identification and validation of seven new loci showing

1

Identification and validation of seven new loci showing differential DNA methylation

related to serum lipid profile: an epigenome-wide approach. The REGICOR study.

Sayols-Baixeras S: Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital

del Mar Medical Research Institute), Barcelona 08003, Catalonia, Spain; Universitat Pompeu

Fabra (UPF), Barcelona 08003, Catalonia, Spain.

Subirana I: CIBER Epidemiology and Public Health, Barcelona 08003, Catalonia, Spain;

Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical

Research Institute), Barcelona 08003, Catalonia, Spain.

Lluis-Ganella C: Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del

Mar Medical Research Institute), Barcelona 08003, Catalonia, Spain.

Civeira F: Unidad Clínica y de Investigación en Lípidos y Arteriosclerosis, Hospital Universitario

Miguel Servet, Instituto de Investigación Sanitaria Aragón, Zaragoza 50009, Spain.

Roquer J: Department of Neurology, Neurovascular Research Group, IMIM (Hospital del Mar

Medical Research Institute), Barcelona 08003, Catalonia, Spain.

Do AN: Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL,

United States of America

Absher D: Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States of America

Cenarro A: Unidad Clínica y de Investigación en Lípidos y Arteriosclerosis, Hospital Universitario


Muñoz D: Cardiovascular Risk and Nutrition Research Group, IMIM (Hospital del Mar Medical


Soriano-Tárraga C: Department of Neurology, Neurovascular Research Group, IMIM (Hospital

del Mar Medical Research Institute), Barcelona 08003, Catalonia, Spain.

Jiménez-Conde J: Department of Neurology, Neurovascular Research Group, IMIM (Hospital


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Ordovas J: Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University,

Boston, MA, United States of America.

Senti M: Department of Experimental and Health Sciences, Pompeu Fabra University,

Barcelona 08003, Catalonia, Spain.

Aslibekyan S: Department of Epidemiology, School of Public Health, University of Alabama at

Birmingham, Birmingham, AL, United States of America

Marrugat J: Cardiovascular Epidemiology and Genetics Research Group. IMIM (Hospital del


Arnett DK: Dean's Office, College of Public Health, University of Kentucky, Lexington, KY,

United States of America.

Elosua R: Cardiovascular Epidemiology and Genetics Research Group. IMIM (Hospital del Mar


Author for correspondence:

Roberto Elosua, MD, PhD

IMIM, Hospital del Mar Medical Research Institute

Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain

Telephone: (+34) 933 160800

Fax: (+34) 933 160796

Email: [email protected]

mailto:[email protected]

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ABSTRACT

Lipid traits (total, low-density and high-density lipoprotein cholesterol, and triglycerides) are

risk factors for cardiovascular disease. DNA methylation is an inherited but also modifiable

epigenetic mark that has been related to cardiovascular risk factors. Our aim was to identify

loci showing differential DNA methylation related to serum lipid levels. Blood DNA methylation

was assessed using the Illumina HumanMethylation450 BeadChip. A two-stage epigenome-

wide association study was performed, with a discovery sample in the REGICOR study (n=645)

and validation in the Framingham Offspring Study (n=2,542). Fourteen CpG sites located in 9

genes (SREBF1, SREBF2, PHOSPHO1, SYNGAP1, ABCG1, CPT1A, MYLIP, TXNIP and SLC7A11) and

2 intergenic regions showed differential methylation in association with lipid traits. Six of these

genes and 1 intergenic region were new discoveries showing differential methylation related

to total cholesterol (SREBF2), HDL-cholesterol (PHOSPHO1, SYNGAP1 and an intergenic region

in chromosome 2) and triglycerides (MYLIP, TXNIP and SLC7A11). These CpGs explained 0.7%,

9.5% and 18.9% of the variability of total cholesterol, HDL cholesterol and triglycerides in the

Framingham Offspring Study, respectively. The expression of the genes SREBF2 and SREBF1

was inversely associated with methylation of their corresponding CpGs (p-value=0.0042 and

0.0045, respectively) in participants of the GOLDN study (n=98). In turn, SREBF1 expression

was directly associated with HDL cholesterol (p-value=0.0429). Genetic variants in SREBF1,

PHOSPHO1, ABCG1 and CPT1A were also associated with lipid profile. Further research is

warranted to functionally validate these new loci and assess the causality of new and

established associations between these differentially methylated loci and lipid metabolism.

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1. Introduction

Total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein

cholesterol (HDL-c), and triglycerides (TG) are among the most important risk factors for

cardiovascular disease, the leading cause of death worldwide. (1,2) Serum lipid levels are

determined by a complex interplay between environmental, lifestyle and genetic factors. (3)

In recent years, new technological advances have allowed study of epigenetic mechanisms that

affect chromatin structure and influence transcription levels. In the field of cardiovascular

diseases, several studies have analyzed the association between DNA methylation and lipid

traits. (4-7) DNA methylation is a heritable but reversible addition of a methyl group to a

nucleotide. This process usually occurs in cytosine nucleotides in the presence of cytosine-

phosphate-guanine (CpG), and can now be analyzed by epigenome-wide association studies

(EWAS) using arrays that cover thousands of CpGs across the genome.

The aim of the present study was to identify and validate new individual CpGs showing

differential methylation related to serum lipid traits (TC, LDL-c, HDL-c and TG) in a population-

based survey using an EWAS design. Additionally, we used shotgun transcriptomics (RNASeq)

data to assess the associations between methylation at each validated CpG site and gene

transcript level, as well as between gene transcript level and lipid phenotypes.

2. Results

2.1. Discovery stage of the EWAS analysis

After quality control steps, the discovery analysis included 645 individuals (99.5%; 3 individuals

were excluded) and 427,948 probes (88.7%; 57,629 probes were excluded). A descriptive

analysis of the main sociodemographic and clinical characteristics of the included individuals is

shown in Table 1.

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The relationship between observed and predicted p-values for all the association tests

between methylation levels and each lipid trait is shown in QQ and Manhattan plots

(Supplementary Figure S1). In the discovery sample, we identified 113 CpGs (27 using model 1

–adjusted for covariates but not for surrogates variables– and 105 using model 2–adjusted for

covariates and surrogates variables–) showing a suggestive association between methylation

levels and lipid traits with an arbitrary p-value threshold <1x10-5 (Supplementary Table 1 and

Figure 1-a). These CpG sites were located in 88 genes, 3 lncRNA and 17 intergenic regions. In

model 1 (Figure 1-b), 4 CpG sites were associated with TC, 4 with HDL-c, 18 with TG and 1 with

both TG and HDL-c; in model 2 (Figure 1-c), 16 CpGs were associated with TC, 7 with LDL-c, 39

with HDL-c, 35 with TG, 5 with both TC and LDL-c and 3 with HDL-c and TG.

We also performed sensitivity analyses excluding those participants taking cholesterol-

lowering drugs and adjusting for diabetes and body mass index (BMI). The results remained

consistent (Supplementary Table 2).

2.2. Validation stage of the EWAS analysis

After applying the same quality control steps as in the discovery analysis, the validation study

included 2,542 individuals (99.0%; 26 individuals excluded) and all the CpG sites identified in

the discovery stage. The characteristics of the population included in the validation stage are

shown in Table 1. The associations observed between the 113 CpGs selected and the lipid

traits in the Framingham Offspring study are shown in Supplementary Table 1.

2.3. Meta-analyses

After meta-analysis of the results obtained in the REGICOR and Framingham Offspring studies,

we validated 12 CpG sites using model 1, and 2 additional CpGs using model 2 (Table 2). Of the

14 hits, one CpG was associated with TC, 3 CpGs with HDL-c, 7 with TG and 3 CpGs with both

TG and HDL-c (Table 2 and Figure 1-d). Validated CpG sites were located in 9 genes and 2

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intergenic regions. One gene (SREBF2) was associated with TC, 4 (SYNGAP1, SREBF1,

PHOSPHO1 and ABCG1) with HDL-c and 6 (TXNIP, SLC7A11, MYLIP, CPT1A, SREBF1 and ABCG1)

with TG.

These 14 CpGs explained 3.84%, 10.33% and 16.07% of the variability of TC, HDL-c and TG, in

REGICOR, and 0.74%, 9.51% and 18.89% in Framingham, respectively (Table 3, Supplementary

Figure S2).

2.4. Gene expression analyses

The results of the Genetics of Lipid-lowering Drugs and Diet Network (GOLDN) study showed

that the methylation of cg16000331 and cg11024682 was inversely associated with the

expression of the genes SREBF2 and SREBF1, respectively (Table 4). In turn, SREBF1 expression

was directly associated with higher levels of HDL cholesterol (Table 4).

2.5. Genetic variation and lipid profile

The aggregated results of the Global Lipids Genetics Consortium showed some genetic variants

in SREBF1, PHOSPHO1, ABCG1 and CPT1A associated with the lipid trait of interest (Table 5,

Supplementary Table 4).

3. Discussion

In this EWAS we have identified and validated 14 CpG sites located in 9 genes (SREBF1, SREBF2,

PHOSPHO1, SYNGAP1, ABCG1, CPT1A, MYLIP, TXNIP and SLC7A11) and 2 intergenic regions

that showed differential methylation in association with 3 lipid traits: TC, HDL-c and TG. This

differential methylation in the validated CpGs explained around 10% of the variability of HDL-c

and around 16-18% of the variability of TG. These results replicated previous findings showing

an association between lipid traits and DNA methylation in three genes (ABCG1, SREBF1 and

CPT1A) and 1 intergenic region. (5,6,8,9) In addition, we identified 6 new genes and 1

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intergenic region showing differential methylation in relation to TC (SREBF2), HDL-c

(PHOSPHO1, SYNGAP1 and an intergenic region located in chromosome 2) and TG (MYLIP,

TXNIP and SLC7A11). The expression of the genes SREBF2 and SREBF1 was inversely associated

with methylation of their corresponding CpGs. In turn, the expression of SREBF1 was

associated with higher levels of HDL cholesterol. Finally, genetic variants in SREBF1,

PHOSPHO1, ABCG1 and CPT1A were also associated with the lipid profile.

Previous findings associated ABCG1 methylation with TG and HDL-c levels. (6,8,9) A direct

relationship of ABCG1 methylation with coronary artery disease and aging has also been

reported. (6,9,10) Reduced levels of DNA methylation in the ABCG1 promoter region have also

been observed in patients under aspirin therapy. (11) Our results on SREBF1 methylation and

TG are also consistent with previous findings, validating the direction and the magnitude of the

association. (5,6) Furthermore, we observed a statistically significant association between

methylation levels of SREBF1 and HDL-c in the opposite direction to that observed with TG.

Previous studies also found an association between BMI and methylation of CpG sites located

in CPT1A and SREBF1. (12,13) In a sensitivity analysis, we further adjusted our models including

BMI as a potential intermediate variable; the magnitude of the association between

methylation in these CpGs and TG or HDL-c was slightly reduced (16-28%; Supplementary

Table 3), suggesting that this association is only partially BMI-dependent. In this study we also

provide data supporting that SREBF1 methylation is related to SREBF1 expression, which in

turn is associated with HDL cholesterol. Moreover, genetic variants in this gene are also

associated with HDL cholesterol. Globally, these results support the causal association

between SREBF1 and HDL cholesterol and suggest a potential functional mechanism.

Novel findings in the present study include an association between lipids traits and different

CpG methylation levels in SREBF2, PHOSPHO1, SYNGAP1, TXNIP, MYLIP and SLC7A11. Four of

these genes, SREBF2, PHOSPHO1, TXNIP and MYLIP, merit detailed comment (See

Supplementary Material for further discussion).

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Sterol regulatory element binding factor 2 (SREBF2) is similar to SREBF1 and encodes

membrane-bound transcription factors that control the metabolism of cholesterol and fatty

acids. A common genetic variant of SREBF2 has been associated with intima-media thickness.

(14) In the present study, we report a positive association between SREBF2 methylation and

TC, in the same direction as the association between SREBF1 and TG. We also report an inverse

association between SREBF2 methylation and expression. These results suggest a potential

role of increased SRBEF2 methylation in atherosclerosis progression through lipid metabolism

regulation.

Phosphatase orphan 1 (PHOSPHO1) plays an important role at early steps of inorganic

phosphate-induced and matrix vesicle-mediated calcification. Published studies show an up-

regulation of PHOSPHO1 in vascular smooth muscle cells; administration of PHOSPHO1

inhibitors reduced vascular smooth calcification by 2.5-fold. Therefore, a procalcific role of

PHOSPHO1 in pathologic vascular ossification is plausible. (15,16) The present study found a

direct association between the CpG methylation at this locus and HDL-cholesterol levels; other

recent studies found an association with diabetes. (17,18) The complex interrelations between

lipids, diabetes and arterial calcifications merit additional studies, (19-22) our data suggest that

the low methylation level at this locus could be associated with higher PHOSPHO1 levels. This

could induce calcification due to low HDL cholesterol levels and altered glucose homeostasis or

other potential mechanisms.

Thioredoxin-interacting protein (TXNIP) is involved in redox homeostasis. It is induced by

glucose but suppressed by insulin, and acts as a regulator of glucose homeostasis in humans.

Recent studies have shown different methylation levels of TXNIP gene in relation to type 2

diabetes. (17,18,23-26) TXNIP has also been related with regulation of TG levels. It was

proposed as a candidate gene for familial combined hyperlipidemia; however, other studies

have not replicated this finding. (27,30) A TXNIP genetic variant was associated with TG levels

in diabetic participants. (31) In addition, the same TXNIP methylation CpG site was reported to

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be associated with TG levels, even though the association did not reach the statistical

significance threshold in the meta-analyses. (6) Additional adjustment of our models including

diabetes as a potential confounder variable did not modify the magnitude of the association

between methylation in this CpG and TG levels (Supplementary Table S2), suggesting that the

association is independent of diabetes. In summary, low TXNIP methylation is associated with

high triglycerides and altered glucose homeostasis and could increase the risk of

atherosclerosis-related diseases.

Finally, we report a direct association between methylation in myosin regulatory light chain

interacting protein (MYLIP), a ubiquitin ligase, and TG. MYLIP was recently identified as a novel

regulator of LDL receptor in a genome-wide association study, so now it is also called

MYLIP/IDOL (inducible degrader of the LDL receptor). (32,33) The induction of MYLIP in

macrophages and liver leads to the ubiquitination of LDL receptors, whereas MYLIP

downregulation by RNA silencing increases LDL receptors levels and enhances LDL uptake. (34)

This mechanism could be similar to that of PCSK9 inhibitors, making it a new therapeutic target

if causality between MYLIP methylation and increased lipid levels can be demonstrated. (35)

Ours findings and previously published results support the hypothesis that high MYLIP

methylation could decrease MYLIP expression and increase triglycerides by decreasing LDL

receptor availability, increasing the risk of atherosclerosis-related diseases.

A major strength of the study was the use of standardized protocols to remove non-biological

sources of variation. Moreover, we used a powerful statistical method that reduces outlier

effects (robust linear regression) and adjusted for residual confounding factors (surrogate

variables). We replicated and meta-analyzed data in a very large external population in order

to improve the quality of our evidence. We also have analyzed the association between DNA

methylation and gene expression, and between gene expression and lipid traits.

Some limitations of the study should be considered. First, some heterogeneity exists between

the REGICOR and Framingham Offspring studies. To address the differences, we carried out a

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meta-analysis of CpG sites with significant coefficient differences between studies, using the

random effects method, and the results did not change. Second, the design of the study was

cross-sectional and therefore we cannot infer causality in the reported association between

lipid traits and DNA methylation levels. Proper Mendelian randomization studies or

prospective data are warranted to assess this issue. (36)

In summary, this study replicated 4 loci (ABCG1, SREBF1, CPT1A and 1 intergenic region at

chromosome 10) and discovered and validated 7 new loci (SREBF2, PHOSPHO1, SYNGAP1,

TXNIP, MYLIP, SLC7A11, and one intergenic region at chromosome 2) showing differential

methylation related to serum lipid profile. The findings point out some genes and pathways

that may be related to lipid metabolism regulation and atherosclerosis. We also report a

potential functional explanation for the association between SREBF1 methylation and HDL

cholesterol that could be mediated by gene expression. Further research is needed to

functionally validate the new loci and assess the causality of these associations.

4. Materials and methods

4.1. Study design and participants

A cross-sectional two-stage epigenome-wide association study was designed.

i) Discovery stage: we used the REGICOR (REgistre GIroní del COR) study, a population-based

cohort that includes participants from different towns representing the urban and rural

diversity of Girona Province in Catalonia (Spain). For this study we considered those individuals

initially enrolled in a survey performed during 2003-2005 (n=6,352; response rate 71.5%) who

were still residing in these towns and attended a follow-up visit during 2009-2013 (n=4,980

participants; response rate 78.4%). From those participants we randomly selected a subsample

of 648 participants, all of whom reported that they were of European descent. All the

participants gave written informed consent before their participation. This study follows the

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principles expressed in the Declaration of Helsinki and the legislation in Spain, and was

approved by the local ethics committee.

ii) Validation stage: We obtained methylation and phenotype data from the Framingham

Offspring Study through the Database of Genotypes and Phenotypes (dbGAP;

http://dbgap.ncbi.nlm.nih.gov; project number #9047). The Framingham Offspring Study

started in 1971 and included 5,209 offspring from the participants in the original Framingham

Heart Study. Those participants attending exam 8 and with available DNA methylation data

were included in the present analysis.

4.2. Serum lipid profile.

In the REGICOR study a team of trained nurses collected fasting blood samples, which were

centrifuged between 15 and 30 minutes after extraction. Both serum and plasma samples

were aliquoted and frozen at -80ºC until analysis. Serum concentrations of TC and TG were

determined enzymatically (Horiba ABX, Montpellier, France). Serum HDL-c concentrations

were measured as soluble cholesterol determined by an accelerator selective detergent

method (Horiba ABX). Analyses were performed in an ABX Pentra 400 (Horiba ABX,

Montpellier, France). External quality assessment was performed with External Quality Control

BIORAD (Bio-Rad, Hercules, California, USA) and Assessment-SEQC (Sociedad Española Química

Clínica, Barcelona, Spain). LDL-c was calculated by the Friedewald equation when TG levels

were lower than 300 mg/dL.

In the Framingham Offspring Study, lipid traits of interest were obtained from examination 8

data through dbGaP. Fasting TC, HDL-c and TG were determined directly and LDL-c was

estimated by the Friedewald equation.

4.3. Other covariates.

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In the REGICOR study, the same group of trained nurses examined and administered all

validated and standardized questionnaires and methods used to collect sociodemographic,

lifestyle and cardiovascular risk factors information. In the Framingham Offspring study, the

covariates of interest were obtained from examination 8 data through dbGaP.

Smoking status was self-reported and then categorized in four different groups: current

smokers (smoked on average ≥1 cigarette/day at the time of the visit or gave up smoking <1

year before the visit); former smokers, between 1 and 5 years (gave up smoking up to 5 years

before the visit); former smokers, more than 5 years; and never smokers (never smoked

regularly, defined as an average ≥1 cigarette/day). Other phenotypes of interest are available

in supplementary material.

4.4 Infinium Methylation 450K technology

In the REGICOR study, DNA was extracted from whole peripheral blood collected in 10 mL

EDTA tubes using a standardized method (Puregen TM; Gentra Systems). In the Framingham

Offspring Study, DNA was extracted from buffy coat using the same method. DNA methylation

was assessed using the Illumina HumanMethylation450 BeadChip (Illumina), which

interrogates 485,577 CpGs, following the Illumina Infinium HD Methylation protocol in both

studies. (37,38) Infinium Methylation 450K is an array-based technology allowing a maximum

of 12 samples for each Beadchip. Each analysis runs onto a plate where it is possible to

accommodate 8 Beadchips, permitting processing of 96 samples in a batch. (39)

The 645 REGICOR samples were analyzed in 7 batches in 2 laboratories of the Spanish National

Genotyping Centre: the Centre for Genomic Regulation in Barcelona (n=187) and the Centro

Nacional de Investigaciones Oncológicas in Madrid (n= 458). Two duplicated samples were

included in all the batches as an internal quality control. In the Framingham Offspring Study,

2,542 samples were analyzed distributed in 30 batches in two different laboratories (n=499

and 2,043). (5,40) Duplicated samples were also included.

