Relationship between ethanol consumption and TBL2 rs17145738 on LDL-C concentration in Japanese adults: a four season 3-day weighed diet record study

Akimoto, S.; Goto, C.; Kuriki, K.

doi:10.1186/s40795-019-0315-6

Table 3 Associations between SNPs and LDL-C concentration in a cross-sectional study and a seasonal variation study

From: Relationship between ethanol consumption and TBL2 rs17145738 on LDL-C concentration in Japanese adults: a four season 3-day weighed diet record study

Gene/season	rs ID/season	CHR	Position	Alleles^a	MAF	Genotype^b			P_HWE	Complete case dataset^c			Observed subject dataset^d			Multiple imputation dataset (m = 100)^e
Gene/season	rs ID/season	CHR	Position	Alleles^a	MAF	AA	Aa	aa	P_HWE	β	S.E.	P	β	S.E.	P	β	S.E.	P
Cross-sectional study^f
Number of observations (person · season)											51			72			78
PSRC1	rs599839	1	109279544	A>G	0.08	66	11	1	0.79	-7.1 × E-2	4.0 × E-2	0.08	-8.6 × E-2	3.5 × E-2	0.01	-8.0 × E-2	3.4 × E-2	0.02
HMGCR	rs12654264	5	75352778	T>A	0.44	25	38	15	1.00	3.5 × E-2	3.7 × E-2	0.35	2.1 × E-2	2.9 × E-2	0.47	2.3 × E-2	2.7 × E-2	0.40
TIMD4	rs6882076	5	156963286	C>T	0.15	56	21	1	0.82	-1.9 × E-2	3.7 × E-2	0.61	2.2 × E-2	2.8 × E-2	0.44	1.9 × E-2	2.7 × E-2	0.50
TBL2	rs17145738	7	73568544	C>T	0.11	62	15	1	1.00	-5.1 × E-2	3.6 × E-2	0.17	-5.5 × E-2	2.9 × E-2	0.06	-5.1 × E-2	2.9 × E-2	0.09
-	rs651007	9	133278431	C>T	0.28	37	39	2	0.08	5.6 × E-2	3.0 × E-2	0.06	4.8 × E-2	2.4 × E-2	0.05	4.8 × E-2	2.4 × E-2	0.05
TOMM40	rs1160985	19	44900155	C>T	0.35	32	38	8	0.80	-5.3 × E-2	3.2 × E-2	0.11	-6.4 × E-2	2.6 × E-2	0.01	-6.7 × E-2	2.5 × E-2	0.009
APOC1	rs445925	19	44912383	G>A	0.10	64	12	2	0.35	-2.0 × E-2	4.8 × E-2	0.68	-5.9 × E-2	3.3 × E-2	0.08	-5.8 × E-2	3.2 × E-2	0.07
Seasonal variation research^g
Number of observations (person · season)											204			262			312
PSRC1	rs599839									-4.8 × E-2	3.6 × E-2	0.19	-4.8 × E-2	3.1 × E-2	0.12	-4.7 × E-2	3.2 × E-2	0.15
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.5 × E-2	8.9 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.08	-1.1 × E-2	1.1 × E-2	0.34
HMGCR	rs12654264									3.9 × E-2	3.3 × E-2	0.24	2.6 × E-2	2.4 × E-2	0.28	2.5 × E-2	2.6 × E-2	0.33
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.4 × E-2	8.9 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.07	-1.1 × E-2	1.1 × E-2	0.34
TIMD4	rs6882076									6.5 × E-3	3.2 × E-2	0.84	1.8 × E-2	2.4 × E-2	0.45	1.9 × E-2	2.6 × E-2	0.47
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.4 × E-2	8.9 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.07	-1.1 × E-2	1.1 × E-2	0.34
TBL2	rs17145738									-4.6 × E-2	3.2 × E-2	0.16	-4.8 × E-2	2.6 × E-2	0.08	-4.7 × E-2	2.8 × E-2	0.09
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.4 × E-2	8.9 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.08	-1.1 × E-2	1.1 × E-2	0.34
-	rs651007									5.0 × E-2	2.7 × E-2	0.07	4.7 × E-2	2.1 × E-2	0.03	4.7 × E-2	2.3 × E-2	0.04
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.4 × E-2	9.0 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.11	-1.5 × E-2	8.2 × E-3	0.07	-1.1 × E-2	1.1 × E-2	0.34
TOMM40	rs1160985									-4.7 × E-2	2.8 × E-2	0.11	-5.9 × E-2	2.2 × E-2	0.01	-5.9 × E-2	2.4 × E-2	0.01
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.4 × E-2	9.0 × E-3	0.11	-1.6 × E-2	7.8 × E-3	0.04	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.8 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.07	-1.1 × E-2	1.1 × E-2	0.33
APOC1	rs445925									-1.4 × E-2	4.3 × E-2	0.74	-4.9 × E-2	2.8 × E-2	0.08	-4.9 × E-2	3.0 × E-2	0.11
Season	- Winter									Reference			Reference			Reference
	- Spring									-1.5 × E-2	8.9 × E-3	0.11	-1.7 × E-2	7.8 × E-3	0.03	-1.6 × E-2	1.1 × E-2	0.13
	- Summer									-2.8 × E-2	8.9 × E-3	0.002	-2.4 × E-2	7.7 × E-3	0.002	-2.2 × E-2	1.1 × E-2	0.04
	- Autumn									-1.4 × E-2	9.0 × E-3	0.12	-1.5 × E-2	8.2 × E-3	0.07	-1.1 × E-2	1.1 × E-2	0.34

Abbreviations: SNP single nucleotide polymorphism, LDL-C LDL cholesterol, CHR chromosome, MAF minor allele frequency, PHWE P-value for Hardy-Weinberg equilibrium, m number of imputations. The following variables were log-transformed to improve the normality: LDL-C concentration; BMI; physical activity; ethanol consumption. P-value <0.05 was shown as bold. ^aAlleles were shown as following: major allele>minor allele. ^bA major allele was shown as 'A', and a minor allele was shown 'a'. ^cComplete case dataset was composed of subjects without missing values on four seasons. ^dObserved subjects dataset was used for the analysis of all of values collected in each season even if there were missing values. ^eMultiple imputation datasets were calculated by means of applying observed subjects dataset to the MI procedure. ^fMultiple regression models were applied for analyzing the associations between SNPs and LDL-C concentration with adjustment for age, sex (0: men, 1: women), BMI, physical activity, ethanol consumption, smoking status (0: non-smoker, 1: smoker). ^gMixed-effect models were applied for analyzing the associations between SNPs and LDL-C concentration with age, sex (0: men, 1: women), BMI, physical activity, ethanol consumption, smoking status (0: non-smoker, 1: smoker) and season (1: winter, 2: spring, 3: summer, 4: autumn) as fixed effects and subject ID as random intercept

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