Table 3

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

RAF (%)

RAF vs. N/S score


SNP (locus)

Central European

Southern European

χ2 P value

rxy

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


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.

Alonso-Perez et al. Arthritis Research & Therapy 2012 14:R94   doi:10.1186/ar3818

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