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M-values were calculated according to Equation 1 and β-values were calculated using Equation

2:

(1)

i

ivalue

U

MM 2log (2)

ii

ivalue

UM

M

Where: Mi is the intensity of methylated probes, Ui is the intensity of unmethylated probes

and α is a constant offset that takes values of 1 and 100 in the respective equations.

An M-value close to 0 means the CpG site is about half-methylated. Positive M-values mean

that there are more methylated than unmethylated cytosines; negative M-values indicate the

opposite ratio. β-value ranges between 0 (completely unmethylated) to 1 (completely

methylated). M-value was the main outcome variable due to its good statistical properties.

(42,42)

We assessed the quality control of the methylation data using a well-defined pipeline (see

Supplementary material) and standardized the M-values for batches following Equation 3:

(3)

)1(

)(

)(

2

n

XX

XXZ ;

Where: Z = standardized M-value (M-stand), X= M-value for a specific individual, X = mean of

M-value for a specific batch and n= sample size.

4.5. Statistical analysis

All the analyses were carried out by robust multivariable linear regression. For each association

test, methylation was considered as the independent variable and lipid traits (TC, LDL-c, HDL-c

and logarithm of TG) were considered as the outcome or dependent variables. We defined two

models for each lipid trait: Model 1, adjusted for a pre-defined set of variables including sex,

age, smoking status, batch effect and estimated cell count, and Model 2, additionally adjusted

for surrogate variables to control for unmeasured potential confounding variables, including

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technical, environmental or demographic variables. (43) Cell count was estimated using

Houseman’s algorithm implemented in R::minfi and surrogate variables were estimated using

the R::sva R package. (44-46)

We passed on to the validation stage those CpG sites associated with lipid traits which

exceeded an arbitrary p-value threshold of 1x10-05 for either of the two models.

Finally, we performed a fixed-effects meta-analysis using data from the REGICOR study and

Framingham Offspring Study for both models. We declared as statistically significant any

association that fulfilled the Bonferroni criteria applied according to the number of probes that

passed the quality control (p-value <1.17x10-07; 0.05/427,948 probes that passed the quality

control). We also performed sensitivity analyses to detect for possible confounding factors,

excluding those participants receiving treatment for dyslipidemia and adjusting for diabetes

and BMI. We did not include the patients with stroke in the meta-analysis as they are not

representative of the general population and lipid traits were measured during the acute

phase of the stroke.

We calculated the statistical power of the meta-analysis to replicate those CpGs identified in

the discovery stage: the magnitudes of the associations for the 113 CpGs included in the

validation stage that could be considered as statistically significant, accepting an alpha risk of

1.17x10-07, in a two-sided test and an 80% power are shown in Supplementary Table 3.

4.6. Additional functional and genetic validation

4.6.1. Methylation, gene expression and lipid profile analyses: the GOLDN study

The GOLDN study included families of self-reported European descent with at least two

siblings, recruited from two centers in the National Heart, Lung, and Blood Institute Family

Heart Study: Minneapolis, Minnesota, and Salt Lake City, Utah. (47) An extended description of

the study is provided in the supplementary material.

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Briefly, we used data from the baseline GOLDN visit for the present analysis. The Infinium

HumanMethylation450 BeadChip (Illumina, San Diego, CA, USA) was used to quantify DNA

methylation in CD4+ T-cells. (48,49) For transcriptional profiling, we selected 102 unrelated

GOLDN participants from the extremes of the BMI distribution. We extracted RNA from buffy

coats using the TRIzol method (ThermoFisher Scientific, Waltham, MA, USA) and evaluated the

quality of each RNA using Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to ensure

integrity. We fragmented purified poly A+ RNA by controlled hydrolysis with a weak base,

followed by conversion to cDNA with random-primed reverse transcriptase. We then

incorporated the cDNA into the Illumina libraries and sequenced on the HiSeq2000 platform.

We used the STAR-2 pass method (50) to align pair-end read sequences. We obtained the

aligned read count information for each gene transcript from the STAR output using the

HTSeq-count program. (51) Two samples appeared as outliers and another two individuals

were missing covariate data; the final sample in the analysis was 98 GOLDN participants.

We fitted linear mixed models to test for associations between methylation scores at each CpG

site and gene transcript level, as well as between gene transcript level and lipid phenotypes.

We only used CpG sites that could be mapped to a known gene in the methylation vs.

expression analyses. We set the statistical significance level according to the Bonferroni

principle, α=0.05/9 genes=0.0056.

4.6.2. Genetic variation and lipid profile: aggregated results of the Global Lipid Research

Consortium

We accessed the publicly available and aggregated summary data of the Global Lipid Genetics

Consortium to explore the additive association between genetic variants in the loci of interest

and their corresponding lipid trait. (33)

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5. Funding

This work was supported by the following sources: Agència de Gestió Ajuts Universitaris de

Recerca [2014 SGR 240]; the Spanish Ministry of Economy through the Carlos III Health

Institute [ISCIII-FIS-FEDER-ERDF PI12-00232, PI12-01238, PI11-01801, PI08-1327, PI05-1251,

PI05-1297, PI02-0471, FIS99/0013-01, FIS96/0026-01, FIS93/0568, FIS92/0009-05], and the Red

de Investigación Cardiovascular [RD12/0042/0013, RD12/0042/0020, RD12/0042/0055,

RD12/0042/0061]. S.S-B. was funded by a contract from Instituto de Salud Carlos III FEDER

[IFI14/00007].

GOLDN: The GOLDN study (AND, DA, JO, SA, DKA) was funded by the US National Institute of

Health (NIH)/National Heart, Lung and Blood Institutes (http://www.nhlbi.nih.gov) grants

R01HL104135 and U01HL72524.

6. Conflict of Interest

None declared.

7. Acknowledgments

Elaine M. Lilly, PhD, Writers First Aid, for revision of the English text.

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22

Figure 1: a) Venn diagrams of discovery hits in REGICOR study using model 1 and model 2. b) Venn diagrams of discovery hits in REGICOR study using model 1. c) Venn diagrams of discovery hits in REGICOR study using model 2. d) Venn diagrams of meta-analysis hits in REGICOR study and Framingham Offspring study using model 2.

Model 1 is adjusted for age, sex, smoking exposure, batch effect and estimated cell count, whereas model 2 is adjusted for age, sex, smoking exposure, batch effect, estimated cell count and surrogate variablesTC= total cholesterol, LDL= low-density lipoprotein, HDL=high-density lipoprotein and TG= triglycerides.

23

Table 1: Descriptive characteristics of the participants in the discovery (REGICOR study) and

validation (Framingham Offspring Study) stage.

REGICOR

Framingham Offspring Study

p-value

N=645 N=2,542

Age 63.2 (11.7) 66.3 (8.9) <0.001

Sex, female, n (%) 329 (51.0) 1,378 (54.2) 0.158

Total cholesterol, mg/dL* 208.0 (36.5) 186.0 (37.2) <0.001

LDL cholesterol, mg/dL*‡ 135 (32.3) 105 (31.3) <0.001

HDL cholesterol, mg/dL*‡ 53.0 (12.3) 57.3 (18.2) <0.001

Triglycerides, mg/dL† 89.0 [67.0; 121.0] 102.0 [73.0; 142.0] <0.001

SBP, mmHg*‡ 131.0 (18.5) 126.0 (17.1) <0.001

DBP, mmHg*‡ 76.0 (9.9) 71.6 (10.2) <0.001

Hypertension, n(%) 302 (47.0) 1442 (57.0) <0.001

Diabetes, n (%) 63 (9.8) - -

Glucose, mg/dl‡ 97.7 (20.4) 107 (23.7) <0.001

BMI, Kg/m2‡ 26.9 (4.1) 28.2 (5.4) <0.001

Waist (cm) * 94.2 (11.5) 101 (14.6) <0.001

Obesity, n (%) 128 (19.9) 792 (31.3) <0.001

Smoking status, n (%):

<0.001

Current smokers 107 (16.6) 252 (10.0)

Former 1 to 5 years 31 (4.8) 56 (2.2)

Former >5 years 165 (25.6) 10 (0.4)

Never smokers 342 (53.0) 2212 (87.4)

Cholesterol treatment, n (%) 154 (24.0) 1098 (43.3) <0.001

Diabetes treatment, n (%) 44 (6.9) - -

Blood pressure treatment , n (%) 200 (31.2) 1236 (48.8) <0.001

*Mean (Standard deviation) † Median (Interquartile range) ‡ LDL, Low density lipoprotein; HDL, High density lipoprotein; SBP, Systolic blood pressure; DBP, Diastolic blood pressure; Hypertension, defined as previous treatment or SBP≥140 mmHg or DBP≥90 mmHg; Diabetes, defined as previous treatment or glycaemia ≥126 mg/dL; BMI, Body mass index; Obesity, defined as BMI ≥30 kg/m2.

24

Table 2: Significant CpG sites differentially methylated in relation to different lipids traits (total cholesterol, low-density lipoprotein, high-density lipoprotein and triglycerides) in the discovery, replication and meta-analysis phase using model 2. CpG id, associated gene or transcript, chromosome (chr) location, genomic position, and observed coefficient (coeff) and standard error (SE) of M-stand, q value (p value adjusted for FDR), comparison of coefficients between model 1 and model 2 and heterogeneity (i).

Total Cholesterol (TC)

Previously associated with:

Features Discovery Phase: REGICOR Replication Phase: Framingham Offspring

Study Meta-analysis (Phase1 + Phase2)

CpG Chr. Pos. Gene Coeff SE P-value Coeff SE P-value Coeff SE P-value

cg16000331 22 42230138 SREBF2 9.00 2.03 8.96E-06 3.99 0.96 3.08E-05 4.91 0.87 1.46E-08 -

Low-density lipoprotein (LDL) cholesterol





- - - - - - - - - - - - - -

High-density lipoprotein (HDL) cholesterol





ch.2.101965435R 2 102599003 NA 2.61 0.57 4.77E-06 2.06 0.44 2.33E-06 2.26 0.35 6.57E-11 -

cg09572125 6 33400477 SYNGAP1 -4.22 0.90 2.96E-06 -3.72 0.73 3.41E-07 -3.92 0.57 5.08E-12 Age(52)

cg11024682 17 17730094 SREBF1 -2.72 0.60 5.81E-06 -3.76 0.41 3.10E-20 -3.43 0.34 0.00E+00 TG(6), BMI(12) and

diabetes(17,18)

cg02650017 17 47301614 PHOSPHO1 2.83 0.51 2.81E-08 2.23 0.41 4.49E-08 2.47 0.32 9.77E-15 Diabetes(17,18)

cg27243685 21 43642366 ABCG1 -2.44 0.54 5.72E-06 -4.54 0.40 2.81E-30 -3.80 0.32 0.00E+00 TG(6) and BMI(12)

cg06500161 21 43656587 ABCG1 -3.47 0.63 3.08E-08 -6.16 0.41 4.00E-52 -5.37 0.34 0.00E+00 TG(6), HDL-c(6),

BMI(12) and diabetes(17,18)

Triglycerides





cg19693031 1 145441552 TXNIP -0.04 0.01 1.68E-06 -0.05 0.00 5.72E-26 -0.05 0.00 0.00E+00 Diabetes(17,18,25,26)

cg06690548 4 139162808 SLC7A11 -0.04 0.01 4.86E-07 -0.04 0.00 5.38E-22 -0.04 0.00 0.00E+00 Diabetes(17)

cg03717755 6 16136539 MYLIP 0.06 0.01 7.31E-09 0.05 0.01 2.45E-14 0.05 0.01 0.00E+00 -

cg07504977 10 102131012 NA 0.04 0.01 7.54E-07 0.04 0.01 1.98E-15 0.04 0.00 0.00E+00 Age (52) and BMI(13,53)

25

cg00574958 11 68607622 CPT1A -0.05 0.01 4.68E-06 -0.08 0.01 4.21E-56 -0.07 0.00 0.00E+00 TG(5,6), BMI(12,13) and

diabetes(17)

cg11024682 17 17730094 SREBF1 0.07 0.01 5.63E-09 0.06 0.01 9.81E-26 0.06 0.01 0.00E+00 TG(6), BMI(12) and

diabetes(17,18)

cg27243685 21 43642366 ABCG1 0.06 0.01 2.46E-10 0.07 0.01 2.59E-38 0.06 0.00 0.00E+00 TG(6) and BMI(12)

cg01881899 21 43652704 ABCG1 0.05 0.01 7.41E-07 0.05 0.01 9.56E-19 0.05 0.00 0.00E+00 -

cg02370100 21 43655256 ABCG1 0.05 0.01 4.74E-06 0.04 0.01 6.91E-13 0.04 0.00 0.00E+00 BMI(53)

cg06500161 21 43656587 ABCG1 0.08 0.01 3.34E-19 0.09 0.01 2.28E-67 0.09 0.00 0.00E+00 TG(6), HDL-c(6),

BMI(12) and diabetes(17,18)

NA: Non-annotated gene; All P values were calculated using standardized M values.

26

Table 3. Variability of total and HDL cholesterol, and triglycerides explained by differential methylation of the validated CpG.

Phenotype CpG

Explained variability (%)

REGICOR Framingham

Offspring Study

Total cholesterol

cg16000331 3.84 0.74

LDL cholesterol - - -

HDL cholesterol

cg06500161 4.05 5.53

cg27243685 2.16 2.98

cg02650017 2.13 0.64

cg11024682 1.56 1.41

ch.2.101965435R 1.16 0.82

cg09572125 0.02 0.00

cg06500161+ cg27243685+ cg02650017+ cg11024682+ ch.2.101965435R +

cg09572125 10.33 9.51

Triglycerides

cg06500161 5.00 5.76

cg27243685 3.66 3.36

cg19693031 3.18 3.22

cg00574958 2.96 7.49

cg06690548 2.77 3.34

cg11024682 2.44 1.91

cg01881899 2.37 1.49

cg03717755 1.95 1.17

cg07504977 1.71 2.18

cg02370100 0.69 0.92

cg06500161+ cg27243685+ cg19693031+ cg00574958+ cg06690548+ cg11024682+ cg01881899+ cg03717755+ cg07504977+

cg02370100

16.07

18.89

27

Table 4. Results of the GOLDN study corresponding to the association between methylation at the CpGs of interest and gene expression, and between gene

expression and the corresponding lipid trait.

Methylation-Gene Expression Gene Expression-Lipid trait

Lipid trait CpG Gen Read count Beta SE P-value Beta SE P-value

Total cholesterol

cg16000331 SREBF2 ENSG00000198911 -3182 1080 0.0042 -0.397 0.733 0.5897

HDL cholesterol

cg09572125 SYNGAP1 ENSG00000197283 -812 454 0.0775 1.047 1.98 0.5985

cg11024682 SREBF1 ENSG00000072310 -3329 1139 0.0045 6.706 3.261 0.0429

cg02650017 PHOSPHO1 ENSG00000173868 -55600 42230 0.1918 -44.39 33.01 0.1825

cg06500161 ABCG1 ENSG00000160179 364 542 0.5036 1.921 1.966 0.3314

cg27243685 ABCG1 ENSG00000160179 -318 908 0.7274

cg01881899 ABCG1 ENSG00000160179 -391 2017 0.8468

cg02370100 ABCG1 ENSG00000160179 -1891 1058 0.0778

Triglycerides

cg19693031 TXNIP ENSG00000117289 -59270 30320 0.0542 25.34 20.25 0.2142

cg06690548 SLC7A11 ENSG00000151012 -38 36 0.2950 -0.01 0.018 0.5616

cg03717755 MYLIP ENSG00000007944 -318 598 0.5968 -0.726 0.37 0.0533

cg00574958 CPT1A ENSG00000110090 -7725 3048 0.0133 0.1147 0.87 0.8955

cg11024682 SREBF1 ENSG00000072310 -3329 1139 0.0045 -0.541 0.484 0.2670

cg06500161 ABCG1 ENSG00000160179 364 542 0.5036 -0.332 0.286 0.2499

Beta: linear regression coefficient; SE: standard error of the regression coefficient.

28

Table 5. Aggregated results of the Global Lipids Genetic Consortium: selection of the SNP

showing the lowest p-value for the associations between genetic variants in the loci of interest

and the corresponding lipid trait. (Adapted from Reference 33)

Gene rsID chr pos A1 A2 A1 allele frequency

Regression coefficient

Standard Error

P-value

Total cholesterol

SREBF2 rs2267443 22 42287454 G A 0.5989 0.0115 0.0054 0.0828

HDL-Cholesterol

SYNGAP1 rs211456 6 33389381 T G 0.3654 0.0062 0.0036 0.0618

SREBF1 rs11653007 17 17716662 G C 1 0.0388 0.0112 0.0013

PHOSPHO1 rs648980 17 47303456 C T 0.4617 0.0079 0.0050 0.0120

ABCG1 rs482303 21 43691469 C G NA 0.0261 0.0089 0.0051

Triglycerides

TXNIP rs7212 1 145442254 G C 1.0000 0.0281 0.0120 0.0608

SLC7A11 rs13141329 4 139125405 A T NA 0.0058 0.0047 0.3340

MYLIP rs2072781 6 16147349 T C 0.9195 0.0139 0.0075 0.1270

CPT1A rs7938117 11 68598054 A G 0.3259 0.0155 0.0035 0.0004

SREBF1 rs11653007 17 17716662 C G NA 0.0301 0.0108 0.0087

ABCG1 rs450808 21 43706944 T C 0.2098 0.0192 0.0090 0.0836

29

Abbreviations

TC: total cholesterol

LDL-c: low-density lipoprotein cholesterol

HDL-c: high-density lipoprotein cholesterol

TG: triglycerides

CpG: cytosine-phosphate-guanine

EWAS: epigenome wide association studies

QQ plot: quantile-quantile plot

lncRNA: long non coding RNA

REGICOR: REgistre GIroní del COR

SREBF1: sterol regulatory element binding transcription factor 1

SREBF2: sterol regulatory element binding transcription factor 2

PHOSPHO1: phosphatase, orphan 1

SYNGAP1: synaptic Ras GTPase activating protein 1

ABCG1: ATP binding cassette subfamily G member 1

CPT1A: carnitine palmitoyltransferase 1A

MYLIP: myosin regulatory light chain interacting protein

TXNIP: thioredoxin interacting protein

SLC7A11: solute carrier family 7 (anionic amino acid transporter light chain, xc- system),

member 11

IDOL: inducible degrader of the LDL receptor

PCSK9: proprotein convertase subtilisin/kexin type 9

dbGAP: Database of Genotypes and Phenotypes

1

Identification and validation of seven new loci showing differential DNA methylation

related to serum lipid profile: an epigenome-wide approach. The REGICOR study.

Sayols-Baixeras S: Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital

del Mar Medical Research Institute), Barcelona 08003, Catalonia, Spain; Universitat Pompeu

Fabra (UPF), Barcelona 08003, Catalonia, Spain.

Subirana I: CIBER Epidemiology and Public Health, Barcelona 08003, Catalonia, Spain;

Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical


Lluis-Ganella C: Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del


Civeira F: Unidad Clínica y de Investigación en Lípidos y Arteriosclerosis, Hospital Universitario


Roquer J: Department of Neurology, Neurovascular Research Group, IMIM (Hospital del Mar


Do AN: Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL,

United States of America

Absher D: Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States of America

Cenarro A: Unidad Clínica y de Investigación en Lípidos y Arteriosclerosis, Hospital Universitario


Muñoz D: Cardiovascular Risk and Nutrition Research Group, IMIM (Hospital del Mar Medical


Soriano-Tárraga C: Department of Neurology, Neurovascular Research Group, IMIM (Hospital


Jiménez-Conde J: Department of Neurology, Neurovascular Research Group, IMIM (Hospital


2

Ordovas J: Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University,

Boston, MA, United States of America.

