Table 2.

SNP Data and Analysis

A. Counts and Frequencies of Individual SNP Genotypes*
	All PBC (n = 351)	Control (n = 205)	AMA+ PBC (n = 303)	AMA− PBC (n = 44)	OLT PBC (n = 29)	Non-OLT PBC (n = 322)
CTLA4 49AG
AA	131 (0.37)	79 (0.39)	112 (0.37)	19 (0.43)	8 (0.28)	123 (0.38)
AG	161 (0.46)	99 (0.48)	134 (0.44)	24 (0.55)	12 (0.41)	149 (0.46)
GG	59 (0.17)	27 (0.13)	57 (0.19)	1 (0.02)	9 (0.31)	50 (0.16)
CTLA4 CT60
GG	117 (0.33)	70 (0.34)	105 (0.35)	10 (0.23)	15 (0.52)	102 (0.32)
AG	168 (0.48)	94 (0.46)	142 (0.47)	24 (0.55)	13 (0.45)	155 (0.48)
AA	66 (0.19)	41 (0.20)	56 (0.18)	10 (0.23)	1 (0.03)	65 (0.20)
PDCD1 PD1.3
GG	267 (0.76)	161 (0.79)	236 (0.78)	29 (0.66)	22 (0.76)	245 (0.76)
AG	80 (0.23)	40 (0.20)	64 (0.21)	15 (0.34)	5 (0.17)	75 (0.23)
AA	4 (0.01)	4 (0.02)	3 (0.01)	0	2 (0.07)	2 (0.01)

B. Statistical Analysis of SNP Genotypes Based on Logistic Regression and Adjusted for Age and Sex
	All PBC Versus Controls		AMA+ Versus AMA− PBC		OLT Versus Non-OLT PBC
	OR (95% CI)	P value	OR (95% CI)	P value	OR (95% CI)	P value
CTLA4 49AG
Log-additive	1.11 (0.86–1.42)	0.44	1.67 (1.03–2.71)	0.04	1.69 (1.00–2.88)	0.05
Dominant	1.05 (0.73–1.51)	0.79	1.35 (0.71–2.58)	0.36	1.71 (0.73–4.00)	0.22
Recessive (GG)	1.33 (0.81–2.20)	0.26	9.96 (1.34–73.97)	0.02	2.46 (1.05–5.76)	0.04
CTLA4 CT60
Log-additive	1.00 (0.78–1.27)	0.97	0.71 (0.45–1.12)	0.14	0.44 (0.24–0.81)	0.008
Dominant	1.05 (0.72–1.52)	0.80	0.55 (0.26–1.17)	0.12	0.43 (0.20–0.93)	0.03
Recessive (AA)	0.92 (0.59–1.43)	0.71	0.73 (0.34–1.58)	0.43	0.13 (0.02–0.99)	0.05
PDCD1 PD1.3
Log-additive	1.05 (0.72–1.55)	0.78	0.62 (0.33–1.17)	0.14	1.35 (0.62–2.93)	0.46
Dominant	1.12 (0.74–1.71)	0.59	0.54 (0.27–1.08)	0.08	1.01 (0.41–2.47)	0.99
Recessive (AA)	0.55 (0.13–2.36)	0.43	–	–	14.74 (1.89–114.9)	0.01

^*Values are expressed as count (frequency).

Bold text indicates statistically significant findings (i.e., P ≤ 0.05).