Table 3.

Independent SNPs Associated with Liver-Enzyme Levels with Genome-wide Significance in Combined GWAS Analysis of Discovery and Replication Data Sets

SNPa	CHR	Positionb	Nearest Gene	Region	Minor Allelec	MAFd	Three Discovery Collections (n = 7,715)		Three Replication Collections (n = 4,704)		Six Collections (n = 12,419)
							Pooled Beta-Coefficient (standard error)	Combined p Value	Pooled Beta-Coefficient (standard error)	Combined p Value	Pooled Beta-Coefficient (standard error)	Combined p Value
ALT
rs11597390	10	101851425	CPN1	intergenic	A	0.36	−0.044 (0.008)	2.9 × 10−8	−0.023 (0.013)	0.08	−0.039 (0.007)	1.5 × 10−8
rs11597086	10	101943695	CHUK	Intronic	C	0.43	−0.038 (0.007)	3.6 × 10−7	−0.030 (0.012)	0.01	−0.036 (0.006)	1.8 × 10−8
rs11591741	10	101966491	CHUK	intronic	C	0.43	−0.038 (0.007)	4.5 × 10−7	−0.029 (0.012)	0.02	−0.035 (0.006)	3.0 × 10−8
rs2281135	22	42657471	PNPLA3	intronic	T	0.18	0.065 (0.010)	8.2 × 10−12	0.051 (0.012)	1.3 × 10−5	0.060 (0.007)	8.4 × 10−16
rs2143571	22	42716587	SAMM50	intronic	A	0.19	0.046 (0.009)	9.4 × 10−7	0.038 (0.012)	1.8 × 10−3	0.043 (0.007)	7.2 × 10−9
GGT
rs1169313	12	119905390	HNF1A	intronic	C	0.38	−0.007 (0.001)	3.2 × 10−8	−0.003 (0.001)	7.0 × 10−5	−0.005 (0.001)	1.8 × 10−10
rs4820599	22	23314767	GGT1	intronic	G	0.31	0.006 (0.001)	3.9 × 10−6	0.008 (0.002)	1.8 × 10−6	0.007 (0.001)	4.0 × 10−11
ALP
rs1780324	1	21567063	NBPF3-ALPL	intergenic	T	0.43	0.032 (0.005)	1.4 × 10−10	0.031 (0.007)	1.0 × 10−5	0.031 (0.004)	7.0 × 10−15
rs9461011	6	24548330	GPLD1	intronic	G	0.23	0.033 (0.006)	4.4 × 10−8	0.030 (0.009)	0.001	0.032 (0.005)	1.9 × 10−10
rs9467160	6	24549725	GPLD1	intronic	A	0.24	0.033 (0.006)	2.2 × 10−8	0.035 (0.009)	1.3 × 10−4	0.034 (0.005)	1.2 × 10−11
rs8176720	9	133162427	ABO	synonymous	G	0.32	0.031 (0.005)	1.4 × 10−8	0.031 (0.008)	7.0 × 10−5	0.031 (0.004)	4.3 × 10−12
rs641959	9	133163253	ABO	intronic	G	0.26	0.035 (0.006)	6.8 × 10−10	0.024 (0.008)	0.004	0.031 (0.005)	2.1 × 10−11
rs514708	9	133163297	ABO	intronic	T	0.26	0.035 (0.006)	6.2 × 10−10	0.024 (0.008)	0.004	0.031 (0.005)	1.9 × 10−11
rs672316	9	133167679	ABO	intronic	C	0.27	0.032 (0.006)	1.4 × 10−8	0.023 (0.008)	0.006	0.029 (0.005)	4.4 × 10−10
rs657152	9	133168819	ABO	intronic	T	0.39	−0.057 (0.005)	4.6 × 10−29	−0.029 (0.007)	4.9 × 10−5	−0.047 (0.004)	1.7 × 10−30
rs474279	9	133169171	ABO	intronic	T	0.24	0.030 (0.006)	3.4 × 10−7	0.023 (0.008)	0.006	0.028 (0.005)	8.3 × 10−9
rs552148	9	133183035	ABO	upstream	T	0.24	0.032 (0.006)	3.1 × 10−8	0.022 (0.008)	0.008	0.029 (0.005)	1.2 × 10−9
rs12355784	10	64791571	JMJD1C	intronic	A	0.48	0.026 (0.005)	4.7 × 10−7	0.025 (0.007)	2.7 × 10−4	0.025 (0.004)	5.0 × 10−10
rs10761779	10	64944933	REEP3	intergenic	G	0.49	0.025 (0.005)	3.9 × 10−7	0.024 (0.007)	4.5 × 10−4	0.025 (0.004)	6.9 × 10−10

^aIndependent SNPs (r² < 0.4) were selected from each loci.

^bPosition is of NCBI Build 35.

^cMinor allele corresponds to forward strand and is of NCBI Build 35.

^dMAF, Minor allele frequency. It is based on CoLaus study.