Senti M: Department of Experimental and Health Sciences, Pompeu Fabra University,

Barcelona 08003, Catalonia, Spain.

Aslibekyan S: Department of Epidemiology, School of Public Health, University of Alabama at

Birmingham, Birmingham, AL, United States of America

Marrugat J: Cardiovascular Epidemiology and Genetics Research Group. IMIM (Hospital del


Arnett DK: Dean's Office, College of Public Health, University of Kentucky, Lexington, KY,

United States of America.

Elosua R: Cardiovascular Epidemiology and Genetics Research Group. IMIM (Hospital del Mar


Author for correspondence:

Roberto Elosua, MD, PhD

IMIM, Hospital del Mar Medical Research Institute

Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain

Telephone: (+34) 933 160800

Fax: (+34) 933 160796

Email: [email protected]

mailto:[email protected]

3

Supplementary Material

1. Discussion

Protein encoded by Synaptic Ras GTPase-activating protein 1 (SYNGAP1) is a neuron-specific

Ras and Rap GTPase-activating protein found in high concentrations in the postsynaptic

density; it accelerates inactivation of the small GTPases Ras and Rap. Mutations in this gene

are the major cause of nonsyndromic cognitive disability in humans and in patients with

associated epilepsy or autism. (1) Methylation levels in this SYNGAP1 CpG site also have been

associated with age. (2)

In addition, we discovered an association between SLC7A11 methylation levels and

triglycerides. Solute carrier family 7 (anionic amino acid transporter light chain, system xc–),

member 11 (SLC7A11) encodes a subunit of the xCT transport system, which is responsible for

intracellular cysteine import and has an important role in the intracellular redox state

controlling the glutathione intracellular levels that protect cells from oxidative stress. (3)

Expression of SLC7A11 promotes tumorigenesis and chemotherapy resistance (4) and its

differential expression in U937 cells in response to oxidized LDL has been reported, suggesting

a potential role in the process of atherosclerosis. (5) However, in vivo human data are lacking

and further research is warranted to establish the potential role of this gene in lipid

metabolism regulation.

2.- Methods.

2.1. Other variables

Other related variables were measured for both studies. In the REGICOR study, glucose

concentration was determined by direct methodology (Roche Diagnostics, Basel, Switzerland).

Blood pressure was measured with a periodically calibrated sphygmomanometer (OMRON

4

711). Two systolic (SBP) and diastolic blood pressure (DBP) measurements were taken and the

lower value for each was recorded for the study. A precision scale of easy calibration was used

for weight and height measurement with participants in underwear and barefoot; body mass

index (BMI) was determined as weight divided by squared height (kg/m2). Waist girth at

umbilicus was measured. Diabetes was defined as glycaemia ≥126 mg/dL or self-reported

treatment; obesity was defined as BMI >30 kg/m2.

In the Framingham Offspring Study, glucose concentration was determined by direct

methodology. Two blood pressure measurements were taken and the lower SBP and DBP

values were used in the validation step. Weight and height were measured barefoot and

rounded to the nearest pound and the next lower ¼ inch, respectively. Waist circumference at

umbilicus was also measured to the next lower ¼ inch. Weight, height and waist

measurements were converted to international system unit (kg and cm) for analysis. Body

mass index was determined as weight divided by squared height (kg/m2). Diabetes was defined

as glycaemia ≥126 mg/dL or self-reported treatment.

2.2. Description of the GOLDN study

The GOLDN study included families of self-reported European descent with at least two

siblings, recruited from two centers in the National Heart, Lung, and Blood Institute Family

Heart Study: Minneapolis, Minnesota, and Salt Lake City, Utah. (6) The primary goal of the

GOLDN study was to identify genetic and epigenetic contributions to variability in lipid

response to two interventions: 1) a dietary fat challenge and 2) a 3-week treatment with 160

mg of fenofibrate. For the current analysis, we used samples from the baseline visit, obtained

prior to both interventions. In addition to non-European ancestry, other exclusion criteria

were: age < 18 years; hyperlipidemia, defined as fasting triglycerides ≥1500 mg/dL; history of

5

cardiovascular, renal, or metabolic disease; pregnancy, lactation, or not using contraception in

women of childbearing age.

Methylation: We used the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA,

USA) to quantify DNA methylation in CD4+ T-cells obtained from GOLDN participants using

previously described protocols. (7, 8) Briefly, we generated β scores and detection P-values

using proprietary Illumina Genome Studio software. If the detection P-value exceeded 0.01,

samples were missing more than 1.5% data points, or probes failed to deliver adequate

intensity on 10% or more samples, we excluded these measurements from analysis. We

normalized the β scores that passed such quality control using the ComBat R package (9) to

account for batch effects, and adjusted for differences between Illumina I and II chemistries as

described in a prior publication. (7) Finally, we removed any CpG sites with mismatches

between the annotation file and the mapping of the probe sequence. (7)

RNA-Seq: For transcriptional profiling, we selected 102 unrelated GOLDN from the extremes of

the body mass index distribution, subject to the availability of samples. We extracted RNA

from buffy coats using the TRIzol method (ThermoFisher Scientific, Waltham, MA, USA). We

evaluated the quality of each RNA using Bioanalyzer (Agilent Technologies, Santa Clara, CA,

USA) to ensure integrity. We fragmented purified poly A+ RNA by controlled hydrolysis with a

weak base, followed by conversion to cDNA with random-primed reverse transcriptase. This

fragmentation step randomizes the subsequent sequencing reads across the length of a

transcript, avoiding bias that comes from using only 3’ ends to make cDNA, and yields a

uniform distribution of fragments with a mean size of 150-250 bp. Following second strand

synthesis, the double-stranded cDNA is subjected to end repair, ligation to Illumina sequencing

adapters, and subsequent PCR amplification. We then incorporated the cDNA into the Illumina

libraries and sequenced on the HiSeq2000 platform. We used the STAR-2 pass method (10) to

align pair-end read sequences. We obtained the aligned read count information for each gene

6

transcript from the STAR output using the HTSeq-count program. (11) We loaded the resulting

raw read count files into the R workspace and used EdgeR library's proprietary DGEList data

structure to encapsulate the read counts and all the associated metadata –e.g., sample names,

gene names, and normalization factors. The HTSeq-count procedure, in combination with the

human genome (hg19) Ensembl-based gene transcript file, identified approximately 63,678

gene transcripts. We retained gene transcripts that were represented at least 1 counts per

million reads in at least two samples, yielding the final set of 31,718 gene transcripts. We used

the trimmed mean of M-values method in EdgeR to normalize RNA-Seq data both within and

between samples. We conducted sample-level quality control examining inter-sample

relationships via a multidimensional scaling (MDS) plot. Two samples appeared as outliers on

the MDS plot and another two individuals were missing covariate data; the final sample in the

analysis was 98 GOLDN participants.

Statistical Analysis: We fit linear mixed models to test for associations between methylation

scores at each CpG site and gene transcript level, as well as between gene transcript level and

lipid phenotypes. We only used CpG sites that could be mapped to a known gene in the

methylation vs. expression analyses. That set of models adjusted for age, sex, study site, the

first 4 methylation principal components generated to capture T-cell purity, and the first 6

expression principal components generated to control for batch effects in RNA-seq data as

fixed effects, as well as pedigree as a random effect (lmekin function of the kinship package in

R). The second set of models, fit to test the association between candidate gene expression

and lipid phenotypes, adjusted for age, sex, study site, first 6 expression principal components

as fixed effects, and pedigree as a random effect. We set the statistical significance level

according to the Bonferroni principle, α=0.05/9=0.0056.

7

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Kimberly,R.P. (2013) Genome-wide DNA methylation analysis of systemic lupus erythematosus

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lipids in the Genetics of Lipid-lowering Drugs and Diet Network study. Circulation, 130, 565-72.

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1185-91.

11. Anders,S., Pyl,P.T., Huber,W. (2015) HTSeq—a Python framework to work with high-

throughput sequencing data. Bioinformatics, 31, 166-9.

8

12. Global Lipids Genetics Consortium. (2013) Discovery and refinement of loci associated with

lipid levels. Nat. Genet., 45, 1274–1283.

9

Supplementary Figure 1: a) Manhattan plots for each lipid trait. Continuous line is a threshold for –log10(1E-5), the CpG sites we validated in the

Framingham Offspring studies and meta-analysis; dotted line shows Bonferroni criteria. b) QQ plot showing the relationship between observed and

predicted p-values for each trait.

10

Supplementary Figure 2: Correlation plots between lipid traits and the methylation level of the validated CpGs. Circles represent values of the variable of

the left axis, and continuous line represents the correlation between left axis and bottom axis. In the case of CpGs associated with HDL cholesterol and

triglycerides triangles represent values of the variable of the right axis and dashed line represents the correlation between right axis and bottom axis.

a) Total cholesterol

b) HDL cholesterol

11

c) Triglycerides

12

d) HDL cholesterol and triglycerides

13

Supplementary Table 1: CpG sites differentially methylated in relation to different lipids traits (total cholesterol, low-density lipoprotein, high-density lipoprotein and triglycerides) in the discovery, replication and meta-analysis phase. CpG id, chromosome (chr) location, genomic position, associated gene or transcript, observed Coeffficient (Coeff), standard error (SE) of M-stand, P-value.

Total Cholesterol

Features Discovery Phase: REGICOR Replication Phase: Framingham Offspring Study Meta-analysis (Phase1+Phase2)

Model 1 Model 2 Model 1 Model 2 Model 1 Model 2

cpg chr pos Gene Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value

cg26226879 1 34642305 C1orf94 5.464 1.245 1.1E-05 5.767 1.276 6.2E-06 -1.040 0.686 1.3E-01 -0.949 0.716 1.8E-01 0.475 0.601 4.3E-01 0.659 0.624 2.9E-01

cg00449821 1 155053823 EFNA3 -6.092 1.280 1.9E-06 -6.609 1.388 1.9E-06 -1.343 0.718 6.1E-02 -1.115 0.757 1.4E-01 -2.479 0.626 7.5E-05 -2.376 0.665 3.5E-04

cg05876625 2 108723177 NA 7.060 1.654 2.0E-05 8.115 1.788 5.7E-06 0.481 0.828 5.6E-01 0.747 0.866 3.9E-01 1.799 0.740 1.5E-02 2.148 0.779 5.9E-03

cg24078828 3 149375789 WWTR1 3.623 1.346 7.1E-03 7.404 1.673 9.6E-06 -1.300 0.708 6.6E-02 -1.022 0.957 2.9E-01 -0.233 0.627 7.1E-01 1.057 0.831 2.0E-01

cg06650596 5 1041028 NA -4.630 1.384 8.3E-04 -7.280 1.617 6.8E-06 -0.676 0.682 3.2E-01 -0.506 0.837 5.5E-01 -1.448 0.612 1.8E-02 -1.938 0.744 9.1E-03

cg17878141 5 81521184 ATG10 6.288 1.382 5.4E-06 6.783 1.613 2.6E-05 -0.376 0.710 6.0E-01 -0.408 0.707 5.6E-01 1.014 0.631 1.1E-01 0.751 0.648 2.5E-01

cg24050047 7 33767686 NA 7.934 1.789 9.2E-06 7.856 1.898 3.5E-05 1.467 0.773 5.8E-02 1.383 0.803 8.5E-02 2.485 0.709 4.6E-04 2.366 0.740 1.4E-03

cg23245289 8 37698900 GPR124 -7.135 1.599 8.1E-06 -7.026 1.609 1.3E-05 -0.763 0.845 3.7E-01 -0.547 0.865 5.3E-01 -2.154 0.747 3.9E-03 -1.999 0.762 8.7E-03

cg13457700 10 5708797 ASB13 3.598 1.427 1.2E-02 8.990 1.922 2.9E-06 -0.821 0.677 2.3E-01 -0.257 0.957 7.9E-01 -0.008 0.612 9.9E-01 1.581 0.857 6.5E-02

cg06224551 11 124670268 C11orf61 3.379 1.182 4.2E-03 6.551 1.377 1.9E-06 -0.648 0.717 3.7E-01 -0.386 0.867 6.6E-01 0.435 0.613 4.8E-01 1.584 0.734 3.1E-02

cg23206311 13 33002447 N4BP2L1 5.855 1.527 1.3E-04 7.061 1.594 9.5E-06 0.268 0.690 7.0E-01 0.927 0.847 2.7E-01 1.214 0.629 5.3E-02 2.278 0.748 2.3E-03

cg22138573 13 60718665 DIAPH3 -3.570 1.572 2.3E-02 -9.787 2.085 2.7E-06 -0.677 0.708 3.4E-01 -0.540 0.920 5.6E-01 -1.165 0.646 7.1E-02 -2.048 0.842 1.5E-02

cg26345203 14 23005866 NA 8.898 2.207 5.5E-05 12.122 2.567 2.3E-06 0.755 1.043 4.7E-01 1.314 1.182 2.7E-01 2.242 0.943 1.7E-02 3.205 1.074 2.8E-03

cg26343512 14 77413728 NA 4.084 1.451 4.9E-03 8.059 1.794 7.1E-06 -1.873 0.685 6.2E-03 -2.366 0.990 1.7E-02 -0.788 0.619 2.0E-01 0.065 0.867 9.4E-01

cg10289790 14 105359915 KIAA0284 -2.896 1.453 4.6E-02 -9.827 2.147 4.7E-06 -0.023 0.709 9.7E-01 0.615 0.973 5.3E-01 -0.575 0.637 3.7E-01 -1.163 0.886 1.9E-01

cg24252746 15 45248932 C15orf43 -4.354 1.428 2.3E-03 -7.707 1.664 3.6E-06 0.411 0.723 5.7E-01 0.323 0.778 6.8E-01 -0.561 0.645 3.8E-01 -1.116 0.705 1.1E-01

cg00624589 16 1094742 NA -5.955 1.397 2.0E-05 -6.476 1.398 3.6E-06 -0.997 0.674 1.4E-01 -1.211 0.697 8.2E-02 -1.933 0.607 1.5E-03 -2.259 0.623 2.9E-04

cg04552480 16 12209538 SNX29 6.850 1.567 1.2E-05 8.443 1.829 3.9E-06 -0.789 0.774 3.1E-01 -0.791 0.824 3.4E-01 0.708 0.694 3.1E-01 0.767 0.751 3.1E-01

cg05609864 16 24550579 RBBP6 3.611 1.377 8.7E-03 9.885 2.071 1.8E-06 -1.073 0.750 1.5E-01 -0.687 1.181 5.6E-01 -0.002 0.658 1.0E+00 1.906 1.026 6.3E-02

cg01771247 16 61846623 CDH8 7.134 1.849 1.1E-04 9.034 2.015 7.3E-06 0.898 0.867 3.0E-01 1.314 0.938 1.6E-01 2.021 0.785 1.0E-02 2.689 0.850 1.6E-03

14

cg10361950 18 12039173 NA 3.818 1.390 6.0E-03 7.932 1.743 5.3E-06 0.069 0.748 9.3E-01 1.313 0.977 1.8E-01 0.910 0.658 1.7E-01 2.896 0.852 6.8E-04

cg06747543 19 18589894 ELL 4.069 1.515 7.2E-03 11.458 2.349 1.1E-06 0.335 0.683 6.2E-01 2.472 1.051 1.9E-02 0.965 0.623 1.2E-01 3.971 0.959 3.5E-05

cg20319775 20 10653482 JAG1 3.743 1.463 1.0E-02 9.379 2.031 3.9E-06 -0.932 0.704 1.9E-01 -0.400 1.033 7.0E-01 -0.053 0.634 9.3E-01 1.609 0.920 8.0E-02

cg16000331 22 42230138 SREBF2 5.646 1.608 4.5E-04 8.997 2.026 9.0E-06 2.531 0.828 2.2E-03 3.995 0.959 3.1E-05 3.183 0.736 1.5E-05 4.910 0.867 1.5E-08

Low-density Lipoprotein Cholesterol




cg07962812 1 183441443 SMG7 3.866 1.193 1.2E-03 6.479 1.428 5.7E-06 -0.261 0.608 6.7E-01 -0.032 0.702 9.6E-01 0.591 0.542 2.8E-01 1.234 0.630 5.0E-02

cg00753676 4 38662991 FLJ13197 -3.758 1.354 5.5E-03 -8.595 1.874 4.5E-06 -2.183 0.659 9.3E-04 -2.880 0.804 3.4E-04 -2.484 0.593 2.8E-05 -3.768 0.738 3.4E-07

cg15619673 7 16625816 NA -4.350 1.226 3.9E-04 -6.597 1.448 5.2E-06 -0.783 0.603 1.9E-01 -0.934 0.671 1.6E-01 -1.478 0.541 6.3E-03 -1.935 0.609 1.5E-03

cg15123809 10 105254427 NEURL -5.224 1.354 1.1E-04 -6.378 1.434 8.7E-06 -0.464 0.663 4.8E-01 -0.283 0.750 7.1E-01 -1.385 0.596 2.0E-02 -1.591 0.664 1.7E-02

cg04413986 12 57119373 NACA 4.097 1.235 9.1E-04 7.590 1.557 1.1E-06 -0.372 0.620 5.5E-01 -0.129 0.769 8.7E-01 0.527 0.554 3.4E-01 1.385 0.690 4.5E-02

cg15899743 14 22985112 NA 6.341 1.929 1.0E-03 11.276 2.477 5.3E-06 1.201 0.951 2.1E-01 2.224 1.176 5.9E-02 2.206 0.853 9.7E-03 3.888 1.062 2.5E-04

cg26345203 14 23005866 NA 7.541 2.023 1.9E-04 10.482 2.322 6.4E-06 1.159 0.917 2.1E-01 1.759 1.048 9.3E-02 2.246 0.835 7.1E-03 3.236 0.955 7.1E-04

cg10289790 14 105359915 KIAA0284 -2.622 1.285 4.1E-02 -8.492 1.918 9.5E-06 0.191 0.602 7.5E-01 0.705 0.816 3.9E-01 -0.316 0.545 5.6E-01 -0.705 0.751 3.5E-01

cg24252746 15 45248932 C15orf43 -4.046 1.241 1.1E-03 -7.116 1.496 2.0E-06 -0.209 0.612 7.3E-01 -0.309 0.657 6.4E-01 -0.959 0.549 8.0E-02 -1.410 0.601 1.9E-02

cg05609864 16 24550579 RBBP6 3.326 1.228 6.8E-03 9.204 1.836 5.4E-07 -0.676 0.646 3.0E-01 -0.572 1.016 5.7E-01 0.192 0.572 7.4E-01 1.721 0.889 5.3E-02

cg22322184 19 7734203 RETN -4.778 1.656 3.9E-03 -10.384 2.345 9.5E-06 -0.186 0.875 8.3E-01 0.298 1.100 7.9E-01 -1.188 0.774 1.2E-01 -1.630 0.996 1.0E-01

cg06747543 19 18589894 ELL 3.834 1.363 4.9E-03 10.415 2.172 1.6E-06 0.459 0.613 4.5E-01 1.975 0.912 3.0E-02 1.027 0.559 6.6E-02 3.239 0.841 1.2E-04

High-density Lipoprotein Cholesterol




cg07395004 1 1310147 AURKAIP1 1.252 0.436 4.1E-03 2.632 0.567 3.5E-06 0.303 0.329 3.6E-01 0.592 0.466 2.0E-01 0.647 0.263 1.4E-02 1.414 0.360 8.6E-05

cg20312179 1 51981505 EPS15 1.742 0.479 2.7E-04 2.603 0.548 2.0E-06 0.217 0.387 5.7E-01 0.131 0.419 7.5E-01 0.820 0.301 6.4E-03 1.045 0.333 1.7E-03

