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. Author manuscript; available in PMC: 2012 Sep 1.
Published in final edited form as: J Hepatol. 2012 Apr 18;57(2):366–375. doi: 10.1016/j.jhep.2012.03.031

Table 2.

Allele frequencies and results from the association analyses for SNPs with association results reaching nominal significance with consistent effect sizes in the replication.

Genome-wide analysis Replication analysis
Allele frequencies (Cases/Controls) Allele frequencies (Cases/Controls)
Chr SNP Position Locus Al Scandinavia
(332/262)		 Germany
(383/2700)		 P-value* OR (95% CI)* Scandinavia
(289/820)		 Central
Europe
(561/2063)		 United
States
(371/625)		 P -value† OR (95% CI) † BD P
value		 Combined
P -value		 Het P-
Value		 SNP
selection
strategy
1 rs3748816 2,516,606 TNFRSF14/MMEL1 G/A 0.29/0.34 0.28/0.33 6.5×10−4 0.79 (0.69–0.90) 0.31/0.35 0.30/0.34 0.27/0.35 8.7×10−6 0.79 (0.71–0.88) 0.45 2.1×10−8 0.92 I
4 rs13132245 123,269,042 KIAA1109/IL2/IL21 G/A 0.16/0.21 0.12/0.17 7.3×10−5 0.69 (0.57–0.83) 0.13/0.18 0.12/0.14 0.12/0.15 3.0×10−4 0.77 (0.67–0.89) 0.65 1.2×10−7 0.40 II
4 rs13119723 123,437,763 KIAA1109/IL2/IL21 G/A 0.13/0.18 0.09/0.14 4.1×10−5 0.65 (0.53–0.80) 0.15/0.19 0.13/0.15 0.12/0.16 4.0×10−4 0.78 (0.68–0.90) 0.87 9.9×10−8 0.32 II
9 rs4077515 138,386,317 CARD9 T/C 0.48/0.45 0.43/0.40 0.045 1.14 (1.00–1.31) 0.49/0.45 0.47/0.42 0.45/0.42 5.3×10−4 1.18 (1.08–1.30) 0.95 7.6×10−5 0.55 I
16 rs2903692 11,146,284 CLEC16A A/G 0.28/0.33 0.31/0.36 0.0014 0.80 (0.92–0.70) 0.27/0.33 0.32/0.35 0.32/0.36 0.0012 0.85 (0.76–0.94) 0.43 6.4×10−6 0.64 I
2 rs13017599 61,017,835 REL A/G 0.40/0.35 0.40/0.37 0.027 1.16 (1.32–1.02) 0.40/0.36 0.42/0.38 0.38/0.37 0.0026 1.16 (1.05–1.28) 0.42 1.9×10−4 0.88 I
21 rs11203203 42,709,255 UBASH3A A/G 0.39/0.35 0.42/0.37 0.0025 1.22 (1.39–1.07) 0.39/0.34 0.39/0.36 0.40/0.36 0.0033 1.16 (1.05–1.28) 0.68 2.9×10−5 0.60 I
19 rs602662 53,898,797 FUT2 A/G 0.56/0.50 0.53/0.46 7.7×10−5 1.30 (1.49–1.14) 0.53/0.47 0.48/0.45 0.51/0.50 0.0034 1.15 (1.05–1.27) 0.29 1.9×10−6 0.21 II
21 rs9976767 42,709,459 UBASH3A G/A 0.48/0.46 0.48/0.44 0.028 1.15 (1.02–1.30) 0.45/0.43 0.47/0.44 0.49/0.43 0.0055 1.14 (1.04–1.26) 0.44 4.0×10−4 0.99 I
19 rs601338 53,898,486 FUT2 A/G 0.50/0.44 0.47/0.40 4.5×10−5 1.33 (1.52–1.16) 0.51/0.44 0.46/0.42 0.48/0.48 0.0061 1.14 (1.04–1.26) 0.062 2.7×10−6 0.14 II
2 rs11682163 3,727,421 ALLC C/T 0.49/0.39 0.49/0.44 7.9×10−5 1.29 (1.47–1.14) 0.50/0.45 0.49/0.44 0.43/0.45 0.010 1.13 (1.03–1.24) 0.048 7.6×10−6 0.14 II
19 rs281377 53,898,415 FUT2 T/C 0.43/0.49 0.46/0.52 9.3×10−6 0.71 (0.61–0.83) 0.39/0.47 0.47/0.49 0.44/0.44 0.011 0.88 (0.80–0.97) 0.025 2.1×10−6 0.059 II
22 rs5771069 48,777,607 IL17REL A/G 0.48/0.54 0.49/0.53 0.0057 0.82 (0.95–0.72) 0.45/0.49 0.47/0.50 0.48/0.50 0.028 0.90 (0.82–0.99) 0.89 5.8×10−4 0.43 I
4 rs11936230 123,236,205 KIAA1109/IL2/IL21 T/C 0.38/0.30 0.41/0.35 1.9×10−5 1.33 (1.17–1.52) 0.38/0.34 0.38/0.36 0.38/0.36 0.039 1.11 (1.01–1.22) 0.79 1.9×10−5 0.040 II
12 rs4149056 21,222,816 SLCO1B1 C/T 0.13/0.17 0.16/0.17 0.044 0.84 (1.00–0.70) 0.14/0.17 0.15/0.16 0.13/0.15 0.043 0.87 (0.76–1.00) 0.60 0.0045 0.76 I
22 rs4820599 23,320,213 GGT1 G/A 0.29/0.24 0.31/0.28 0.035 1.16 (1.01–1.33) 0.29/0.28 0.29/0.27 0.31/0.28 0.043 1.11 (1.00–1.23) 0.77 0.0038 0.69 I
12 rs3184504 110,368,991 SH2B3 T/C 0.54/0.52 0.57/0.51 0.0016 1.23 (1.08–1.40) 0.47/0.45 0.51/0.49 0.51/0.47 0.050 1.10 (1.00–1.21) 0.67 4.6×10−4 0.21 I

Complete association results for SNPs reaching nominal significance with consistent effect sizes in the replication. For the genome-wide analysis, the allele frequencies were calculated based on allele dosages and are listed separately for the German and Scandinavian discovery panels. For the replication analysis, allele frequencies are given for all three panels making up the combined replication panel. The combined P-values for the genome-wide analysis and the replication analysis were generated using the METAL software [34]. The genomic positions refer to NCBI’s build 36. SNP selection strategies I and II indicate SNPs selected based on the two SNP selection strategies. The HLA association was confirmed for rs4143332 (Prepl=4.1×10−77, Pcomb=4.4×10−123) (not listed in the table).

Chr, chromosome; Al, alleles; OR, Odds Ratio; CI, Confidence Interval; BD, Breslow-Day; Het, heterogeneity

*

Odds ratios and P-values derived from logistic regressions of allele dosages including the six first principal components from the principal components analysis as covariates.

†

P-values generated by using the Cochrane-Mantel-Haenszel test