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Table 1 SNPs with opposite risk profiles in different autoimmune diseases

From: Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

SNP Gene Chra A1b Annotation Diseasesc Ref
      RA-AS-  
rs11752919 ZSCAN23 6 C in small intron   [3]
      T1D/ATD-MS  
     Asp527Asn (in CDSN); less than 2.6 RA-AS-  
rs3130981 CDSN/PSORS1C1 6 A    [3]
     kb from rs1265048 T1D/ATD-MS  
     intergenic; 1.2kb upstream of RA-AS-  
rs1265048   6 C    [3]
     PSORS1C1 T1D/ATD-MS  
      RA-AS-  
rs151719 HLA-DMB 6 G in small intron   [3]
      T1D/ATD-MS  
      ATD-MS/RA-  
rs10484565 TAP2 6 T in 3' UTR   [3]
      AS-T1D  
      RA-AS-  
0rs1264303 VARS2 6 G in 5'UTR   [3]
      T1D/ATD-MS  
      RA-AS-  
rs2076530 BTNL2 6 G splice site altering/protein truncation   [3]
      T1D/ATD-MS  
     intergenic; 0.7 kb downstream RA-AS-MS/T1D-  
rs3129953   6 T    [3]
     BTNL2 ATD  
      RA-AS-  
rs757262 TRIM40 6 T Thr183Met   [3]
      T1D/ATD-MS  
     intronic; close to alternatively spliced RA-AS-T1D-  
rs2517646 TRIM10 6 G    [3]
     exon ATD/MS  
      RA-AS-  
rs2071286 NOTCH4 6 A intronic   [3]
      T1D/ATD-MS  
      CD/T1D-RA-  
rs2476601 PTPN22 1 T Arg620TRP   [6, 6064]
      SLE-GD  
     about 1kb downstream the   
rs3024505 IL10 1 A   T1D/CD-UC [4]
     transcription end site   
     about 1kb downstream the   
rs917997 IL18RAP 2 T   T1D/CD [4]
     transcription end site   
rs9388489   6 G intergenic CD/T1D [4]
rs4788084   16 T intergenic T1D/CD [4]
      T1D-ATD-  
rs1063635 MICA 6 A Gln274Arg   [3]
      MS/AS  
rs1634717   6 A intergenic RA/T1D-ATD- [3]
      MS  
      RA-AS-MS/T1D-  
rs204991 GPSM3 6 C intronic   [3]
      ATD  
rs2242655 C6orf47 6 C Lys92Asn ATD-MS/RA- [3]
      AS-T1D  
      ATD-MS/RA-  
rs2299851 MSH5 6 T Intronic   [3]
      AS-T1D  
      AS/RA-T1D-  
rs2248462   6 A intergenic   [3]
      ATD-MS  
     intronic; close to alternatively spliced RA-AS-  
rs2844463 BAT3 6 T    [3]
     exon ATD/T1D-MS  
      RA-AS-MS/T1D-  
rs3135363   6 C intergenic   [3]
      ATD  
      RA-AS-MS/T1D-  
rs4428528   6 C intergenic   [3]
      ATD  
      MS/RA-AS-T1D-  
rs887464   6 A intergenic (upstream PSORS1C3)   [3]
      ATD  
      ATD-MS/RA-  
rs9267954   6 T intergenic   [3]
      AS-T1D  
rs2201841 IL23R 1 G intronic UC/psoriasis [65, 66]
rs744166 STAT3 17 G intronic CD/MS [67, 68]
  1. a chromosome
  2. b minor allele in CEU
  3. c diseases are shown in order depending on the predisposing/protective effect of the minor allele.