15

ch.2.101965435R 2 102599003 NA 1.152 0.415 5.5E-03 2.610 0.570 4.8E-06 1.186 0.339 4.7E-04 2.060 0.436 2.3E-06 1.173 0.263 8.1E-06 2.263 0.346 6.6E-11

cg03555914 2 121554810 GLI2 -1.242 0.403 2.1E-03 -3.269 0.692 2.3E-06 0.166 0.310 5.9E-01 -0.275 0.624 6.6E-01 -0.357 0.246 1.5E-01 -1.617 0.463 4.8E-04

cg03128029 2 203143288 NOP58 1.922 0.626 2.1E-03 3.611 0.785 4.3E-06 1.214 0.511 1.7E-02 1.419 0.606 1.9E-02 1.497 0.396 1.6E-04 2.237 0.480 3.1E-06

cg00959259 3 122281975 PARP9; DTX3L

1.881 0.419 7.1E-06 2.342 0.434 6.6E-08 0.112 0.361 7.6E-01 0.046 0.371 9.0E-01 0.866 0.273 1.5E-03 1.015 0.282 3.1E-04

cg01277372 3 169378764 MECOM -1.591 0.457 5.0E-04 -3.079 0.671 4.4E-06 -0.532 0.384 1.7E-01 -0.897 0.504 7.5E-02 -0.971 0.294 9.7E-04 -1.683 0.403 2.9E-05

cg27338287 3 190580644 LOC647309 -2.249 0.501 7.3E-06 -2.812 0.557 4.5E-07 -0.363 0.363 3.2E-01 -0.341 0.400 3.9E-01 -1.012 0.294 5.8E-04 -1.180 0.325 2.8E-04

cg03838769 4 168156467 SPOCK3 1.891 0.431 1.2E-05 2.234 0.460 1.2E-06 -0.207 0.327 5.3E-01 -0.276 0.336 4.1E-01 0.559 0.260 3.2E-02 0.598 0.272 2.8E-02

cg02111504 5 93954110 C5orf36; ANKRD32; C5orf36

1.052 0.424 1.3E-02 2.753 0.617 8.1E-06 -0.119 0.322 7.1E-01 -0.506 0.535 3.4E-01 0.309 0.256 2.3E-01 0.893 0.404 2.7E-02

cg08530041 5 168093430 SLIT3 -1.394 0.409 6.4E-04 -2.776 0.628 9.8E-06 0.513 0.313 1.0E-01 0.602 0.404 1.4E-01 -0.193 0.249 4.4E-01 -0.388 0.340 2.5E-01

cg09572125 6 33400477 SYNGAP1 -4.029 0.876 4.2E-06 -4.222 0.903 3.0E-06 -3.647 0.702 2.1E-07 -3.716 0.729 3.4E-07 -3.797 0.548 4.2E-12 -3.915 0.567 5.1E-12

cg03667621 7 1478715 MICALL2 -1.435 0.422 6.7E-04 -2.750 0.601 4.8E-06 0.394 0.324 2.2E-01 0.539 0.624 3.9E-01 -0.283 0.257 2.7E-01 -1.166 0.433 7.1E-03

cg08549335 7 30387954 ZNRF2 1.630 0.449 2.8E-04 2.220 0.480 3.7E-06 1.104 0.381 3.7E-03 1.202 0.413 3.6E-03 1.324 0.290 5.1E-06 1.635 0.313 1.7E-07

cg02902261 7 72991150 TBL2 -1.757 0.398 1.0E-05 -3.004 0.533 1.8E-08 -0.196 0.326 5.5E-01 -0.488 0.420 2.5E-01 -0.823 0.252 1.1E-03 -1.451 0.330 1.1E-05

cg19126110 7 115263754 NA 1.635 0.437 1.8E-04 2.450 0.495 7.5E-07 0.398 0.355 2.6E-01 0.346 0.411 4.0E-01 0.890 0.275 1.2E-03 1.203 0.316 1.4E-04

cg25097801 8 23315147 ENTPD4 1.127 0.405 5.4E-03 2.230 0.500 8.4E-06 0.016 0.317 9.6E-01 0.006 0.446 9.9E-01 0.438 0.249 7.9E-02 0.989 0.333 3.0E-03

cg27342720 8 120033982 NA 1.842 0.525 4.4E-04 3.356 0.664 4.3E-07 1.061 0.415 1.1E-02 1.177 0.475 1.3E-02 1.362 0.326 2.9E-05 1.915 0.387 7.2E-07

cg14364472 9 139394549 NOTCH1 -1.934 0.423 4.8E-06 -2.061 0.440 2.9E-06 -0.042 0.320 9.0E-01 -0.106 0.324 7.4E-01 -0.732 0.255 4.1E-03 -0.794 0.261 2.4E-03

cg18659867 10 80007739 NA 1.468 0.571 1.0E-02 3.881 0.772 5.0E-07 0.446 0.476 3.5E-01 0.552 0.625 3.8E-01 0.865 0.365 1.8E-02 1.869 0.486 1.2E-04

cg14758812 10 103090818 NA 1.514 0.440 5.8E-04 2.331 0.519 7.2E-06 0.392 0.363 2.8E-01 0.332 0.388 3.9E-01 0.847 0.280 2.5E-03 1.047 0.311 7.5E-04

cg13613180 11 74560694 XRRA1 -1.622 0.424 1.3E-04 -2.267 0.506 7.5E-06 -0.683 0.353 5.3E-02 -1.065 0.402 8.1E-03 -1.068 0.271 8.3E-05 -1.530 0.315 1.2E-06

cg12669088 12 25541364 NA 1.809 0.648 5.2E-03 4.101 0.862 2.0E-06 1.023 0.535 5.6E-02 1.395 0.724 5.4E-02 1.342 0.413 1.1E-03 2.514 0.555 5.8E-06

cg07511188 12 51442144 LETMD1 1.250 0.424 3.2E-03 2.486 0.562 9.7E-06 0.422 0.317 1.8E-01 0.791 0.462 8.7E-02 0.720 0.254 4.6E-03 1.474 0.357 3.6E-05

cg25736198 12 72345225 TPH2 1.685 0.504 8.2E-04 2.674 0.584 4.7E-06 0.632 0.396 1.1E-01 0.631 0.444 1.5E-01 1.034 0.311 8.9E-04 1.378 0.353 9.5E-05

cg11827629 12 115822424 NA 1.474 0.492 2.7E-03 2.897 0.646 7.4E-06 0.504 0.373 1.8E-01 0.507 0.448 2.6E-01 0.858 0.297 3.9E-03 1.282 0.368 4.9E-04

cg10415314 14 33949227 NPAS3 2.052 0.598 6.0E-04 3.086 0.688 7.3E-06 1.146 0.430 7.7E-03 1.232 0.482 1.1E-02 1.455 0.349 3.1E-05 1.841 0.395 3.1E-06

cg26948596 14 93078627 RIN3 -1.270 0.405 1.7E-03 -2.988 0.652 4.6E-06 -0.048 0.310 8.8E-01 -0.689 0.512 1.8E-01 -0.499 0.246 4.3E-02 -1.566 0.403 1.0E-04

16

cg16743005 16 50403128 BRD7 1.131 0.444 1.1E-02 2.861 0.609 2.6E-06 0.224 0.316 4.8E-01 0.514 0.512 3.2E-01 0.529 0.257 4.0E-02 1.485 0.392 1.5E-04

cg07839457 16 57023022 NLRC5 2.212 0.482 4.4E-06 1.946 0.475 4.1E-05 0.315 0.369 3.9E-01 0.269 0.382 4.8E-01 0.930 0.291 1.4E-03 1.019 0.299 6.6E-04

cg16411857 16 57023191 NLRC5 2.459 0.485 4.0E-07 1.634 0.416 8.4E-05 0.361 0.352 3.0E-01 0.331 0.375 3.8E-01 0.892 0.268 8.9E-04 1.126 0.296 1.5E-04

cg26561196 16 68344680 SLC7A6OS; PRMT7

2.559 0.540 2.2E-06 1.353 0.415 1.1E-03 0.125 0.327 7.0E-01 0.151 0.463 7.4E-01 0.595 0.257 2.1E-02 1.172 0.352 8.6E-04

cg11024682 17 17730094 SREBF1 -2.718 0.600 5.8E-06 -1.556 0.427 2.7E-04 -2.382 0.331 6.5E-13 -3.762 0.408 3.1E-20 -2.072 0.262 2.4E-15 -3.431 0.337 0.0E+00

cg27466042 17 36896370 PCGF2 -2.354 0.507 3.4E-06 -1.560 0.404 1.1E-04 0.201 0.304 5.1E-01 0.094 0.365 8.0E-01 -0.436 0.243 7.3E-02 -0.742 0.296 1.2E-02

cg02650017 17 47301614 PHOSPHO1 2.827 0.509 2.8E-08 1.757 0.428 4.1E-05 1.494 0.350 2.0E-05 2.234 0.408 4.5E-08 1.599 0.271 3.7E-09 2.466 0.319 9.8E-15

cg18942579 17 57915773 TMEM49 2.289 0.517 9.7E-06 1.808 0.475 1.4E-04 0.494 0.385 2.0E-01 0.445 0.419 2.9E-01 1.014 0.299 7.0E-04 1.176 0.326 3.1E-04

cg08533242 20 62195615 PRIC285 -2.375 0.506 2.7E-06 -1.559 0.401 1.0E-04 0.245 0.323 4.5E-01 0.171 0.392 6.6E-01 -0.464 0.251 6.5E-02 -0.783 0.310 1.2E-02

cg27243685 21 43642366 ABCG1 -2.438 0.537 5.7E-06 -1.665 0.391 2.1E-05 -3.218 0.334 5.1E-22 -4.540 0.397 2.8E-30 -2.564 0.254 0.0E+00 -3.798 0.319 0.0E+00

cg06500161 21 43656587 ABCG1 -3.475 0.628 3.1E-08 -1.925 0.403 1.7E-06 -4.048 0.329 8.2E-35 -6.159 0.405 4.0E-52 -3.199 0.255 0.0E+00 -5.369 0.341 0.0E+00

cg14627538 21 48082402 PRMT2 -3.139 0.666 2.5E-06 -1.257 0.417 2.6E-03 -0.135 0.310 6.6E-01 -0.705 0.483 1.4E-01 -0.533 0.249 3.2E-02 -1.544 0.391 7.9E-05

cg03339016 22 19279085 CLTCL1 3.092 0.599 2.5E-07 1.203 0.432 5.3E-03 -0.359 0.308 2.4E-01 -0.893 0.470 5.7E-02 0.167 0.251 5.0E-01 0.623 0.370 9.2E-02

cg16838132 22 39913220 SMCR7L -1.722 0.385 7.8E-06 -1.557 0.366 2.1E-05 -0.339 0.327 3.0E-01 -0.337 0.323 3.0E-01 -0.880 0.244 3.0E-04 -0.909 0.248 2.4E-04

Triglycerides




cg21268984 1 8720599 RERE 0.037 0.011 4.3E-04 0.070 0.014 1.3E-06 0.015 0.007 3.0E-02 0.024 0.008 2.7E-03 0.021 0.006 2.0E-04 0.035 0.007 6.8E-07

cg19693031 1 145441552 TXNIP -0.033 0.009 1.4E-04 -0.043 0.009 1.7E-06 -0.041 0.004 1.0E-20 -0.051 0.005 5.7E-26 -0.039 0.004 0.0E+00 -0.049 0.004 0.0E+00

cg04282029 1 149890655 SV2A 0.036 0.008 6.6E-06 0.052 0.010 4.2E-07 -0.002 0.005 6.1E-01 -0.005 0.006 3.5E-01 0.007 0.004 7.7E-02 0.008 0.005 1.1E-01

cg24926185 1 151557485 NA 0.035 0.007 3.3E-06 0.041 0.009 3.0E-06 -0.001 0.004 7.3E-01 -0.002 0.004 6.9E-01 0.007 0.004 5.2E-02 0.007 0.004 8.6E-02

cg14615868 1 236558696 EDARADD 0.026 0.007 2.1E-04 0.038 0.008 1.4E-06 -0.001 0.004 7.8E-01 0.000 0.005 9.8E-01 0.006 0.004 8.8E-02 0.009 0.004 1.6E-02

cg15707428 2 11679845 GREB1 0.032 0.007 6.2E-06 0.036 0.008 1.2E-05 0.003 0.004 4.8E-01 0.004 0.005 4.1E-01 0.011 0.004 2.8E-03 0.012 0.004 3.3E-03

cg25265126 2 113891507 IL1RN 0.045 0.010 7.9E-06 0.045 0.011 2.5E-05 0.008 0.006 2.1E-01 0.008 0.007 2.3E-01 0.018 0.005 6.6E-04 0.018 0.006 1.2E-03

cg15353603 2 162915902 DPP4 -0.036 0.012 2.4E-03 -0.079 0.015 2.4E-07 -0.009 0.008 2.6E-01 -0.010 0.009 2.3E-01 -0.016 0.006 1.0E-02 -0.027 0.008 3.2E-04

17

cg15726700 3 196370254 LRRC33 0.037 0.012 1.7E-03 0.066 0.014 5.9E-06 0.001 0.007 9.3E-01 0.006 0.009 4.9E-01 0.011 0.006 8.6E-02 0.023 0.008 2.8E-03

cg16868776 4 976565 SLC26A1 0.035 0.008 5.3E-06 0.039 0.009 6.6E-06 0.000 0.005 9.8E-01 -0.002 0.005 7.3E-01 0.009 0.004 2.2E-02 0.008 0.004 5.6E-02

cg14577840 4 16257979 FLJ39653 0.034 0.008 9.8E-06 0.036 0.008 1.7E-05 0.003 0.004 5.2E-01 0.003 0.005 5.9E-01 0.011 0.004 5.3E-03 0.011 0.004 9.6E-03

cg02951062 4 74269908 ALB 0.033 0.007 7.9E-06 0.036 0.008 1.6E-05 -0.003 0.004 5.0E-01 -0.004 0.005 3.7E-01 0.007 0.004 8.1E-02 0.005 0.004 1.9E-01

cg02941135 4 81122314 PRDM8 0.029 0.007 1.6E-05 0.032 0.007 8.6E-06 -0.005 0.004 2.8E-01 -0.005 0.005 2.6E-01 0.005 0.004 1.4E-01 0.005 0.004 1.6E-01

cg06690548 4 139162808 SLC7A11 -0.033 0.008 2.1E-05 -0.040 0.008 4.9E-07 -0.042 0.005 1.5E-20 -0.044 0.005 5.4E-22 -0.040 0.004 0.0E+00 -0.043 0.004 0.0E+00

cg07285213 5 1292339 TERT 0.037 0.007 6.9E-07 0.041 0.008 3.0E-07 0.002 0.005 6.5E-01 0.001 0.005 9.0E-01 0.011 0.004 3.0E-03 0.012 0.004 4.8E-03

cg22656956 5 137475177 NME5 0.033 0.010 8.6E-04 0.064 0.014 3.6E-06 0.007 0.006 2.5E-01 0.015 0.007 4.1E-02 0.014 0.005 6.8E-03 0.026 0.006 7.3E-05

cg03717755 6 16136539 MYLIP 0.049 0.009 2.2E-07 0.062 0.011 7.3E-09 0.038 0.006 2.0E-10 0.051 0.007 2.5E-14 0.041 0.005 4.4E-16 0.054 0.006 0.0E+00

cg26222229 6 36842844 PPIL1 -0.022 0.008 5.5E-03 -0.060 0.013 2.3E-06 -0.002 0.004 5.9E-01 0.002 0.007 7.7E-01 -0.007 0.004 6.9E-02 -0.013 0.006 3.8E-02

cg02127509 6 135516936 MYB 0.042 0.011 1.5E-04 0.062 0.013 3.8E-06 0.003 0.006 6.5E-01 0.006 0.007 4.2E-01 0.012 0.005 2.5E-02 0.018 0.006 3.8E-03

cg27462497 7 2633190 IQCE -0.029 0.007 8.1E-05 -0.036 0.008 2.4E-06 0.004 0.004 3.4E-01 0.004 0.004 3.6E-01 -0.005 0.004 2.3E-01 -0.006 0.004 1.1E-01

cg15140703 7 99775532 STAG3; GPC2

0.037 0.008 1.1E-05 0.041 0.008 1.6E-06 0.000 0.005 9.9E-01 0.001 0.005 8.7E-01 0.010 0.004 2.4E-02 0.012 0.004 7.4E-03

cg09608424 7 141630158 CLEC5A 0.033 0.007 9.8E-06 0.042 0.009 6.8E-07 0.003 0.004 5.6E-01 0.003 0.005 5.6E-01 0.010 0.004 6.1E-03 0.013 0.004 2.7E-03

cg22643879 8 10149407 MSRA 0.034 0.008 1.0E-05 0.045 0.010 6.5E-06 -0.005 0.005 2.3E-01 -0.007 0.005 1.5E-01 0.005 0.004 2.2E-01 0.004 0.005 4.1E-01

cg00721800 8 77618385 ZFHX4 -0.018 0.007 1.2E-02 -0.042 0.009 8.1E-06 -0.002 0.004 6.2E-01 -0.003 0.006 6.5E-01 -0.006 0.004 8.1E-02 -0.013 0.005 6.5E-03

cg17293161 10 80141089 NA -0.031 0.009 3.4E-04 -0.040 0.009 9.0E-06 0.005 0.004 3.0E-01 0.007 0.005 1.7E-01 -0.003 0.004 4.8E-01 -0.004 0.004 3.7E-01

cg07504977 10 102131012 NA 0.034 0.008 8.7E-06 0.044 0.009 7.5E-07 0.033 0.005 8.5E-12 0.042 0.005 2.0E-15 0.033 0.004 4.4E-16 0.043 0.005 0.0E+00

cg00574958 11 68607622 CPT1A -0.031 0.008 1.0E-04 -0.050 0.011 4.7E-06 -0.063 0.004 1.0E-44 -0.080 0.005 4.2E-56 -0.055 0.004 0.0E+00 -0.075 0.005 0.0E+00

cg21958090 11 112752496 NA 0.029 0.007 8.8E-06 0.031 0.007 1.4E-05 -0.002 0.005 7.2E-01 -0.001 0.005 7.9E-01 0.008 0.004 2.7E-02 0.009 0.004 2.4E-02

cg13046832 14 29254680 C14orf23 0.039 0.010 1.1E-04 0.047 0.010 4.6E-06 0.005 0.005 3.8E-01 0.007 0.006 2.3E-01 0.013 0.005 8.7E-03 0.017 0.005 8.9E-04

cg16058274 14 94179847 NA -0.031 0.008 1.4E-04 -0.045 0.009 1.5E-07 0.004 0.005 3.5E-01 0.006 0.005 2.5E-01 -0.004 0.004 3.1E-01 -0.007 0.004 1.1E-01

cg10845124 15 101984550 PCSK6 -0.023 0.010 2.0E-02 -0.063 0.014 7.8E-06 0.000 0.005 9.6E-01 0.002 0.006 7.8E-01 -0.005 0.004 2.7E-01 -0.009 0.006 1.2E-01

cg08708323 16 1728724 HN1L -0.034 0.007 4.8E-06 -0.034 0.008 9.7E-06 -0.003 0.004 5.1E-01 -0.003 0.005 5.8E-01 -0.011 0.004 3.4E-03 -0.011 0.004 6.0E-03

cg11024682 17 17730094 SREBF1 0.036 0.008 3.3E-06 0.065 0.011 5.6E-09 0.039 0.005 3.2E-16 0.061 0.006 9.8E-26 0.038 0.004 0.0E+00 0.062 0.005 0.0E+00

cg06971602 17 35306010 AATF 0.023 0.008 2.8E-03 0.045 0.010 5.3E-06 -0.005 0.004 2.1E-01 -0.005 0.006 3.6E-01 0.001 0.004 7.4E-01 0.007 0.005 1.3E-01

cg27657459 17 54853771 NA 0.035 0.008 2.5E-06 0.041 0.009 2.7E-06 0.001 0.004 8.3E-01 0.000 0.004 9.2E-01 0.010 0.004 1.0E-02 0.009 0.004 2.7E-02

18

cg22244768 17 55634551 MSI2 -0.021 0.007 3.1E-03 -0.041 0.009 2.7E-06 0.007 0.004 1.1E-01 0.010 0.005 3.9E-02 0.000 0.004 9.0E-01 -0.002 0.004 6.4E-01

cg03148858 19 3047978 TLE2 0.038 0.009 5.2E-05 0.046 0.010 2.1E-06 -0.004 0.005 4.8E-01 -0.003 0.005 6.0E-01 0.006 0.004 1.9E-01 0.009 0.005 6.4E-02

cg27243685 21 43642366 ABCG1 0.044 0.008 6.5E-08 0.061 0.010 2.5E-10 0.047 0.004 6.7E-28 0.065 0.005 2.6E-38 0.047 0.004 0.0E+00 0.064 0.004 0.0E+00

cg01881899 21 43652704 ABCG1 0.034 0.008 1.4E-05 0.047 0.010 7.4E-07 0.037 0.005 9.9E-15 0.050 0.006 9.6E-19 0.036 0.004 0.0E+00 0.049 0.005 0.0E+00

cg02370100 21 43655256 ABCG1 0.027 0.008 1.0E-03 0.047 0.010 4.7E-06 0.029 0.005 2.3E-09 0.040 0.006 6.9E-13 0.028 0.004 9.5E-12 0.041 0.005 0.0E+00

cg06500161 21 43656587 ABCG1 0.049 0.007 5.0E-11 0.083 0.009 3.3E-19 0.060 0.004 4.6E-43 0.090 0.005 2.3E-67 0.057 0.004 0.0E+00 0.088 0.005 0.0E+00

cg02288017 X 16803667 CXorf15 0.039 0.008 2.0E-07 0.040 0.008 4.1E-07 -0.001 0.005 7.6E-01 -0.001 0.005 8.1E-01 0.010 0.004 1.1E-02 0.010 0.004 1.5E-02

cg01275664 X 34405983 NA -0.045 0.010 7.7E-06 -0.049 0.011 3.7E-06 -0.011 0.005 3.3E-02 -0.012 0.005 2.5E-02 -0.018 0.005 8.8E-05 -0.019 0.005 4.5E-05

NA: Non-annotated gene; All P values were calculated using standardized M values.

