and T1D susceptibility loci in AD. This cohort study used data from German National Health Insurance beneficiaries aged 40years or younger (n=655,815) from 2005 through 2011. Prevalent AD in the period 2005 to 2006 was defined as primary exposure, and incident RA, IBD, and T1D in the period 2007 to 2011 were defined as primary outcomes. Risk ratios were calculated with generalized linear models. Established RA, IBD, and T1D loci were explored in high-density genotyping data from 2,425 cases with AD and 5,449 controls. Patients with AD (n=49,847) were at increased risk for incident RA (risk ratio [RR], 1.72; 95% CI, 1.25-2.37) and/or IBD (CD: RR, 1.34; 95% CI, 1.11-1.61; UC: RR, 1.25; 95% CI, 1.03-1.53). After adjusting for health care utilization, there was a nominally significant inverse effect on T1D risk (RR, 0.72; 95% CI, 0.53-0.998). There was no disproportionate occurrence of known RA, CD, UC, or T1D risk alleles in AD. AD is a risk factor for the development of RA and IBD. This excess comorbidity cannot be attributed to major known IBD and RA genetic risk factors.

Genetic Case-Control Study for Eight Polymorphisms Associated with Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is an autoimmune disease which has a significant socio-economic impact. The aim of the current study was to investigate eight candidate RA susceptibility loci to identify the associated variants in Egyptian population. Eight single nucleotide polymorphisms (SNPs) (MTHFR—C677T and A1298C, TGFβ1 T869C, TNFB A252G, and VDR—ApaI, BsmI, FokI, and TaqI) were tested by genotyping patients with RA (n = 105) and unrelated controls (n = 80). Associations were tested using multiplicative, dominant, recessive, and co-dominant models. Also, the linkage disequilibrium (LD) between the VDR SNPs was measured to detect any indirect association. By comparing RA patients with controls (TNFB, BsmI, and TaqI), SNPs were associated with RA using all models. MTHFR C677T was associated with RA using all models except the recessive model. TGFβ1 and MTHFR A1298C were associated with RA using the dominant and the co-dominant models. The recessive model represented the association for ApaI variant. There were no significant differences for FokI and the presence of RA disease by the used models examination. For LD results, There was a high D′ value between BsmI and FokI (D′ = 0.91), but the r2 value between them was poor. All the studied SNPs may contribute to the susceptibility of RA disease in Egyptian population except for FokI SNP.

Replication of PTPRC as genetic biomarker of response to TNF inhibitors in patients with rheumatoid arthritis.

Genetic biomarkers could be useful for orienting treatment of patients with rheumatoid arthritis (RA), but none has been convincingly validated yet. Putative biomarkers include 14 single nucleotide polymorphisms that have shown association with response to TNF inhibitors (TNFi) in candidate gene studies and that we assayed here in 755 RA patients. Three of them, in the PTPRC, IL10 and CHUK genes, were significantly associated with response to TNFi. The most significant result was obtained with rs10919563 in PTPRC, which is a confirmed RA susceptibility locus. Its RA risk allele was associated with improved response (B=0.33, P=0.006). This is the second independent replication of this biomarker (P=9.08 × 10(-8) in the combined 3003 RA patients). In this way, PTPRC has become the most replicated genetic biomarker of response to TNFi. In addition, the positive but weaker replication of IL10 and CHUK should stimulate further validation studies.

RADB: a database of rheumatoid arthritis-related polymorphisms.

Rheumatoid arthritis (RA) is an autoimmune disease that has a complex genetic basis. Therefore, it is important to explore the genetic background of RA. The extensive recent application of polymorphic genetic markers, especially single nucleotide polymorphisms, has presented us with a large quantity of genetic data. In this study, we developed the Database of Rheumatoid Arthritis-related Polymorphisms (RADB), to integrate all the RA-related genetic polymorphisms and provide a useful resource for researchers. We manually extracted the RA-related polymorphisms from 686 published reports, including RA susceptibility loci, polymorphisms associated with particular clinical features of RA, polymorphisms associated with drug response in RA and polymorphisms associated with a higher risk of cardiovascular disease in RA. Currently, RADB V1.0 contains 3235 polymorphisms that are associated with 636 genes and refer to 68 countries. The detailed information extracted from the literature includes basic information about the articles (e.g. PubMed ID, title and abstract), population information (e.g. country, geographic area and sample size) and polymorphism information (e.g. polymorphism name, gene, genotype, odds ratio and 95% confidence interval, P-value and risk allele). Meanwhile, useful annotations, such as hyperlinks to dbSNP, GenBank, UCSC, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway, are included. In addition, a tool for meta-analysis was developed to summarize the results of multiple studies. The database is freely available at http://www.bioapp.org/RADB.Database URL: http://www.bioapp.org/RADB.

Association of susceptible genetic markers and autoantibodies in rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic autoimmune disorder of unknown aetiology resulting in inflammation of the synovium, cartilage and bone. The disease has a heterogeneous character, consisting of clinical subsets of anti-citrullinated protein antibody (ACPA)-positive and APCA-negative disease. Although, the pathogenesis of RA is incompletely understood, genetic factors play a vital role in susceptibility to RA as the heritability of RA is between 50 and 60%, with the human leukocyte antigen (HLA) locus accounting for at least 30% of overall genetic risk. Non-HLA genes, i.e. tumour necrosis factor-α (TNF-α) within the MHC (major histocompatibility complex) have also been investigated for association with RA. Although, some contradictory results have originated from several studies on TNF-α gene, the data published so far indicate the possible existence of TNF-α gene promoter variants that act as markers for disease severity and response to treatment in RA. The correlation of HLA and non-HLA genes within MHC region is apparently interpreted. A considerable number of confirmed associations with RA and other autoimmune disease susceptibility loci including peptidylarginine deiminase type 4 (PADI4), protein tyrosine phosphatase non-receptor type 22 (PTPN22), signal transducer and activator of transcription (STAT4), cluster of differentiation 244 (CD244) and cytotoxic T lymphocyte-associated antigen 4 (CTLA4), located outside the MHC have been reported recently. In this review, we aim to give an update on recent progress in RA genetics, the importance of the combination of HLA-DRB1 alleles, non-HLA gene polymorphism, its detection and autoantibodies as susceptibility markers for early RA disease.

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci

A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data. We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45,790 European case-control samples. We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5×10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs. This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases.