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Table 3 Risk allele frequencies in Central and Southern European controls and relationship with the North/South score

From: Bias in effect size of systemic lupus erythematosus susceptibility loci across Europe: a case-control study

  RAF (%) RAF vs. N/S score
SNP (locus) Central European Southern European χ2 P value r xy Slope P value
rs3131379 (MSH5) 14.9 4.6 4.9 × 10-26 0.92 4.15 2.0 × 10-6
rs2187668 (HLA-DQA1) 15.7 8.7 1.9 × 10-9 0.88 4.93 4.0 × 10-5
rs2476601 (PTPN22) 11.8 6.1 1.5 × 10-8 0.74 4.21 2.7 × 10-3
rs13277113 (C8orf13-BLK) 31.0 23.2 2.2 × 10-6 0.20 0.95 NS
rs6445975 (PXK) 29.0 22.6 7.5 × 10-5 0.66 2.67 0.01
rs1143679 (ITGAM) 11.9 16.7 4.9 × 10-4 -0.59 -4.79 0.03
rs2205960 (TNFSF4) 25.2 20.7 4.9 × 10-3 0.15 1.08 NS
rs1801274 (FCGR2A) 44.5 48.6 0.03 -0.40 -1.25 NS
rs4963128 (KIAA1542) 69.1 65.3 0.03 0.58 2.83 0.03
rs10488631 (IRF5) 11.6 9.3 0.046 0.46 3.64 0.10
rs17435 (MECP2)a 20.9 22.8 NS -0.57 -2.84 0.03
rs573775 (ATG5) 28.2 26.3 NS 0.51 4.10 0.06
rs7574865 (STAT4) 23.3 23.8 NS -0.51 -4.63 0.06
rs6920220 (TNFAIP3) 19.3 17.8 NS 0.49 2.74 0.07
rs10798269 (1q25.1) 66.2 69.0 NS -0.17 -1.16 NS
rs5754217 (UBE2L3) 22.8 20.8 NS 0.16 1.28 NS
rs2304256 (TYK2) 73.1 71.0 NS 0.06 0.23 NS
rs2230926 (TNFAIP3) 3.5 4.3 NS -0.21 -3.42 NS
rs729302 (IRF5) 67.8 69.0 NS -0.00 -0.03 NS
rs17266594 (BANK1) 71.2 70.9 NS 0.32 1.99 NS
  1. Comparison of the risk allele frequencies (RAFs) between Central and Southern European controls, and linear regression of RAFs to the North/South score (N/S score) of population differentiation (from Table 1). NS, not significant. aAnalysis performed only in women because the locus is in the X chromosome.