Model 1 is adjusted for age, sex, smoking exposure, batch effect and estimated cell count. Model 2 is adjusted for age, sex, smoking exposure, batch effect, estimated cell

count and surrogate variables.

19

Supplementary Table 2: Sensitivity analysis using Model 1 and Model 2 further adjusted for diabetes, BMI and exclusion of participants taking cholesterol-lowering drugs.

CpG id, observed coefficient (Coeff), standard error (SE) of M-stand, P-value.

Total Cholesterol

Features Model 1 Model 2

Diabetes BMI Excluding Treated Participants Diabetes BMI Excluding Treated Participants

cpg Coeff SE P-value Coeff. SE P-value Coeff SE P-value Coeff. SE P-value Coeff SE P-value Coeff SE P-value

cg26226879 4.814 1.262 1.37E-04 5.556 1.257 9.83E-06 5.474 1.466 1.88E-04 5.124 1.267 5.22E-05 5.828 1.274 4.80E-06 6.215 1.472 2.43E-05

cg00449821 -5.756 1.242 3.61E-06 -6.004 1.296 3.59E-06 -4.430 1.504 3.23E-03 -6.128 1.376 8.44E-06 -6.500 1.403 3.58E-06 -4.620 1.606 4.02E-03

cg05876625 7.058 1.602 1.05E-05 7.007 1.670 2.72E-05 7.200 1.843 9.38E-05 8.231 1.755 2.72E-06 7.982 1.832 1.32E-05 8.545 2.034 2.66E-05

cg24078828 3.299 1.320 1.24E-02 3.622 1.351 7.34E-03 3.676 1.709 3.14E-02 7.076 1.597 9.35E-06 7.344 1.693 1.44E-05 7.528 2.211 6.61E-04

cg06650596 -4.461 1.431 1.83E-03 -4.940 1.340 2.26E-04 -4.181 1.651 1.13E-02 -6.909 1.646 2.71E-05 -7.820 1.525 2.91E-07 -7.277 2.184 8.65E-04

cg17878141 6.300 1.374 4.51E-06 6.465 1.383 2.95E-06 6.694 1.674 6.36E-05 6.762 1.554 1.35E-05 6.936 1.613 1.71E-05 7.614 2.017 1.60E-04

cg24050047 7.404 1.784 3.32E-05 7.948 1.826 1.34E-05 8.476 2.104 5.64E-05 7.293 1.897 1.21E-04 7.839 1.955 6.06E-05 8.440 2.173 1.03E-04

cg23245289 -6.863 1.504 5.01E-06 -7.117 1.600 8.65E-06 -6.181 1.978 1.78E-03 -6.746 1.523 9.40E-06 -7.016 1.603 1.21E-05 -6.169 1.984 1.87E-03

cg13457700 3.176 1.372 2.06E-02 3.614 1.423 1.11E-02 3.981 1.691 1.85E-02 8.595 1.903 6.30E-06 9.009 1.920 2.72E-06 9.893 2.291 1.57E-05

cg06224551 3.539 1.156 2.20E-03 3.421 1.188 3.97E-03 4.203 1.411 2.89E-03 6.842 1.354 4.32E-07 6.625 1.378 1.54E-06 7.243 1.615 7.33E-06

cg23206311 5.804 1.506 1.17E-04 5.761 1.523 1.55E-04 7.032 1.874 1.76E-04 6.939 1.568 9.64E-06 6.988 1.594 1.16E-05 8.125 1.913 2.16E-05

cg22138573 -4.037 1.554 9.41E-03 -3.338 1.566 3.30E-02 -4.702 1.787 8.52E-03 -10.136 2.079 1.09E-06 -9.587 2.128 6.65E-06 -11.160 2.350 2.05E-06

cg26345203 8.591 2.232 1.18E-04 8.910 2.223 6.11E-05 9.733 2.405 5.20E-05 11.906 2.544 2.87E-06 11.959 2.591 3.92E-06 14.513 2.960 9.48E-07

cg26343512 3.772 1.456 9.58E-03 4.145 1.458 4.47E-03 4.410 1.680 8.68E-03 7.774 1.719 6.13E-06 8.078 1.794 6.68E-06 8.349 2.028 3.83E-05

cg10289790 -2.960 1.449 4.10E-02 -2.842 1.451 5.02E-02 -2.958 1.745 9.00E-02 -9.255 2.170 2.00E-05 -9.971 2.159 3.86E-06 -9.300 2.609 3.64E-04

cg24252746 -3.855 1.432 7.09E-03 -4.317 1.423 2.42E-03 -5.092 1.664 2.22E-03 -7.144 1.703 2.74E-05 -7.683 1.668 4.11E-06 -8.550 1.955 1.22E-05

cg00624589 -5.491 1.400 8.74E-05 -5.783 1.415 4.35E-05 -5.608 1.558 3.18E-04 -6.050 1.404 1.65E-05 -6.303 1.411 7.95E-06 -6.132 1.576 1.00E-04

cg04552480 7.065 1.538 4.35E-06 6.954 1.587 1.18E-05 6.993 1.902 2.37E-04 8.756 1.749 5.53E-07 8.516 1.855 4.41E-06 9.064 2.270 6.52E-05

cg05609864 3.176 1.400 2.33E-02 3.642 1.380 8.31E-03 4.547 1.604 4.59E-03 9.377 2.142 1.20E-05 9.829 2.080 2.28E-06 12.165 2.414 4.67E-07

cg01771247 6.717 1.757 1.32E-04 7.095 1.858 1.35E-04 7.980 1.986 5.88E-05 8.623 1.934 8.27E-06 8.914 2.043 1.28E-05 10.833 2.287 2.17E-06

cg10361950 3.580 1.413 1.13E-02 3.861 1.392 5.53E-03 3.904 1.684 2.04E-02 7.739 1.672 3.70E-06 7.928 1.747 5.65E-06 7.700 2.040 1.60E-04

cg06747543 3.557 1.492 1.71E-02 4.102 1.516 6.82E-03 3.498 1.748 4.54E-02 10.705 2.420 9.73E-06 11.438 2.390 1.70E-06 10.129 2.851 3.81E-04

cg20319775 3.250 1.473 2.73E-02 3.743 1.459 1.03E-02 4.227 1.732 1.47E-02 8.746 1.962 8.30E-06 9.243 2.045 6.21E-06 10.167 2.282 8.40E-06

cg16000331 4.872 1.578 2.02E-03 5.704 1.613 4.04E-04 5.342 2.020 8.19E-03 8.036 1.979 4.91E-05 8.950 2.052 1.30E-05 8.322 2.454 6.96E-04

20




cpg Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff. SE P-value

cg07962812 3.590 1.189 2.52E-03 3.886 1.200 1.20E-03 3.235 1.386 1.96E-02 6.122 1.412 1.45E-05 6.507 1.437 5.97E-06 5.787 1.662 4.96E-04

cg00753676 -3.832 1.363 4.93E-03 -3.657 1.352 6.84E-03 -4.486 1.622 5.68E-03 -8.347 1.868 7.92E-06 -8.572 1.892 5.90E-06 -9.606 2.419 7.18E-05

cg15619673 -4.064 1.215 8.22E-04 -4.257 1.233 5.56E-04 -3.953 1.455 6.60E-03 -6.188 1.461 2.29E-05 -6.517 1.453 7.31E-06 -5.990 1.725 5.15E-04

cg15123809 -4.830 1.314 2.36E-04 -5.226 1.358 1.18E-04 -6.385 1.509 2.31E-05 -5.819 1.378 2.41E-05 -6.444 1.433 6.87E-06 -7.729 1.675 3.92E-06

cg04413986 3.438 1.236 5.41E-03 4.190 1.243 7.46E-04 4.654 1.518 2.18E-03 6.695 1.640 4.46E-05 7.734 1.568 8.14E-07 8.658 1.949 8.92E-06

cg15899743 5.960 1.906 1.77E-03 6.413 1.930 8.89E-04 6.677 2.288 3.51E-03 10.744 2.453 1.19E-05 11.223 2.501 7.24E-06 12.535 2.925 1.82E-05

cg26345203 7.271 1.991 2.60E-04 7.566 2.004 1.59E-04 8.009 2.112 1.49E-04 10.315 2.300 7.29E-06 10.420 2.345 8.82E-06 12.078 2.563 2.44E-06

cg10289790 -2.649 1.291 4.01E-02 -2.571 1.295 4.71E-02 -2.918 1.523 5.53E-02 -7.992 1.963 4.69E-05 -8.581 1.914 7.38E-06 -8.369 2.301 2.76E-04

cg24252746 -3.650 1.239 3.21E-03 -4.008 1.238 1.20E-03 -4.725 1.469 1.29E-03 -6.603 1.476 7.63E-06 -7.095 1.501 2.27E-06 -7.931 1.757 6.37E-06

cg05609864 3.045 1.209 1.18E-02 3.369 1.227 6.04E-03 3.693 1.422 9.42E-03 8.984 1.927 3.14E-06 9.173 1.848 6.88E-07 10.513 2.315 5.61E-06

cg22322184 -4.380 1.624 7.00E-03 -4.617 1.689 6.26E-03 -5.125 1.870 6.13E-03 -9.213 2.340 8.23E-05 -10.227 2.407 2.14E-05 -10.391 2.797 2.03E-04

cg06747543 3.473 1.358 1.06E-02 3.874 1.369 4.64E-03 3.282 1.644 4.59E-02 9.794 2.208 9.14E-06 10.483 2.200 1.88E-06 9.311 2.612 3.64E-04




cpg Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value

cg07395004 1.111 0.424 8.82E-03 1.210 0.427 4.60E-03 1.372 0.508 6.93E-03 2.539 0.574 9.57E-06 2.444 0.544 7.07E-06 2.660 0.604 1.06E-05

cg20312179 1.579 0.474 8.60E-04 1.647 0.474 5.11E-04 2.138 0.548 9.46E-05 2.360 0.546 1.53E-05 2.409 0.535 6.62E-06 3.060 0.639 1.67E-06

ch.2.101965435R 0.967 0.399 1.54E-02 1.084 0.408 7.81E-03 1.264 0.473 7.55E-03 2.324 0.568 4.29E-05 2.379 0.573 3.34E-05 2.613 0.635 3.90E-05

cg03555914 -1.237 0.406 2.29E-03 -1.134 0.417 6.53E-03 -1.362 0.471 3.80E-03 -3.237 0.675 1.65E-06 -3.141 0.668 2.59E-06 -3.593 0.783 4.49E-06

cg03128029 1.796 0.633 4.58E-03 1.708 0.627 6.49E-03 1.883 0.757 1.28E-02 3.503 0.796 1.07E-05 3.152 0.788 6.29E-05 3.461 0.922 1.75E-04

cg00959259 1.871 0.388 1.42E-06 1.952 0.394 7.00E-07 1.833 0.470 9.54E-05 2.324 0.422 3.73E-08 2.378 0.410 6.39E-09 2.220 0.509 1.26E-05

cg01277372 -1.568 0.454 5.46E-04 -1.344 0.461 3.52E-03 -1.375 0.551 1.26E-02 -2.906 0.648 7.22E-06 -2.682 0.674 6.89E-05 -2.853 0.833 6.17E-04

cg27338287 -2.070 0.496 3.01E-05 -2.067 0.485 2.03E-05 -2.018 0.606 8.76E-04 -2.532 0.554 4.91E-06 -2.606 0.560 3.26E-06 -2.438 0.682 3.48E-04

cg03838769 1.705 0.431 7.55E-05 1.725 0.423 4.53E-05 2.531 0.485 1.76E-07 2.049 0.444 3.94E-06 2.013 0.448 6.93E-06 2.993 0.508 3.93E-09

cg02111504 0.974 0.403 1.56E-02 0.991 0.426 2.01E-02 1.119 0.504 2.63E-02 2.685 0.602 8.14E-06 2.485 0.626 7.18E-05 2.676 0.719 2.00E-04

cg08530041 -1.297 0.409 1.53E-03 -1.321 0.397 8.74E-04 -1.171 0.479 1.45E-02 -2.583 0.640 5.46E-05 -2.801 0.606 3.82E-06 -2.362 0.726 1.15E-03

21

cg09572125 -3.955 0.791 5.66E-07 -3.255 0.877 2.07E-04 -4.343 1.025 2.27E-05 -4.095 0.817 5.38E-07 -3.421 0.915 1.84E-04 -4.618 1.080 1.89E-05

cg03667621 -1.405 0.422 8.67E-04 -1.360 0.433 1.69E-03 -1.412 0.491 4.01E-03 -2.728 0.601 5.75E-06 -2.722 0.591 4.12E-06 -2.753 0.696 7.60E-05

cg08549335 1.438 0.435 9.36E-04 1.492 0.459 1.14E-03 1.745 0.538 1.19E-03 1.981 0.469 2.40E-05 1.973 0.476 3.40E-05 2.353 0.581 5.21E-05

cg02902261 -1.653 0.396 2.95E-05 -1.516 0.403 1.71E-04 -1.990 0.473 2.63E-05 -2.804 0.528 1.07E-07 -2.705 0.534 4.06E-07 -3.483 0.635 4.12E-08

cg19126110 1.421 0.435 1.08E-03 1.552 0.429 2.97E-04 1.799 0.518 5.14E-04 2.146 0.491 1.24E-05 2.265 0.487 3.31E-06 2.711 0.590 4.38E-06

cg25097801 0.882 0.388 2.31E-02 1.019 0.398 1.05E-02 1.427 0.494 3.88E-03 1.878 0.513 2.52E-04 1.958 0.518 1.57E-04 2.471 0.573 1.59E-05

cg27342720 1.711 0.503 6.65E-04 1.724 0.519 9.07E-04 2.279 0.559 4.58E-05 3.121 0.639 1.03E-06 2.997 0.647 3.66E-06 4.069 0.710 1.00E-08

cg14364472 -1.770 0.422 2.69E-05 -1.649 0.447 2.24E-04 -2.189 0.509 1.72E-05 -1.902 0.436 1.31E-05 -1.760 0.453 1.02E-04 -2.321 0.532 1.27E-05

cg18659867 1.406 0.558 1.17E-02 1.420 0.562 1.16E-02 1.736 0.716 1.53E-02 3.865 0.765 4.32E-07 3.539 0.739 1.65E-06 4.170 0.886 2.51E-06

cg14758812 1.550 0.429 3.04E-04 1.442 0.424 6.67E-04 1.732 0.528 1.04E-03 2.332 0.505 3.80E-06 2.155 0.487 9.46E-06 2.564 0.609 2.59E-05

cg13613180 -1.589 0.432 2.39E-04 -1.402 0.416 7.41E-04 -1.417 0.528 7.29E-03 -2.235 0.513 1.33E-05 -2.006 0.485 3.50E-05 -1.972 0.629 1.71E-03

cg12669088 1.651 0.613 7.05E-03 1.855 0.618 2.70E-03 2.017 0.799 1.15E-02 3.741 0.835 7.36E-06 4.014 0.880 5.05E-06 4.588 1.079 2.12E-05

cg07511188 1.072 0.415 9.83E-03 1.259 0.420 2.73E-03 1.406 0.496 4.60E-03 2.212 0.547 5.19E-05 2.416 0.556 1.38E-05 2.524 0.640 7.96E-05

cg25736198 1.624 0.490 9.21E-04 1.707 0.483 4.04E-04 1.893 0.594 1.44E-03 2.538 0.570 8.45E-06 2.604 0.575 5.91E-06 2.946 0.667 1.01E-05

cg11827629 1.254 0.469 7.51E-03 1.396 0.474 3.26E-03 1.641 0.570 3.99E-03 2.502 0.614 4.57E-05 2.646 0.632 2.85E-05 3.059 0.743 3.83E-05

cg10415314 1.900 0.596 1.42E-03 1.797 0.576 1.81E-03 2.293 0.678 7.17E-04 2.830 0.678 3.02E-05 2.659 0.679 9.03E-05 3.468 0.772 6.97E-06

cg26948596 -1.203 0.394 2.27E-03 -1.123 0.401 5.15E-03 -1.276 0.493 9.64E-03 -2.832 0.646 1.18E-05 -2.813 0.620 5.67E-06 -3.135 0.779 5.72E-05

cg16743005 1.075 0.433 1.32E-02 1.144 0.417 6.09E-03 0.837 0.505 9.74E-02 2.858 0.599 1.83E-06 2.836 0.609 3.19E-06 2.089 0.713 3.41E-03

cg07839457 2.040 0.442 3.95E-06 1.920 0.456 2.60E-05 2.084 0.545 1.33E-04 2.336 0.453 2.46E-07 2.153 0.461 3.04E-06 2.379 0.569 2.89E-05

cg16411857 1.524 0.409 1.96E-04 1.618 0.412 8.60E-05 1.730 0.478 2.97E-04 2.363 0.477 7.17E-07 2.389 0.478 5.73E-07 2.573 0.550 2.95E-06

cg26561196 1.269 0.395 1.33E-03 1.285 0.401 1.35E-03 1.457 0.486 2.73E-03 2.472 0.523 2.28E-06 2.359 0.531 9.02E-06 2.603 0.638 4.47E-05

cg11024682 -1.301 0.437 2.93E-03 -1.148 0.432 7.88E-03 -1.643 0.503 1.09E-03 -2.206 0.600 2.34E-04 -2.092 0.628 8.58E-04 -3.019 0.695 1.39E-05

cg27466042 -1.444 0.399 2.97E-04 -1.389 0.417 8.57E-04 -1.507 0.464 1.16E-03 -2.224 0.507 1.14E-05 -2.129 0.508 2.74E-05 -2.309 0.598 1.14E-04

cg02650017 1.495 0.411 2.73E-04 1.585 0.432 2.42E-04 1.419 0.521 6.47E-03 2.483 0.499 6.51E-07 2.502 0.521 1.58E-06 2.096 0.595 4.29E-04

cg18942579 1.798 0.478 1.67E-04 1.762 0.482 2.55E-04 1.803 0.583 1.99E-03 2.289 0.521 1.10E-05 2.188 0.522 2.78E-05 2.312 0.635 2.73E-04

cg08533242 -1.485 0.403 2.30E-04 -1.370 0.406 7.41E-04 -1.479 0.467 1.54E-03 -2.243 0.505 9.11E-06 -2.168 0.490 9.56E-06 -2.335 0.588 7.06E-05

cg27243685 -1.478 0.394 1.73E-04 -1.236 0.409 2.53E-03 -1.726 0.472 2.58E-04 -2.160 0.520 3.22E-05 -1.878 0.538 4.79E-04 -2.502 0.614 4.54E-05

cg06500161 -1.720 0.410 2.78E-05 -1.517 0.422 3.22E-04 -1.995 0.495 5.56E-05 -3.077 0.641 1.56E-06 -2.836 0.616 4.20E-06 -3.860 0.757 3.36E-07

cg14627538 -1.243 0.405 2.16E-03 -1.059 0.419 1.15E-02 -1.125 0.482 1.97E-02 -3.095 0.650 1.89E-06 -2.836 0.664 1.93E-05 -3.094 0.819 1.59E-04

cg03339016 1.084 0.412 8.45E-03 1.140 0.421 6.76E-03 1.114 0.503 2.69E-02 2.933 0.591 7.08E-07 2.819 0.573 8.70E-07 2.767 0.731 1.53E-04

cg16838132 -1.627 0.358 5.33E-06 -1.590 0.368 1.59E-05 -1.469 0.437 7.70E-04 -1.824 0.372 9.52E-07 -1.787 0.386 3.69E-06 -1.647 0.471 4.73E-04

