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DIYgenomics Health Risk Web Application

Side-by-side comparison of consumer genomic services (deCODEme, Navigenics, and 23andme) by locus, gene, and variant for 20 conditions (diabetes, cancers, heart disease, etc.). If a company reviews the variant, the underlying research reference is posted in the table below. 'Sample data' displays the normal allele in green, the risk allele in red (risk allele identification methodology). 'Rank' is a composite score assigned to the variant by DIYgenomics per journal ranking, number of cases and controls, p-value, and odds ratio (rank assessment methodology).

NOTE: The information on this page is intended for research and educational purposes only, and is not for diagnostic use.

Variants reviewed for Rheumatoid arthritis

//FOR FIRST APP - HEALTH
Locus Gene VariantdeCO-ooooo-DEme Navigenics 23andMe Nebula NIH SNP (Ref/Alt) Sample data Rank
1p13.2 PTPN22 rs2476601 2 2,3,5,9,10,16,19,20,24,25,26,31,32,37,39 G/C AG 2
1p36.13 PADI4 rs11203366 11,12,30,33,34 A/G AG 1
1p36.32 MMEL1 rs3890745 1,23,26,28,39 A/G CC 4
2p16.1 REL rs13031237 7,8 G/T GG 4
2q32.3 STAT4 rs7574865 29 13,14,17,22,29 G/T GG 3
4q27 IL2/IL21 rs6822844 G/T GG 1
6p21.32 MHC rs6457617 26,39 C/T TT 4
6p21.32 HLA-DRB1 rs660895 A/G AG 4
6q23 rs13192841 A/G AG 3
6q23 rs2327832 1,26,28,35,39 A/G AA 4
6q23.3 TNFAIP3/OLIG3 rs10499194 27 C/T CT 3
6q23.3 TNFAIP3/OLIG3 rs6920220 39 A/G GG 4
9q34 TRAF1/C5 rs3761847 27 4,6,15,26,28,36,38,41 A/G AG 4
20q13.12 CD40 rs1569723 18,21,28 A/C AA 4

Research references cited by consumer genomic companies:

  1. Barton A et al; Rheumatoid arthritis susceptibility loci at chromosomes 10p15 12q13 and 22q13; Nat Genet; 2008 Oct;40(10):1156-9.
  2. Begovich AB et al; A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis; Am J Hum Genet; 2004 Aug;75(2):330-7.
  3. Bottini N et al; A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes; Nat Genet; 2004 Apr;36(4):337-8.
  4. Bradley JR et al; Tumor necrosis factor receptor-associated factors (TRAFs); Oncogene; 2001 Oct 1;20(44):6482-91.
  5. Cloutier JF et al; Cooperative inhibition of T-cell antigen receptor signaling by a complex between a kinase and a phosphatase; J Exp Med; 1999 Jan 4;189(1):111-21.
  6. Cooke TD et al; Identification of immunoglobulins and complement in rheumatoid articular collagenous tissues; Arthritis Rheum; 1975 Nov-Dec;18(6):541-51.
  7. Eyre S et al; Confirmation of association of the REL locus with rheumatoid arthritis susceptibility in the UK population; Ann. Rheum. Dis.; 2010; 69(8):1572-3.
  8. Gregersen PK et al; REL - encoding a member of the NF-kappaB family of transcription factors is a newly defined risk locus for rheumatoid arthritis; Nat. Genet.; 2009; 41(7):820-3.
  9. Hinks A et al; Association between the PTPN22 gene and rheumatoid arthritis and juvenile idiopathic arthritis in a UK population: further support that PTPN22 is an autoimmunity gene; Arthritis Rheum; 2005 Jun;52(6):1694-9.
  10. Hinks A et al; Investigation of genetic variation across the protein tyrosine phosphatase gene in patients with rheumatoid arthritis in the UK; Ann Rheum Dis; 2007 May;66(5):683-6.
  11. Ikari K et al; Association between PADI4 and rheumatoid arthritis: a replication study; Arthritis Rheum; 2005 Oct;52(10):3054-7.
  12. Kang CP et al; A functional haplotype of thePADI4 gene associated with increased rheumatoid arthritis susceptibility in Koreans; Arthritis Rheum; 2006 Jan;54(1):90-6.
  13. Kelley JM et al; Genetic variants of STAT4 associated with rheumatoid arthritis in persons of Asian and European ancestry do not replicate in African Americans; Ann. Rheum. Dis.; 2010; 69(4):625-6.
  14. Kobayashi S et al; Association of STAT4 with susceptibility to rheumatoid arthritis and systemic lupus erythematosus in the Japanese population; Arthritis Rheum.; 2008; 58(7):1940-6.
  15. Kurreeman FA et al; A candidate gene approach identifies the TRAF1/C5 region as a risk factor for rheumatoid arthritis; PLoS Med; 2007 Sep;4(9):e278.
  16. Lee AT et al; The PTPN22 R620W polymorphism associates with RF positive rheumatoid arthritis in a dose-dependent manner but not with HLA-SE status; Genes Immun; 2005 Mar;6(2):129-33.
  17. Lee HS et al.; Association of STAT4 with rheumatoid arthritis in the Korean population; Mol. Med.; 2007; 13(9-10):455-60.
  18. Lee HS et al.; Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations; Arthritis Rheum.; 2009; 60(2):364-71.
  19. Michou L et al; Linkage proof for PTPN22 a rheumatoid arthritis susceptibility gene and a human autoimmunity gene; Proc Natl Acad Sci U S A; 2007 Jan 30;104(5):1649-54.
  20. Orozco G et al; Association of a functional single-nucleotide polymorphism of PTPN22 encoding lymphoid protein phosphatase with rheumatoid arthritis and systemic lupus erythematosus; Arthritis Rheum; 2005 Jan;52(1):219-24.
  21. Orozco G et al; Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study; Ann. Rheum. Dis.; 2010; 69(5):813-6.
  22. Orozco G et al; Association of STAT4 with rheumatoid arthritis: a replication study in three European populations; Arthritis Rheum.; 2008; 58(7):1974-80.
  23. Ouimet T et al; Neprilysin II: A putative novel metalloprotease and its isoforms in CNS and testis; Biochem Biophys Res Commun; 2000 May 19;271(3):565-70.
  24. Pierer M et al; Association of PTPN22 1858 single-nucleotide polymorphism with rheumatoid arthritis in a German cohort: higher frequency of the risk allele in male compared to female patients; Arthritis Res Ther; 2006;8(3):R75.
  25. Plenge RM et al; Replication of putative candidate-gene associations with rheumatoid arthritis in >4 000 samples from North America and Sweden: association of susceptibility with PTPN22 CTLA4 and PADI4; Am J Hum Genet; 2005 Dec;77(6):1044-60.
  26. Plenge RM et al; TRAF1-C5 as a risk locus for rheumatoid arthritis--a genome wide study; N Engl J Med; 2007 Sep 20;357(12):1199-209.
  27. Plenge RM et al; Two independent alleles at 6q23 associated with risk of rheumatoid arthritis; Nat Genet; 2007 Dec;39(12):1477-82.
  28. Raychaudhuri S et al; Common variants atCD40 and other loci confer risk of rheumatoid arthritis; Nat Genet; 2008 Oct;40(10):1216-23.
  29. Remmers EF et al; STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus; N Engl J Med; 2007 Sep 6;357(10):977-86.
  30. Schellekens GA et al; The diagnostic properties of rheumatoid arthritis antibodies recognizing a cyclic citrullinated peptide; Arthritis Rheum; 2000Jan;43(1):155-63.
  31. Simkins HM et al; Association of the PTPN22locus with rheumatoid arthritis in a New Zealand Caucasian cohort; Arthritis Rheum; 2005 Jul;52(7):2222-5.
  32. Steer S et al; Association of R602W in a protein tyrosine phosphatase gene with a high risk of rheumatoid arthritis in a British population: evidence for an early onset/disease severity effect; Arthritis Rheum; 2005 Jan;52(1):358-60.
  33. Suzuki A et al; Functional haplotypes of PADI4 encoding citrullinating enzyme peptidylarginine deiminase 4 are associated with rheumatoid arthritis; Nat Genet; 2003 Aug;34(4):395-402.
  34. Takata Y et al; Replication of reported genetic associations of PADI4 FCRL3 SLC22A4 and RUNX1 genes with rheumatoid arthritis: results of an independent Japanese population and evidence from meta-analysis of East Asian studies; J Hum Genet; 2008;53(2):163-73.
  35. Thomson W et al; Rheumatoid arthritis association at 6q23; Nat Genet; 2007 Dec;39(12):1431-3.
  36. Tsitsikov EN et al; TRAF1 is a negative regulator of TNF signaling. enhanced TNF signaling in TRAF1-deficient mice; Immunity; 2001 Oct;15(4):647-57.
  37. van Oene M et al; Association of the lymphoid tyrosine phosphatase R620W variant with rheumatoid arthritis but not Crohn disease in Canadian populations; Arthritis Rheum; 2005 Jul;52(7):1993-8.
  38. Wang Y et al; A role for complement in antibody-mediated inflammation: C5-deficient DBA/1 mice are resistant to collagen-induced arthritis; J Immunol; 2000 Apr 15;164(8):4340-7.
  39. Wellcome Trust Case Control Consortium et al; Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls; Nature; 2007 Jun7;447(7145):661-78.
  40. Zhernakova A et al; Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases; Am J Hum Genet; 2007 Dec;81(6):1284-8.
  41. Zvaifler NJ et al; The immunopathology of joint inflammation in rheumatoidarthritis; Adv Immunol; 1973;16(0):265-336.

Glossary:
Locus (plural loci): the specific location of a gene or DNA sequence on a chromosome, (e.g.; 8p21.1 is the p21.1 region on Chromosome 8).
Gene: a series of variants at a locus that code for proteins or RNA chains.
Variant: the specific location with two alleles (e.g.; 'CG') or genotype values. Companies may review different variants in the same gene and locus.

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