Genome-wide association study on serum alkaline phosphatase levels in a Chinese population

BMC Genomics

Table 1 SNPs associated with serum ALP levels

SNP	Region	Position^a	Genes	Locus	Minor/major allele	GWAS^b			Validation^b*			Combined^b
SNP	Region	Position^a	Genes	Locus	Minor/major allele	MAF	Effect size (s.e.m)	P values	MAF	Effect size (s.e.m)	P values	MAF	Effect size (s.e.m)	P values
rs1383023	2p23.1	31872045	N/A	-	A/C	0.093	0.087 (0.018)	2.30 × 10^-6	0.075	0.0016 (0.014)	9.05 × 10^-1	0.080	-0.0009(0.005)	8.59 × 10^-1
rs7594727	2p11.2	96853597	CNNM3	Intron	A/C	0.107	-0.070 (0.017)	3.70 × 10^-5	0.116	-0.008 (0.011)	5.01 × 10^-1	0.113	-0.018(0.009)	4.39 × 10^-2
rs8176720	9q34.2	135122694	ABO	Exon	C/T	0.444	0.055 (0.010)	8.19 × 10^-8	0.454	0.038 (0.005)	6.63 × 10^-16	0.452	0.041(0.004)	2.50 × 10^-21
rs651007	9q34.2	135143696	SURF6-ABO	Up-	A/G	0.244	-0.114 (0.012)	1.93 × 10^-21	0.222	-0.077 (0.005)	7.54 × 10^-44	0.226	-0.079(0.005)	1.12 × 10^-56
rs7025162	9q34.2	135156167	SURF6-ABO	Up-	A/G	0.390	-0.064 (0.011)	2.20 × 10^-9	0.383	-0.044 (0.005)	1.10 × 10^-20	0.384	-0.047(0.004)	2.82 × 10^-27
rs7214920	17q21.32	42406128	RPRML	Up-	A/G	0.119	0.068 (0.016)	2.55 × 10^-6	0.119	0.001 (0.011)	9.12 × 10^-1	0.119	0.020(0.009)	2.99 × 10^-2

^aGenome position is based on NCBI build 36.3.
^bThe P values in GWAS stage are based on linear regression analysis on the log-transformed ALP with adjustment for age, gender and the top two eigenvectors in PCA analysis assuming an additive model by PLINK. The validation and combined P values are calculated by linear regression model on the log-transformed ALP and adjusted for age and gender.
^*SNPs of rs8176720, rs651007 and rs7025162 were validated in 8,830 healthy participants, while rs1383023, rs7594727 and rs7214920 were validated in 3,456 participants.

ISSN: 1471-2164