22

Triglycerides



cpg Coeff SE P-value Coeff SE P-value Coeff. SE P-value Coeff SE P-value Coeff SE P-value Coeff SE P-value

cg21268984 0.035 0.011 8.79E-04 0.029 0.010 5.61E-03 0.041 0.012 4.40E-04 0.066 0.014 4.76E-06 0.059 0.015 7.42E-05 0.073 0.017 1.86E-05

cg19693031 -0.030 0.009 6.24E-04 -0.028 0.008 6.79E-04 -0.032 0.011 2.58E-03 -0.039 0.009 2.99E-05 -0.036 0.009 7.87E-05 -0.046 0.012 7.38E-05

cg04282029 0.035 0.008 7.62E-06 0.031 0.007 2.00E-05 0.043 0.009 8.24E-07 0.051 0.010 7.34E-07 0.045 0.010 8.72E-06 0.064 0.012 3.61E-08

cg24926185 0.034 0.007 4.55E-06 0.030 0.007 2.81E-05 0.037 0.008 5.61E-06 0.042 0.009 3.12E-06 0.035 0.009 4.00E-05 0.043 0.010 6.28E-06

cg14615868 0.026 0.007 1.43E-04 0.021 0.007 1.17E-03 0.033 0.008 2.11E-05 0.038 0.008 1.78E-06 0.034 0.008 1.45E-05 0.046 0.009 1.04E-07

cg15707428 0.033 0.007 6.99E-06 0.030 0.007 2.07E-05 0.035 0.009 4.40E-05 0.037 0.008 1.08E-05 0.034 0.008 7.03E-06 0.037 0.010 2.09E-04

cg25265126 0.044 0.010 1.13E-05 0.040 0.010 3.35E-05 0.055 0.012 6.46E-06 0.044 0.010 2.75E-05 0.039 0.010 1.21E-04 0.054 0.013 1.48E-05

cg15353603 -0.036 0.012 2.50E-03 -0.027 0.011 1.58E-02 -0.028 0.014 4.86E-02 -0.077 0.015 4.44E-07 -0.061 0.015 8.63E-05 -0.073 0.018 5.26E-05

cg15726700 0.039 0.012 8.90E-04 0.029 0.012 1.17E-02 0.049 0.014 3.04E-04 0.069 0.015 2.37E-06 0.057 0.014 8.43E-05 0.082 0.017 1.60E-06

cg16868776 0.033 0.008 2.46E-05 0.031 0.008 3.30E-05 0.040 0.009 1.19E-05 0.036 0.009 2.25E-05 0.033 0.008 6.29E-05 0.044 0.010 1.26E-05

cg14577840 0.034 0.008 9.54E-06 0.030 0.008 1.05E-04 0.038 0.009 3.65E-05 0.037 0.009 1.56E-05 0.031 0.008 1.51E-04 0.039 0.010 7.75E-05

cg02951062 0.031 0.007 2.86E-05 0.029 0.007 5.28E-05 0.034 0.009 1.31E-04 0.033 0.008 5.10E-05 0.031 0.008 1.29E-04 0.036 0.010 2.57E-04

cg02941135 0.028 0.007 3.03E-05 0.024 0.007 2.55E-04 0.034 0.009 6.86E-05 0.031 0.007 1.16E-05 0.025 0.007 3.48E-04 0.036 0.009 4.49E-05

cg06690548 -0.032 0.008 3.92E-05 -0.025 0.007 5.04E-04 -0.031 0.010 2.63E-03 -0.038 0.008 1.73E-06 -0.031 0.008 4.92E-05 -0.040 0.010 4.69E-05

cg07285213 0.037 0.007 5.28E-07 0.031 0.007 1.77E-05 0.040 0.009 8.91E-06 0.041 0.008 1.55E-07 0.033 0.008 2.65E-05 0.045 0.010 2.68E-06

cg22656956 0.034 0.010 5.59E-04 0.023 0.010 1.86E-02 0.042 0.011 9.88E-05 0.065 0.014 1.52E-06 0.050 0.014 2.58E-04 0.074 0.015 6.71E-07

cg03717755 0.047 0.009 6.26E-07 0.037 0.009 6.15E-05 0.048 0.011 2.31E-05 0.060 0.011 1.79E-08 0.048 0.010 4.45E-06 0.061 0.014 9.93E-06

cg26222229 -0.021 0.008 8.34E-03 -0.022 0.007 2.04E-03 -0.022 0.010 2.50E-02 -0.058 0.013 5.01E-06 -0.056 0.012 6.46E-06 -0.067 0.015 3.87E-06

cg02127509 0.040 0.011 1.28E-04 0.033 0.010 1.46E-03 0.051 0.013 1.54E-04 0.061 0.013 2.71E-06 0.054 0.013 1.93E-05 0.069 0.016 1.32E-05

cg27462497 -0.030 0.007 4.79E-05 -0.029 0.007 1.85E-05 -0.030 0.009 5.24E-04 -0.036 0.008 3.38E-06 -0.037 0.007 8.25E-07 -0.039 0.009 3.09E-05

cg15140703 0.036 0.008 1.39E-05 0.033 0.008 4.32E-05 0.039 0.009 3.28E-05 0.039 0.008 1.81E-06 0.036 0.008 7.58E-06 0.042 0.009 9.01E-06

cg09608424 0.031 0.007 2.73E-05 0.029 0.007 6.22E-05 0.031 0.009 3.36E-04 0.040 0.009 5.13E-06 0.036 0.008 6.50E-06 0.039 0.011 3.39E-04

cg22643879 0.032 0.007 1.19E-05 0.030 0.007 4.71E-05 0.036 0.009 2.12E-05 0.043 0.009 5.49E-06 0.040 0.010 2.68E-05 0.046 0.011 5.71E-05

cg00721800 -0.018 0.007 1.17E-02 -0.016 0.007 1.62E-02 -0.015 0.008 7.19E-02 -0.042 0.009 8.96E-06 -0.037 0.009 6.71E-05 -0.042 0.011 1.49E-04

cg17293161 -0.032 0.009 1.97E-04 -0.031 0.008 7.55E-05 -0.033 0.011 1.64E-03 -0.041 0.009 7.43E-06 -0.040 0.009 2.89E-06 -0.043 0.011 7.78E-05

cg07504977 0.033 0.008 1.35E-05 0.025 0.008 9.89E-04 0.035 0.010 1.91E-04 0.043 0.009 1.62E-06 0.034 0.009 1.65E-04 0.046 0.012 1.42E-04

cg00574958 -0.030 0.008 3.80E-04 -0.026 0.008 1.25E-03 -0.032 0.010 1.47E-03 -0.047 0.011 1.59E-05 -0.038 0.011 4.42E-04 -0.054 0.014 7.47E-05

cg21958090 0.028 0.006 1.26E-05 0.026 0.006 5.51E-05 0.030 0.007 3.82E-05 0.030 0.007 1.17E-05 0.028 0.007 4.96E-05 0.030 0.008 5.93E-05

23

cg13046832 0.038 0.010 1.51E-04 0.031 0.009 1.22E-03 0.035 0.012 3.37E-03 0.046 0.010 9.83E-06 0.039 0.010 8.32E-05 0.042 0.012 2.99E-04

cg16058274 -0.032 0.009 1.93E-04 -0.027 0.008 4.98E-04 -0.028 0.010 6.58E-03 -0.045 0.009 6.54E-07 -0.039 0.009 1.04E-05 -0.045 0.012 1.24E-04

cg10845124 -0.022 0.010 2.79E-02 -0.020 0.009 1.90E-02 -0.016 0.012 1.88E-01 -0.059 0.014 4.11E-05 -0.052 0.013 8.88E-05 -0.058 0.018 1.15E-03

cg08708323 -0.033 0.007 9.90E-06 -0.028 0.007 1.31E-04 -0.026 0.009 2.97E-03 -0.033 0.008 1.76E-05 -0.028 0.008 3.25E-04 -0.026 0.009 2.84E-03

cg11024682 0.033 0.008 3.54E-05 0.026 0.008 1.24E-03 0.034 0.009 6.04E-05 0.061 0.012 1.34E-07 0.050 0.012 1.22E-05 0.061 0.013 6.59E-06

cg06971602 0.022 0.008 3.76E-03 0.017 0.008 2.08E-02 0.022 0.009 1.38E-02 0.042 0.010 1.38E-05 0.039 0.010 1.42E-04 0.040 0.012 5.33E-04

cg27657459 0.035 0.007 3.09E-06 0.033 0.007 6.70E-06 0.040 0.009 1.31E-05 0.041 0.009 2.45E-06 0.037 0.008 1.05E-05 0.045 0.011 2.19E-05

cg22244768 -0.023 0.007 1.40E-03 -0.020 0.007 3.38E-03 -0.021 0.008 1.07E-02 -0.043 0.009 6.59E-07 -0.037 0.008 9.97E-06 -0.044 0.010 1.53E-05

cg03148858 0.038 0.009 5.55E-05 0.033 0.009 2.87E-04 0.041 0.011 1.45E-04 0.046 0.009 1.25E-06 0.042 0.010 1.16E-05 0.050 0.011 7.09E-06

cg27243685 0.042 0.008 1.70E-07 0.036 0.008 8.33E-06 0.041 0.010 2.74E-05 0.059 0.010 8.85E-10 0.051 0.009 4.50E-08 0.053 0.012 7.59E-06

cg01881899 0.034 0.008 8.97E-06 0.027 0.008 6.45E-04 0.036 0.009 9.37E-05 0.048 0.010 7.34E-07 0.039 0.009 2.18E-05 0.048 0.012 3.80E-05

cg02370100 0.025 0.008 2.16E-03 0.019 0.008 2.02E-02 0.028 0.009 2.09E-03 0.044 0.010 2.25E-05 0.037 0.010 2.26E-04 0.045 0.012 1.89E-04

cg06500161 0.046 0.007 4.36E-10 0.040 0.008 1.45E-07 0.048 0.009 1.13E-07 0.080 0.009 1.85E-17 0.070 0.010 2.56E-13 0.082 0.012 8.54E-12

cg02288017 0.039 0.008 5.50E-07 0.035 0.007 1.87E-06 0.038 0.009 4.41E-05 0.040 0.008 6.59E-07 0.036 0.008 2.05E-06 0.038 0.010 9.72E-05

cg01275664 -0.045 0.010 4.72E-06 -0.040 0.010 7.09E-05 -0.059 0.012 3.11E-07 -0.049 0.010 2.40E-06 -0.043 0.010 2.11E-05 -0.062 0.011 5.02E-08

24

Supplementary Table 3: Statistical power provided by the meta-analysis to validate the selected CpG sites

differentially methylated in relation to lipids traits (total cholesterol, low-density lipoprotein, high-density

lipoprotein and triglycerides) in the discovery stage.

Total Cholesterol

Features Meta-analysis (Phase1+Phase2)

cpg chr pos Gene Coeff Coeff (80% power) P-value

cg26226879 1 34642305 C1orf94 0.659 3.831 2.90E-01

cg00449821 1 155053823 EFNA3 -2.376 4.083 3.50E-04

cg05876625 2 108723177 NA 2.148 4.783 5.90E-03

cg24078828 3 149375789 WWTR1 1.057 5.102 2.00E-01

cg06650596 5 1041028 NA -1.938 4.568 9.10E-03

cg17878141 5 81521184 ATG10 0.751 3.979 2.50E-01

cg24050047 7 33767686 NA 2.366 4.544 1.40E-03

cg23245289 8 37698900 GPR124 -1.999 4.679 8.70E-03

cg13457700 10 5708797 ASB13 1.581 5.262 6.50E-02

cg06224551 11 124670268 C11orf61 1.584 4.507 3.10E-02

cg23206311 13 33002447 N4BP2L1 2.278 4.593 2.30E-03

cg22138573 13 60718665 DIAPH3 -2.048 5.170 1.50E-02

cg26345203 14 23005866 NA 3.205 6.594 2.80E-03

cg26343512 14 77413728 NA 0.065 5.323 9.40E-01

cg10289790 14 105359915 KIAA0284 -1.163 5.440 1.90E-01

cg24252746 15 45248932 C15orf43 -1.116 4.329 1.10E-01

cg00624589 16 1094742 NA -2.259 3.825 2.90E-04

cg04552480 16 12209538 SNX29 0.767 4.611 3.10E-01

cg05609864 16 24550579 RBBP6 1.906 6.300 6.30E-02

cg01771247 16 61846623 CDH8 2.689 5.219 1.60E-03

cg10361950 18 12039173 NA 2.896 5.231 6.80E-04

cg06747543 19 18589894 ELL 3.971 5.888 3.50E-05

cg20319775 20 10653482 JAG1 1.609 5.649 8.00E-02

cg16000331 22 42230138 SREBF2 4.910 5.323 1.50E-08




cg07962812 1 183441443 SMG7 1.234 3.868 5.00E-02

cg00753676 4 38662991 FLJ13197 -3.768 4.531 3.40E-07

cg15619673 7 16625816 NA -1.935 3.739 1.50E-03

cg15123809 10 105254427 NEURL -1.591 4.077 1.70E-02

cg04413986 12 57119373 NACA 1.385 4.237 4.50E-02

cg15899743 14 22985112 NA 3.888 6.521 2.50E-04

cg26345203 14 23005866 NA 3.236 5.864 7.10E-04

cg10289790 14 105359915 KIAA0284 -0.705 4.611 3.50E-01

25

cg24252746 15 45248932 C15orf43 -1.410 3.690 1.90E-02

cg05609864 16 24550579 RBBP6 1.721 5.458 5.30E-02

cg22322184 19 7734203 RETN -1.630 6.115 1.00E-01

cg06747543 19 18589894 ELL 3.239 5.164 1.20E-04




cg07395004 1 1310147 AURKAIP1 1.414 2.210 8.60E-05

cg20312179 1 51981505 EPS15 1.045 2.045 1.70E-03

ch.2.101965435R 2 102599003 NA 2.263 2.124 6.60E-11

cg03555914 2 121554810 GLI2 -1.617 2.843 4.80E-04

cg03128029 2 203143288 NOP58 2.237 2.947 3.10E-06

cg00959259 3 122281975 PARP9;

1.015 1.731 3.10E-04 DTX3L

cg01277372 3 169378764 MECOM -1.683 2.474 2.90E-05

cg27338287 3 190580644 LOC647309 -1.180 1.995 2.80E-04

cg03838769 4 168156467 SPOCK3 0.598 1.670 2.80E-02

cg02111504 5 93954110

C5orf36;

0.893 2.481 2.70E-02 ANKRD32;

C5orf36

cg08530041 5 168093430 SLIT3 -0.388 2.088 2.50E-01

cg09572125 6 33400477 SYNGAP1 -3.915 3.481 5.10E-12

cg03667621 7 1478715 MICALL2 -1.166 2.659 7.10E-03

cg08549335 7 30387954 ZNRF2 1.635 1.922 1.70E-07

cg02902261 7 72991150 TBL2 -1.451 2.026 1.10E-05

cg19126110 7 115263754 NA 1.203 1.940 1.40E-04

cg25097801 8 23315147 ENTPD4 0.989 2.045 3.00E-03

cg27342720 8 120033982 NA 1.915 2.376 7.20E-07

cg14364472 9 139394549 NOTCH1 -0.794 1.603 2.40E-03

cg18659867 10 80007739 NA 1.869 2.984 1.20E-04

cg14758812 10 103090818 NA 1.047 1.910 7.50E-04

cg13613180 11 74560694 XRRA1 -1.530 1.934 1.20E-06

cg12669088 12 25541364 NA 2.514 3.408 5.80E-06

cg07511188 12 51442144 LETMD1 1.474 2.192 3.60E-05

cg25736198 12 72345225 TPH2 1.378 2.167 9.50E-05

cg11827629 12 115822424 NA 1.282 2.260 4.90E-04

cg10415314 14 33949227 NPAS3 1.841 2.425 3.10E-06

cg26948596 14 93078627 RIN3 -1.566 2.474 1.00E-04

cg16743005 16 50403128 BRD7 1.485 2.407 1.50E-04

cg07839457 16 57023022 NLRC5 1.019 1.836 6.60E-04

cg16411857 16 57023191 NLRC5 1.126 1.817 1.50E-04

cg26561196 16 68344680 SLC7A6OS;

1.172 2.161 8.60E-04 PRMT7

26

cg11024682 17 17730094 SREBF1 -3.431 2.069 0.00E+00

cg27466042 17 36896370 PCGF2 -0.742 1.817 1.20E-02

cg02650017 17 47301614 PHOSPHO1 2.466 1.959 9.80E-15

cg18942579 17 57915773 TMEM49 1.176 2.002 3.10E-04

cg08533242 20 62195615 PRIC285 -0.783 1.903 1.20E-02

cg27243685 21 43642366 ABCG1 -3.798 1.959 0.00E+00

cg06500161 21 43656587 ABCG1 -5.369 2.094 0.00E+00

cg14627538 21 48082402 PRMT2 -1.544 2.401 7.90E-05

cg03339016 22 19279085 CLTCL1 0.623 2.272 9.20E-02

cg16838132 22 39913220 SMCR7L -0.909 1.523 2.40E-04

Triglycerides



cg21268984 1 8720599 RERE 0.035 0.043 6.80E-07

cg19693031 1 145441552 TXNIP -0.049 0.025 0.00E+00

cg04282029 1 149890655 SV2A 0.008 0.031 1.10E-01

cg24926185 1 151557485 NA 0.007 0.025 8.60E-02

cg14615868 1 236558696 EDARADD 0.009 0.025 1.60E-02

cg15707428 2 11679845 GREB1 0.012 0.025 3.30E-03

cg25265126 2 113891507 IL1RN 0.018 0.037 1.20E-03

cg15353603 2 162915902 DPP4 -0.027 0.049 3.20E-04

cg15726700 3 196370254 LRRC33 0.023 0.049 2.80E-03

cg16868776 4 976565 SLC26A1 0.008 0.025 5.60E-02

cg14577840 4 16257979 FLJ39653 0.011 0.025 9.60E-03

cg02951062 4 74269908 ALB 0.005 0.025 1.90E-01

cg02941135 4 81122314 PRDM8 0.005 0.025 1.60E-01

cg06690548 4 139162808 SLC7A11 -0.043 0.025 0.00E+00

cg07285213 5 1292339 TERT 0.012 0.025 4.80E-03

cg22656956 5 137475177 NME5 0.026 0.037 7.30E-05

cg03717755 6 16136539 MYLIP 0.054 0.037 0.00E+00

cg26222229 6 36842844 PPIL1 -0.013 0.037 3.80E-02

cg02127509 6 135516936 MYB 0.018 0.037 3.80E-03

cg27462497 7 2633190 IQCE -0.006 0.025 1.10E-01

cg15140703 7 99775532 STAG3;

