Skip to main content

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/seasonrs ID/seasonCHRPositionAllelesaMAFGenotypebPHWEComplete case datasetcObserved subject datasetdMultiple imputation dataset (m = 100)e
AAAaaaβS.E.PβS.E.PβS.E.P
Cross-sectional studyf
 Number of observations (person · season)       51  72  78 
PSRC1rs5998391109279544A>G0.08661110.79-7.1 × E-24.0 × E-20.08-8.6 × E-23.5 × E-20.01-8.0 × E-23.4 × E-20.02
HMGCRrs12654264575352778T>A0.442538151.003.5 × E-23.7 × E-20.352.1 × E-22.9 × E-20.472.3 × E-22.7 × E-20.40
TIMD4rs68820765156963286C>T0.15562110.82-1.9 × E-23.7 × E-20.612.2 × E-22.8 × E-20.441.9 × E-22.7 × E-20.50
TBL2rs17145738773568544C>T0.11621511.00-5.1 × E-23.6 × E-20.17-5.5 × E-22.9 × E-20.06-5.1 × E-22.9 × E-20.09
 -rs6510079133278431C>T0.28373920.085.6 × E-23.0 × E-20.064.8 × E-22.4 × E-20.054.8 × E-22.4 × E-20.05
TOMM40rs11609851944900155C>T0.35323880.80-5.3 × E-23.2 × E-20.11-6.4 × E-22.6 × E-20.01-6.7 × E-22.5 × E-20.009
APOC1rs4459251944912383G>A0.10641220.35-2.0 × E-24.8 × E-20.68-5.9 × E-23.3 × E-20.08-5.8 × E-23.2 × E-20.07
Seasonal variation researchg
 Number of observations (person · season)       204  262  312 
PSRC1rs599839        -4.8 × E-23.6 × E-20.19-4.8 × E-23.1 × E-20.12-4.7 × E-23.2 × E-20.15
 Season- Winter        ReferenceReferenceReference
- Spring        -1.5 × E-28.9 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.08-1.1 × E-21.1 × E-20.34
HMGCRrs12654264        3.9 × E-23.3 × E-20.242.6 × E-22.4 × E-20.282.5 × E-22.6 × E-20.33
 Season- Winter        ReferenceReferenceReference
- Spring        -1.4 × E-28.9 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.07-1.1 × E-21.1 × E-20.34
TIMD4rs6882076        6.5 × E-33.2 × E-20.841.8 × E-22.4 × E-20.451.9 × E-22.6 × E-20.47
 Season- Winter        ReferenceReferenceReference
- Spring        -1.4 × E-28.9 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.07-1.1 × E-21.1 × E-20.34
TBL2rs17145738        -4.6 × E-23.2 × E-20.16-4.8 × E-22.6 × E-20.08-4.7 × E-22.8 × E-20.09
 Season- Winter        ReferenceReferenceReference
- Spring        -1.4 × E-28.9 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.08-1.1 × E-21.1 × E-20.34
 -rs651007        5.0 × E-22.7 × E-20.074.7 × E-22.1 × E-20.034.7 × E-22.3 × E-20.04
 Season- Winter        ReferenceReferenceReference
- Spring        -1.4 × E-29.0 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.11-1.5 × E-28.2 × E-30.07-1.1 × E-21.1 × E-20.34
TOMM40rs1160985        -4.7 × E-22.8 × E-20.11-5.9 × E-22.2 × E-20.01-5.9 × E-22.4 × E-20.01
 Season- Winter        ReferenceReferenceReference
- Spring        -1.4 × E-29.0 × E-30.11-1.6 × E-27.8 × E-30.04-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.8 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.07-1.1 × E-21.1 × E-20.33
APOC1rs445925        -1.4 × E-24.3 × E-20.74-4.9 × E-22.8 × E-20.08-4.9 × E-23.0 × E-20.11
 Season- Winter        ReferenceReferenceReference
- Spring        -1.5 × E-28.9 × E-30.11-1.7 × E-27.8 × E-30.03-1.6 × E-21.1 × E-20.13
- Summer        -2.8 × E-28.9 × E-30.002-2.4 × E-27.7 × E-30.002-2.2 × E-21.1 × E-20.04
- Autumn        -1.4 × E-29.0 × E-30.12-1.5 × E-28.2 × E-30.07-1.1 × E-21.1 × E-20.34
  1. 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