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Table 3 Top single-marker hits in genes from the four genetic pathways associated with SLE

From: Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus

Gene Marker Chr bp MA OR p (Spain) p (EUR) p (meta) Pathway
BCL10 rs12084253 1 85,720,326 T 1.11 0.020 0.0015 0.00012 BCR
FCER1G rs1136224 1 161,184,097 G 0.91 0.023 0.022 0.0024 VASC
FCGR2B rs182968886 1 161,642,985 A 0.86 0.044 0.0018 0.00023 BCR
CD247 rs113305799 1 167,416,006 A 1.17 0.0035 0.044 0.0022 CTLA4
PROC rs6740067 2 128,156,366 T 1.16 0.043 0.018 0.0026 VASC
CTLA4 rs733618 2 204,730,944 C 1.19 0.026 0.0018 0.00016 CTLA4
PPP3CA rs13120190 4 102,056,663 G 0.93 0.025 0.047 0.0060 BCR
IL2 rs45522533 4 123,396,876 T 1.16 0.016 0.0058 0.00044 CTLA4
SLC7A11 rs74843273 4 139,150,464 T 0.81 0.025 0.0066 0.00065 VASC
ITK rs60714766 5 156,602,589 T 1.07 0.015 0.043 0.0042 CTLA4
CARD11 rs6461796 7 3,071,195 C 0.94 0.027 0.033 0.0042 BCR
LYN rs17812659 8 56,889,862 G 0.86 0.013 2.57E-05 1.17E-06 BCR,VASC
ANGPT1 rs79847080 8 108,293,443 G 0.84 0.032 0.0028 0.00031 VASC
VAV2 rs2810536 9 136,812,625 G 1.08 0.030 0.011 0.0013 BCR
KRAS rs17388587 12 25,389,220 G 1.13 0.036 0.048 0.0075 BCR, VASC
PRKCB rs11641223 16 24,020,316 T 1.11 0.041 0.0010 0.00012 BCR
CD19 16:28955702:D 16 28,955,702 I 1.06 0.0077 0.047 0.0034 BCR
SLC7A6 rs55856208 16 68,324,210 T 1.08 0.045 0.049 0.0086 VASC
PLCG2 rs11548656 16 81,916,912 G 1.3 0.014 0.00062 0.000035 BCR
ATP1B2 rs1794287 17 7,578,837 A 0.9 0.023 0.024 0.0026 VASC
ITGB3 rs75211989 17 45,366,261 G 1.11 0.00014 0.020 0.00020 VASC
GRB2 rs36023980 17 73,341,284 T 0.85 0.00039 1.51E-06 4.73E-09 CTLA4, IL4, BCR, VASC
NFATC1 rs111354805 18 77,238,078 T 1.21 0.027 6.58E-05 5.26E-06 BCR
MAP2K2 rs350913 19 4,096,779 T 0.94 0.029 0.030 0.0039 BCR
CD79A rs16975619 19 42,392,441 C 1.52 0.020 0.0099 0.00089 BCR
SIRPG rs11696739 20 1,600,925 A 0.92 0.044 0.0050 0.00069 VASC
RAC2 rs229566 22 37,602,131 A 1.06 0.041 0.03 0.0047 BCR
  1. Suggestive risk variants were identified as those markers showing with the most significant meta-analysis p value (p (meta)), and that are associated in the two genome-wide association study cohorts (p < 0.05) and show the same direction of effect (OR) MA minor allele, OR odds ratio according to minor allele in European ancestry cohort, I insertion allele, Pathway biological pathway/s where the gene has been annotated, BCR B cell receptor pathway, CTLA4 CTLA4 pathway, IL4 interleukin-4 pathway, VASC vascular cell wall pathway