0.012 0.025 7.40E-03 GPC2

cg09608424 7 141630158 CLEC5A 0.013 0.025 2.70E-03

cg22643879 8 10149407 MSRA 0.004 0.031 4.10E-01

cg00721800 8 77618385 ZFHX4 -0.013 0.031 6.50E-03

cg17293161 10 80141089 NA -0.004 0.025 3.70E-01

cg07504977 10 102131012 NA 0.043 0.031 0.00E+00

cg00574958 11 68607622 CPT1A -0.075 0.031 0.00E+00

cg21958090 11 112752496 NA 0.009 0.025 2.40E-02

cg13046832 14 29254680 C14orf23 0.017 0.031 8.90E-04

27

cg16058274 14 94179847 NA -0.007 0.025 1.10E-01

cg10845124 15 101984550 PCSK6 -0.009 0.037 1.20E-01

cg08708323 16 1728724 HN1L -0.011 0.025 6.00E-03

cg11024682 17 17730094 SREBF1 0.062 0.031 0.00E+00

cg06971602 17 35306010 AATF 0.007 0.031 1.30E-01

cg27657459 17 54853771 NA 0.009 0.025 2.70E-02

cg22244768 17 55634551 MSI2 -0.002 0.025 6.40E-01

cg03148858 19 3047978 TLE2 0.009 0.031 6.40E-02

cg27243685 21 43642366 ABCG1 0.064 0.025 0.00E+00

cg01881899 21 43652704 ABCG1 0.049 0.031 0.00E+00

cg02370100 21 43655256 ABCG1 0.041 0.031 0.00E+00

cg06500161 21 43656587 ABCG1 0.088 0.031 0.00E+00

cg02288017 X 16803667 CXorf15 0.010 0.025 1.50E-02

cg01275664 X 34405983 NA -0.019 0.031 4.50E-05

Cpg, CpG id; chr, chromosome location; pos, genomic position; Gene, associated gene or transcript; Coeff, observed

coefficient of M-standardized; Coeff (80% power), coefficient that could be detected as statistically significant with

80% power; P-value, p-value observed in the meta-analysis.

28

Supplementary Table 4: Aggregated results of the Global Lipids Genetic Consortium: associations between genetic

variants in the loci of interest and the corresponding lipid trait. (Adapted from Reference 12)

SREBF2-TC

rsID chr pos A1 A2 Freq_A1 coef SE Pval

rs9607849 22 42229867 G A 0.9921 0.0255 0.0252 1.57E-01

rs1569451 22 42232291 G A 0.3047 0.0069 0.0056 5.36E-01

rs2006638 22 42232577 C T 0.8931 0.0055 0.0084 6.36E-01

rs9607850 22 42235352 C T 0.5317 0.0073 0.0052 2.87E-01

rs5996074 22 42236337 G A 0.3047 0.0070 0.0056 5.09E-01

rs2267438 22 42237565 C T 0.3047 0.0071 0.0056 5.16E-01

rs2267439 22 42237769 C T 0.3047 0.0067 0.0055 5.54E-01

rs7287886 22 42238027 C A 0.1201 0.0067 0.0076 3.34E-01

rs16985978 22 42239222 C T 0.9921 0.0151 0.0238 3.34E-01

rs2284082 22 42240797 C T 0.3047 0.0067 0.0056 5.55E-01

rs2255957 22 42241372 A G 0.1201 0.0077 0.0073 2.67E-01

rs1883205 22 42243020 T C 0.3047 0.0069 0.0056 5.26E-01

rs4501042 22 42245763 C T 0.3047 0.0071 0.0056 5.11E-01

rs9611677 22 42247356 T G 0.9921 0.0267 0.0257 1.55E-01

rs2413660 22 42247360 G A 0.5396 0.0095 0.0052 1.54E-01

rs2839713 22 42253727 A G 0.0950 0.0101 0.0078 1.66E-01

rs133280 22 42255525 G A 0.4670 0.0086 0.0051 1.94E-01

rs9607852 22 42258272 A G 0.0303 0.0048 0.0153 6.83E-01

rs714015 22 42259098 T C 0.4631 0.0090 0.0051 1.74E-01

rs2269657 22 42264269 T G 0.2256 0.0039 0.0058 4.83E-01

rs133290 22 42267605 A C 0.4631 0.0086 0.0051 1.76E-01

rs11702960 22 42269532 C T 0.8575 0.0068 0.0076 3.26E-01

rs133291 22 42269628 T C 0.2361 0.0085 0.0060 3.74E-01

rs9611685 22 42273933 C T 0.9921 0.0022 0.0186 5.62E-01

rs4822062 22 42274287 G A 0.9011 0.0061 0.0084 5.85E-01

rs12165579 22 42278245 G A 0.0303 0.0051 0.0155 6.54E-01

rs13055841 22 42279653 G A 0.3193 0.0075 0.0062 3.79E-01

rs5751174 22 42280135 A G 0.0989 0.0122 0.0077 9.88E-02

rs2269658 22 42280618 C T 0.1201 0.0102 0.0078 3.30E-01

rs9623466 22 42281149 G T 0.0303 0.0051 0.0159 6.54E-01

rs9623467 22 42281255 A C 0.0303 0.0064 0.0160 7.04E-01

rs9623468 22 42281294 G A 0.0303 0.0056 0.0160 6.62E-01

rs1052717 22 42281429 G A 0.4828 0.0085 0.0051 1.87E-01

rs9623469 22 42281587 T C 0.0303 0.0063 0.0160 6.92E-01

rs17002737 22 42282012 T C 0.0871 0.0086 0.0090 4.10E-01

rs6002521 22 42283709 A G 0.0330 0.0075 0.0164 7.60E-01

rs5996078 22 42286255 A G 0.0330 0.0076 0.0166 7.69E-01

rs2267443 22 42287454 G A 0.5989 0.0115 0.0054 8.28E-02

rs6002524 22 42288994 G T 0.0858 0.0070 0.0094 5.82E-01

rs5996080 22 42289466 C T 0.0858 0.0071 0.0094 5.79E-01

rs4822066 22 42289500 G A 0.8681 0.0032 0.0075 9.91E-01

rs12157312 22 42290177 C T 0.0858 0.0141 0.0109 3.09E-01

rs2269660 22 42292923 A G 0.0805 0.0068 0.0094 6.02E-01

rs9620000 22 42296703 C T 0.0831 0.0068 0.0093 6.21E-01

rs6002527 22 42297968 C T 0.0831 0.0067 0.0093 6.08E-01

29

rs17379759 22 42299535 A G 0.8668 0.0051 0.0074 8.11E-01

rs2229442 22 42301748 G A 0.0831 0.0072 0.0094 5.86E-01

rs1009544 22 42239348 C G NA 0.0116 0.0080 2.85E-01

rs9607851 22 42246530 C G NA 0.0286 0.0250 1.36E-01

rs2228314 22 42276742 C G NA 0.0054 0.0059 3.23E-01

rs4822064 22 42279506 G C 1.0000 0.0062 0.0077 3.86E-01

rs2284083 22 42252589 G C 1.0000 0.0092 0.0078 1.99E-01

rs12373973 22 42246564 T A 1.0000 0.0233 0.0238 1.94E-01

rs2269661 22 42295970 C G NA 0.0066 0.0094 6.10E-01

rs17002706 22 42258577 C G NA 0.0036 0.0086 7.91E-01

SYNGAP1-HDL-C

rs211456 6 33389381 T G 0.3654 0.0062 0.0036 6.18E-02

rs2076775 6 33394253 G C 1 0.0031 0.005 3.66E-01

rs413722 6 33398620 C T 0.9208 0.0097 0.0065 2.01E-01

rs9394145 6 33399778 C T 0.6741 0.0008 0.0038 8.83E-01

rs453590 6 33403422 T C 0.3734 0.0033 0.0049 3.39E-01

rs10807124 6 33404064 A G 0.3219 0.0014 0.0053 8.31E-01

rs411136 6 33408542 A G 0.3734 0.0062 0.0036 6.44E-02

rs12204193 6 33415307 G C 1 0.0002 0.0051 7.58E-01

rs2772376 6 33416111 T C 0.3734 0.0037 0.0050 3.03E-01

rs2247385 6 33421577 C T 0.3734 0.0061 0.0036 7.25E-02

rs2274730 6 33422545 G C 0.4129 0.0011 0.0044 8.82E-01

SREBF1-HDL-C

rs11868035 17 17715101 G A 0.6583 0.0065 0.0054 4.99E-01

rs2297508 17 17715317 G C 1 0.0069 0.0051 3.04E-01

rs11653007 17 17716662 G C 1 0.0388 0.0112 1.28E-03

rs4925115 17 17721457 G A 0.5805 0.0075 0.0050 2.27E-01

rs11656665 17 17724789 A G 0.5805 0.0072 0.0050 2.52E-01

rs1108511 17 17726469 C T 0.9380 0.0017 0.0103 6.65E-01

rs9899634 17 17727943 A T NA 0.0079 0.0049 1.42E-01

rs8066560 17 17728043 G A 0.6029 0.0080 0.0049 1.48E-01

rs9902941 17 17733760 T C 0.5963 0.0078 0.0049 1.62E-01

rs1889018 17 17734740 A G 0.5910 0.0080 0.0049 1.58E-01

rs4925118 17 17739163 C T 0.8918 0.0028 0.0085 7.10E-01

PHOSPHO1-HDL-C

rs648980 17 47303456 C T 0.4617 0.0079 0.0050 1.20E-01

rs617182 17 47307274 A G 0.4604 0.0068 0.0049 1.75E-01

ABCG1-HDL-C

rs12626718 21 43618652 A G 0.9169 0.0025 0.0096 9.34E-01

rs4148082 21 43619415 G A 0.9169 0.0018 0.0096 9.02E-01

rs1378577 21 43619665 T G 0.7863 0.0007 0.0060 9.98E-01

rs4148083 21 43620158 C T 0.9169 0.0024 0.0096 9.25E-01

rs4148086 21 43620427 T C 0.9169 0.0033 0.0097 9.87E-01

30

rs9975740 21 43620485 A T NA 0.0003 0.0072 9.78E-01

rs7283103 21 43620856 G A 0.9169 0.0036 0.0095 9.45E-01

rs4148087 21 43622267 G A 0.8694 0.0005 0.0074 9.16E-01

rs10084554 21 43623281 G T 0.7441 0.0033 0.0056 6.72E-01

rs10084555 21 43623379 G A 0.9921 0.0114 0.019 7.14E-01

rs12626951 21 43624272 A G 0.9169 0.0027 0.0098 9.80E-01

rs1117640 21 43625274 T G 0.8707 0.0004 0.0072 9.59E-01

rs1840593 21 43626673 G A 0.7441 0.0035 0.0059 6.48E-01

rs221948 21 43633193 A G 0.1148 0.0091 0.0101 7.65E-01

rs915845 21 43635438 G T 0.1412 0.0001 0.0073 9.77E-01

rs4148095 21 43635956 T C 0.9525 0.0051 0.0116 9.67E-01

rs2234715 21 43638855 A G 0.9261 0.0048 0.0107 9.11E-01

rs4148101 21 43640183 G A 0.8628 0.0005 0.0073 9.53E-01

rs4148102 21 43641347 A G 0.1398 0.0021 0.0070 8.65E-01

rs4148103 21 43641605 G A 0.9222 0.0027 0.0115 9.24E-01

rs9976024 21 43641657 A G 0.1372 0.0008 0.0074 9.16E-01

rs4148104 21 43642438 C T 0.9222 0.0067 0.0122 7.93E-01

rs3787968 21 43650387 G A 0.4367 0.0042 0.0048 3.91E-01

rs3827225 21 43650779 A G 0.2361 0.0097 0.0055 1.44E-01

rs3787970 21 43651556 T C 0.4406 0.0049 0.0048 3.15E-01

rs3787972 21 43651705 C T 0.4406 0.0051 0.0048 3.03E-01

rs881395 21 43652410 T C 0.3311 0.0072 0.0052 2.17E-01

rs225440 21 43653053 T C 0.3931 0.0058 0.0049 3.42E-01

rs915847 21 43657248 A G 0.3285 0.0097 0.0051 9.31E-02

rs225443 21 43658206 A G 0.3509 0.0093 0.0050 9.35E-02

rs225444 21 43658226 C G NA 0.0076 0.0048 1.57E-01

rs225445 21 43658444 C T 0.4367 0.0083 0.0048 1.16E-01

rs225447 21 43658979 G A 0.4367 0.0082 0.0048 1.21E-01

rs225448 21 43659830 C T 0.3681 0.0087 0.0050 1.75E-01

rs9978671 21 43660279 T C 0.0462 0.0025 0.0110 5.40E-01

rs13052462 21 43661920 A C 0.3127 0.0107 0.0054 1.26E-01

rs178744 21 43662796 T C 0.3219 0.0115 0.0054 8.89E-02

rs7283699 21 43663318 A G 0.0488 0.0023 0.0117 6.11E-01

rs9982196 21 43664647 A T NA 0.0015 0.0118 6.45E-01

rs4148117 21 43666065 C T 0.434 0.0092 0.0053 1.13E-01

rs9974658 21 43666701 A G 0.0488 0.0039 0.0118 4.98E-01

rs11909889 21 43667961 G A 0.9802 0.0028 0.0182 8.77E-01

rs9978842 21 43668916 G C 1 0.0011 0.0114 6.39E-01

rs12329683 21 43669610 G T 0.0501 0.0008 0.0114 6.58E-01

rs9982242 21 43671120 G C 1 0.0010 0.015 5.54E-01

rs225374 21 43671633 G C 1 0.0123 0.0074 1.15E-01

rs4148120 21 43673477 G C 1 0.0062 0.008 3.99E-01

rs7279750 21 43674684 T C 0.7731 0.0070 0.0075 2.89E-01

rs7281093 21 43674859 G A 0.7731 0.0065 0.0075 3.12E-01

rs7281345 21 43674982 G A 0.8325 0.0065 0.0077 3.69E-01

rs225378 21 43675694 G A 0.5330 0.0003 0.0054 6.91E-01

rs4148121 21 43675834 C T 0.0079 0.0011 0.0305 9.19E-01

rs183436 21 43677831 C A 0.2995 0.0037 0.0060 6.43E-01

rs3787986 21 43678808 C T 0.8285 0.0075 0.0076 3.12E-01

rs915841 21 43679438 T C 0.8285 0.0077 0.0076 3.04E-01

rs915842 21 43679513 C T 0.8285 0.0079 0.0076 2.89E-01

31

rs915843 21 43679554 C T 0.8285 0.0079 0.0076 2.92E-01

rs9974417 21 43679644 G A 0.9815 0.0209 0.0224 1.62E-01

rs9976804 21 43679862 G A 0.9815 0.0153 0.0224 2.58E-01

rs17114590 21 43681956 A G 0.8325 0.0081 0.0076 2.65E-01

rs225383 21 43682244 C T 0.5026 0.0021 0.0036 7.50E-01

rs4148122 21 43682365 G A 0.9815 0.031 0.0208 6.07E-02

rs225384 21 43682394 A G 0.4974 0.0026 0.0053 4.07E-01

rs225385 21 43682686 A G 0.4974 0.0012 0.0053 5.45E-01

rs225386 21 43682938 G A 0.5158 0.0014 0.0053 6.11E-01

rs9980952 21 43682959 G A 0.9842 0.0101 0.0225 5.75E-01

rs225387 21 43683053 G A 0.4974 0.0025 0.0053 4.04E-01

rs9975218 21 43684299 A G 0.9815 0.0035 0.0208 5.02E-01

rs17767083 21 43684321 C T 0.8760 0.0162 0.0089 1.48E-02

rs225388 21 43684456 A G 0.4960 0.0028 0.0053 3.86E-01

rs225391 21 43684668 A G 0.0857 0.0193 0.0103 4.47E-02

rs225393 21 43685123 G A 0.5185 0.0033 0.0054 4.18E-01

rs225396 21 43687354 T C 0.4974 0.0031 0.0054 3.94E-01

rs225398 21 43688594 G C 1 0.0005 0.0059 9.44E-01

rs532345 21 43689491 T C 0.4116 0.0077 0.0055 5.75E-02

rs691687 21 43689870 G A 0.4116 0.0075 0.0054 6.64E-02

rs482303 21 43691469 C G NA 0.0261 0.0089 5.06E-03

rs2298689 21 43696833 G A 0.9156 0.0057 0.0106 7.01E-01

rs2234718 21 43697195 A G 0.7599 0.0131 0.0061 3.69E-02

rs4148123 21 43698251 G A 0.6227 0.0005 0.0055 7.23E-01

rs3787995 21 43698914 G C 1 0.0028 0.0103 9.10E-01

rs225406 21 43699230 A G 0.1108 0.0238 0.0082 6.13E-03

rs2839482 21 43700432 A G 0.8127 0.0129 0.0061 4.48E-02

rs225410 21 43700907 T C 0.5224 0.0103 0.0053 1.54E-02

rs492338 21 43701977 G A 0.5290 0.0099 0.0054 1.53E-02

rs3788007 21 43706776 A G 0.2005 0.0047 0.0080 4.22E-01

rs450808 21 43706944 C T 0.7902 0.0025 0.0093 8.33E-01

rs425215 21 43707101 G C 1 0.0041 0.0090 7.92E-01

rs7277991 21 43709682 G T 0.6266 0.0071 0.0051 3.26E-01

rs7275482 21 43709700 T C 0.2005 0.0008 0.0065 5.96E-01

rs4148137 21 43710052 T C 0.3786 0.0039 0.0051 7.86E-01

rs2234721 21 43710096 T G 0.3773 0.0044 0.0051 7.36E-01

rs4148139 21 43710774 A G 0.1939 0.0015 0.0072 4.90E-01

rs914189 21 43710909 C G NA 0.0006 0.0064 7.53E-01

rs13050646 21 43712049 T G NA 0.0063 0.0114 9.41E-01

rs9975333 21 43714517 C A 0.5831 0.0069 0.0050 2.28E-01

rs474142 21 43714579 A G 0.0330 0.0004 0.0166 7.94E-01

rs2276235 21 43715013 C A 0.5831 0.0059 0.0049 2.83E-01

rs3788010 21 43716022 A G 0.5871 0.0054 0.0048 3.35E-01

rs1541290 21 43718483 A G 0.5079 0.0123 0.0049 3.11E-02

TXNIP-TG

rs7211 1 145441620 T C 0.0501 0.0288 0.0125 6.62E-02

rs7212 1 145442254 G C 1.0000 0.0281 0.0120 6.08E-02

rs4755 1 145442264 T A 1.0000 0.0567 0.0318 1.19E-01

32

SLC7A11-TG

rs7688870 4 139084657 C A 0.4868 0.0053 0.0047 5.25E-01

rs4560461 4 139086857 A G 0.1069 0.0061 0.0091 5.59E-01

rs7674870 4 139089463 G A 0.4380 0.0058 0.0047 4.75E-01

rs13144383 4 139090804 A G 0.8311 0.0076 0.0066 4.29E-01

rs4504306 4 139093228 C T 0.4789 0.0055 0.0047 5.52E-01

rs11728841 4 139096299 A C 0.4710 0.0028 0.0047 9.50E-01

rs4863767 4 139112222 C A 0.4235 0.0049 0.0048 3.43E-01

rs4863771 4 139113336 T G 0.4235 0.0003 0.0034 9.16E-01

rs11100834 4 139114529 C T 0.4565 0.0056 0.0050 3.33E-01

rs6832143 4 139117012 G A 0.5317 0.0052 0.0049 4.36E-01

rs4330397 4 139118089 C G NA 0.0028 0.0055 7.64E-01

rs4863772 4 139120683 T C 0.4987 0.0053 0.0047 3.98E-01

rs4131888 4 139123748 T C 0.1887 0.0056 0.0059 4.23E-01

rs4602539 4 139125041 G T 0.2704 0.0048 0.0050 5.56E-01

rs13141329 4 139125405 A T NA 0.0058 0.0047 3.34E-01

rs12506333 4 139127861 A G 0.0277 0.0029 0.0122 4.79E-01

rs6537244 4 139129255 A G 0.5000 0.0054 0.0047 3.87E-01

rs11734488 4 139130133 T C 0.4987 0.0051 0.0047 4.09E-01

rs6854381 4 139130390 G A 0.5026 0.0040 0.0047 5.78E-01

rs7682497 4 139135399 G A 0.5013 0.0035 0.0047 6.39E-01

rs4461565 4 139144689 A G 0.1135 0.0037 0.0074 8.26E-01

rs3935420 4 139148186 A G 0.4947 0.0052 0.0047 4.51E-01

rs7666936 4 139150283 C T 0.1504 0.0001 0.0066 9.70E-01

rs2037027 4 139150889 A G 0.1161 0.0005 0.0078 9.15E-01

rs2037026 4 139150941 G C 0.0092 0.0050 0.0157 6.12E-01

rs13140611 4 139152115 T A 1.0000 0.0046 0.0047 5.14E-01

rs17050206 4 139152618 C G NA 0.0094 0.0092 4.68E-01

rs7685529 4 139155804 C T 0.4670 0.0049 0.0047 4.83E-01

rs1018279 4 139156309 G A 0.4987 0.0045 0.0048 5.44E-01

rs10519451 4 139156660 T C 0.3852 0.0046 0.0052 4.66E-01

rs11727731 4 139160397 G A 0.5462 0.0004 0.0034 8.63E-01

rs4343770 4 139164146 T C 0.1425 0.0047 0.0064 7.96E-01

MYLIP-TG

rs760633 6 16128965 C G 0.7876 0.0015 0.0040 4.93E-01

rs909562 6 16130333 G A 0.1201 0.0054 0.0056 3.29E-01

rs2076017 6 16130559 A G 0.9855 0.0007 0.0215 8.90E-01

rs1011616 6 16132409 T C 0.1187 0.0041 0.0055 4.21E-01

rs8180638 6 16135176 C T 0.7942 0.0009 0.0058 7.39E-01

rs2142674 6 16138665 C A 0.7902 0.0011 0.0058 7.07E-01

rs2282813 6 16140631 G T 0.1662 0.0045 0.0075 7.45E-01

rs7756075 6 16141616 G A 0.9195 0.0114 0.0077 2.72E-01

rs7763395 6 16142359 A G 0.7098 0.0066 0.0051 2.74E-01

rs2205796 6 16142997 T G 0.7902 0.0008 0.0057 7.83E-01

rs2072783 6 16143897 G A 0.1504 0.0055 0.0050 4.04E-01

rs2056937 6 16144614 T C 0.7084 0.0064 0.0049 2.42E-01

rs1060913 6 16146740 A G 0.2098 0.0140 0.0183 1.93E-01

rs2072781 6 16147349 T C 0.9195 0.0139 0.0075 1.27E-01

33

CPT1A-TG

rs2278908 11 68523910 C T 0.6939 0.0105 0.0050 1.03E-01

rs897049 11 68528613 C A 0.8945 0.0082 0.0081 9.06E-01

rs897048 11 68529378 G C 1.0000 0.0039 0.0063 9.37E-01

rs7112615 11 68530318 A C 0.9591 0.0044 0.0103 8.86E-01

rs4930608 11 68531596 C T 0.8351 0.0013 0.0064 6.68E-01

rs7942147 11 68531866 C A 0.8351 0.0022 0.0064 7.46E-01

rs2924672 11 68532073 C G NA 0.0044 0.0109 5.00E-01

rs2924671 11 68532605 A G 0.0356 0.0032 0.0108 6.12E-01

rs2123869 11 68538660 A G 0.8351 0.0036 0.0064 9.33E-01

rs3019593 11 68538939 C T 0.0369 0.0014 0.0110 6.93E-01

rs2060981 11 68539869 T C 0.8351 0.0021 0.0064 7.54E-01

rs2060980 11 68539973 C A 1.0000 0.0004 0.0066 4.47E-01

rs3763831 11 68540316 A G 0.8351 0.0058 0.0065 9.06E-01

rs11228346 11 68541540 A G 0.8720 0.0100 0.0076 4.72E-01

rs897047 11 68544438 A G 0.8351 0.0040 0.0064 9.32E-01

rs10791997 11 68544985 T C 0.8351 0.0084 0.0077 5.37E-01

rs3019576 11 68548260 C A 0.0369 0.0027 0.0112 5.48E-01

rs11228349 11 68548468 G A 0.8720 0.0070 0.0076 7.32E-01

rs3829242 11 68548723 T C 0.8351 0.0033 0.0064 9.37E-01

rs2228502 11 68549340 A G 0.0369 0.0049 0.0113 4.39E-01

rs2305508 11 68549546 C T 0.4802 0.0123 0.0050 5.89E-02

rs2924685 11 68550068 C T 0.0356 0.0031 0.0112 5.65E-01

rs11228350 11 68550123 T G 0.8720 0.0085 0.0076 6.13E-01

rs2924683 11 68550304 C G NA 0.0064 0.0114 3.81E-01

rs2924682 11 68550391 A G 0.0356 0.0053 0.0114 4.15E-01

rs4930610 11 68553151 C T 0.8377 0.0023 0.0066 7.27E-01

rs747840 11 68554503 G A 0.0145 0.0044 0.0177 4.26E-01

rs3019578 11 68556380 A C 0.0158 0.0010 0.0172 6.02E-01

rs2924679 11 68556782 A G 0.0158 0.0047 0.0180 4.61E-01

rs12364396 11 68556831 C T 0.8720 0.0051 0.0076 8.64E-01

rs11228358 11 68561757 T C 0.8720 0.0068 0.0077 6.90E-01

rs4930248 11 68565904 T C 0.5937 0.0129 0.0052 6.27E-02

rs2924675 11 68566248 G A 0.0158 0.0072 0.0181 3.52E-01

rs3794021 11 68567825 G C 1.0000 0.0020 0.0073 7.67E-01

rs10896368 11 68569254 T A 1.0000 0.0069 0.0084 7.09E-01

rs3019587 11 68569642 T G 0.0145 0.0033 0.0184 4.40E-01

rs10791999 11 68570838 A G 0.0145 0.0018 0.0186 5.96E-01

rs2924674 11 68571777 A G 0.9855 0.0027 0.0184 8.13E-01

rs3019582 11 68572301 T G 0.0145 0.0005 0.0189 6.10E-01

rs3019581 11 68572332 G A 0.9855 0.0001 0.0191 5.88E-01

rs1037488 11 68576951 A G 0.9604 0.0085 0.0143 4.86E-01

rs2278906 11 68579595 C G NA 0.0100 0.0089 4.91E-01

rs2924689 11 68583671 T C 0.9855 0.0091 0.0167 8.82E-01

rs11228364 11 68583684 C T 0.8575 0.0098 0.0089 5.39E-01

rs3019607 11 68585986 A C 0.9855 0.0052 0.0191 8.43E-01

rs2924697 11 68586939 G C 1.0000 0.0068 0.0084 7.72E-01

rs3019613 11 68589257 A G 0.8404 0.0029 0.0053 8.18E-01

rs12361365 11 68591872 A G 0.8061 0.0129 0.0079 2.14E-01

34

rs11228368 11 68593258 A G 0.4512 0.0133 0.0049 1.86E-02

rs10896369 11 68595970 G A 0.1253 0.0074 0.0069 4.96E-01

rs11228372 11 68596578 G A 0.4525 0.0124 0.0049 2.93E-02

rs10896370 11 68596693 T C 0.1253 0.0086 0.0069 3.72E-01

rs10896371 11 68597104 C T 0.1280 0.0062 0.0069 5.88E-01

rs11228373 11 68597220 G C 1.0000 0.0047 0.0069 7.39E-01

rs11605837 11 68597886 T G 0.3272 0.0110 0.0050 5.44E-02

rs7938117 11 68598054 A G 0.3259 0.0155 0.0035 4.37E-04

rs1017639 11 68598534 C A 0.0383 0.0074 0.0115 4.68E-01

rs1017640 11 68598684 T C 0.0897 0.0077 0.0084 6.36E-01

rs1017641 11 68598783 C T 0.3654 0.0122 0.0049 2.54E-02

rs628399 11 68600592 G T 0.0871 0.0045 0.0084 9.42E-01

rs597539 11 68601974 G C 1.0000 0.0113 0.0050 4.63E-02

rs613084 11 68603157 A C 0.3351 0.0101 0.0050 7.98E-02

rs3019594 11 68605690 C T 0.0844 0.0051 0.0084 8.91E-01

rs597316 11 68610810 C G NA 0.0110 0.0050 5.61E-02

SREBF1-TG

rs11868035 17 17715101 A G 0.3417 0.0113 0.0052 2.27E-02

rs2297508 17 17715317 C G NA 0.0131 0.0049 1.56E-02

rs11653007 17 17716662 C G NA 0.0301 0.0108 8.74E-03

rs4925115 17 17721457 A G 0.4195 0.0133 0.0049 1.30E-02

rs11656665 17 17724789 G A 0.4195 0.0124 0.0049 2.17E-02

rs1108511 17 17726469 T C 0.0620 0.0093 0.0100 6.00E-01

rs9899634 17 17727943 T A 1.0000 0.0120 0.0048 2.37E-02

rs8066560 17 17728043 A G 0.3971 0.0128 0.0048 1.63E-02

rs9902941 17 17733760 C T 0.4037 0.0121 0.0048 2.48E-02

rs1889018 17 17734740 G A 0.4090 0.0118 0.0048 2.70E-02

rs4925118 17 17739163 T C 0.1082 0.0125 0.0083 4.00E-01

ABCG1-TG

rs12626718 21 43618652 A G 0.9169 0.0036 0.0101 4.74E-01

rs4148082 21 43619415 G A 0.9169 0.0033 0.0101 4.86E-01

rs1378577 21 43619665 T G 0.7863 0.0063 0.0060 5.40E-01

rs4148083 21 43620158 C T 0.9169 0.0037 0.0101 4.69E-01

rs4148086 21 43620427 T C 0.9169 0.0035 0.0102 4.69E-01

rs9975740 21 43620485 T A 1.0000 0.0105 0.0071 3.93E-01

rs7283103 21 43620856 G A 0.9169 0.0037 0.0100 4.59E-01

rs4148087 21 43622267 G A 0.8694 0.0079 0.0073 6.53E-01

rs10084554 21 43623281 G T 0.7441 0.0083 0.0055 3.69E-01

rs10084555 21 43623379 G A 0.9921 0.0145 0.0185 6.22E-01

rs12626951 21 43624272 A G 0.9169 0.0033 0.0103 5.05E-01

rs1117640 21 43625274 T G 0.8707 0.0080 0.0070 6.14E-01

rs1840593 21 43626673 G A 0.7441 0.0086 0.0059 3.38E-01

rs221948 21 43633193 A G 0.1148 0.0033 0.0100 7.06E-01

rs915845 21 43635438 T G 0.8588 0.0080 0.0071 6.24E-01

rs4148095 21 43635956 T C 0.9525 0.0167 0.0113 2.61E-01

rs2234715 21 43638855 A G 0.9261 0.0007 0.0113 6.21E-01

rs4148101 21 43640183 G A 0.8628 0.0112 0.0071 3.93E-01

35

rs4148102 21 43641347 G A 0.8602 0.0099 0.0069 5.30E-01

rs4148103 21 43641605 A G 0.0778 0.0008 0.0123 6.85E-01

rs9976024 21 43641657 G A 0.8628 0.0111 0.0072 4.17E-01

rs4148104 21 43642438 T C 0.0778 0.0044 0.0129 9.79E-01

rs3787968 21 43650387 A G 0.5633 0.0067 0.0047 1.98E-01

rs3827225 21 43650779 G A 0.7639 0.0066 0.0054 3.27E-01

rs3787970 21 43651556 C T 0.5594 0.0068 0.0047 2.18E-01

rs3787972 21 43651705 T C 0.5594 0.0070 0.0047 2.06E-01

rs881395 21 43652410 C T 0.6689 0.0059 0.0051 2.72E-01

rs225440 21 43653053 C T 0.6069 0.0077 0.0048 1.85E-01

rs915847 21 43657248 G A 0.6715 0.0065 0.0051 2.00E-01

rs225443 21 43658206 G A 0.6491 0.0061 0.0049 1.89E-01

rs225444 21 43658226 G C 1.0000 0.0076 0.0047 1.59E-01

rs225445 21 43658444 T C 0.5633 0.0073 0.0047 1.70E-01

rs225447 21 43658979 A G 0.5633 0.0076 0.0047 1.50E-01

rs225448 21 43659830 T C 0.6319 0.0084 0.0050 1.67E-01

rs9978671 21 43660279 T C 0.0462 0.0034 0.0104 8.66E-01

rs13052462 21 43661920 C A 0.6873 0.0054 0.0054 4.05E-01

rs178744 21 43662796 C T 0.6781 0.0063 0.0054 3.99E-01

rs7283699 21 43663318 G A 0.9512 0.0017 0.0110 7.63E-01

rs9982196 21 43664647 A T NA 0.0006 0.0111 9.73E-01

rs4148117 21 43666065 T C 0.5660 0.0066 0.0052 2.81E-01

rs9974658 21 43666701 A G 0.0488 0.0013 0.0111 9.81E-01

rs11909889 21 43667961 A G 0.0198 0.0054 0.0177 7.67E-01

rs9978842 21 43668916 G C 1.0000 0.0037 0.0108 8.39E-01

rs12329683 21 43669610 G T 0.0501 0.0037 0.0108 8.28E-01

rs9982242 21 43671120 G C 1.0000 0.0058 0.0142 9.29E-01

rs225374 21 43671633 C G NA 0.0055 0.0072 3.17E-01

rs4148120 21 43673477 G C 1.0000 0.0026 0.0073 4.96E-01

rs7279750 21 43674684 T C 0.7731 0.0064 0.0070 3.07E-01

rs7281093 21 43674859 G A 0.7731 0.0065 0.0070 3.06E-01

rs7281345 21 43674982 G A 0.8325 0.0031 0.0071 4.98E-01

rs225378 21 43675694 G A 0.5330 0.0075 0.0052 2.74E-01

rs4148121 21 43675834 C T 0.0079 0.0272 0.0289 4.98E-01

rs183436 21 43677831 A C 0.7005 0.0062 0.0055 5.54E-01

rs3787986 21 43678808 C T 0.8285 0.0019 0.0069 5.83E-01

rs915841 21 43679438 T C 0.8285 0.0025 0.0069 5.50E-01

rs915842 21 43679513 C T 0.8285 0.0029 0.0069 5.20E-01

rs915843 21 43679554 C T 0.8285 0.0027 0.0069 5.35E-01

rs9974417 21 43679644 A G 0.0185 0.0139 0.0215 5.34E-01

rs9976804 21 43679862 A G 0.0185 0.0137 0.0215 4.86E-01

rs17114590 21 43681956 A G 0.8325 0.0022 0.0069 5.75E-01

rs225383 21 43682244 T C 0.4974 0.0021 0.0034 4.63E-01

rs4148122 21 43682365 A G 0.0185 0.0199 0.0200 3.81E-01

rs225384 21 43682394 A G 0.4974 0.0033 0.0051 6.24E-01

rs225385 21 43682686 A G 0.4974 0.0042 0.0050 5.02E-01

rs225386 21 43682938 G A 0.5158 0.0071 0.0051 2.39E-01

rs9980952 21 43682959 G A 0.9842 0.0109 0.0223 7.09E-01

rs225387 21 43683053 G A 0.4974 0.0057 0.0051 3.33E-01

rs9975218 21 43684299 G A 0.0185 0.0105 0.0201 6.27E-01

rs17767083 21 43684321 T C 0.1240 0.0103 0.0083 1.31E-01

36

rs225388 21 43684456 A G 0.4960 0.0058 0.0051 3.20E-01

rs225391 21 43684668 G A 0.9143 0.0078 0.0099 6.65E-01

rs225393 21 43685123 G A 0.5185 0.0071 0.0052 2.43E-01

rs225396 21 43687354 T C 0.4974 0.0039 0.0051 4.85E-01

rs225398 21 43688594 C G NA 0.0043 0.0055 5.40E-01

rs532345 21 43689491 T C 0.4116 0.0025 0.0052 9.96E-01

rs691687 21 43689870 G A 0.4116 0.0021 0.0051 9.85E-01

rs482303 21 43691469 G C 1.0000 0.0096 0.0085 3.46E-01

rs2298689 21 43696833 G A 0.9156 0.0024 0.0098 5.34E-01

rs2234718 21 43697195 G A 0.2401 0.0039 0.0059 5.70E-01

rs4148123 21 43698251 A G 0.3773 0.0046 0.0052 8.69E-01

rs3787995 21 43698914 G C 1.0000 0.0058 0.0095 3.64E-01

rs225406 21 43699230 G A 0.8892 0.0112 0.0080 1.82E-01

rs2839482 21 43700432 G A 0.1873 0.0009 0.0060 8.99E-01

rs225410 21 43700907 T C 0.5224 0.0015 0.0050 7.08E-01

rs492338 21 43701977 G A 0.5290 0.0012 0.0052 6.15E-01

rs3788007 21 43706776 A G 0.2005 0.0048 0.0076 7.47E-01

rs450808 21 43706944 T C 0.2098 0.0192 0.0090 8.36E-02

rs425215 21 43707101 C G NA 0.0039 0.0085 5.98E-01

rs7277991 21 43709682 T G 0.3734 0.0034 0.0050 7.54E-01

rs7275482 21 43709700 C T 0.7995 0.0084 0.0066 2.22E-01

rs4148137 21 43710052 T C 0.3786 0.0029 0.0052 3.71E-01

rs2234721 21 43710096 T G 0.3773 0.0017 0.0052 4.67E-01

rs4148139 21 43710774 G A 0.8061 0.0085 0.0073 1.89E-01

rs914189 21 43710909 C G NA 0.0075 0.0066 2.62E-01

rs13050646 21 43712049 G T 1.0000 0.0039 0.0114 6.50E-01

rs9975333 21 43714517 A C 0.4169 0.0032 0.0049 7.90E-01

rs474142 21 43714579 A G 0.0330 0.0122 0.0159 8.15E-01

rs2276235 21 43715013 A C 0.4169 0.0031 0.0048 7.95E-01

rs3788010 21 43716022 G A 0.4129 0.0039 0.0047 6.90E-01

rs1541290 21 43718483 G A 0.4921 0.0033 0.0048 7.76E-01

rsID, genetic variant identification; chr, chromosome location; pos, genomic position; A1, risk allele; A2, non-risk

allele; Freq_A1, risk allele frequency; coef, regression coefficient; SE, standard error; pval, p-value of the assocition.

identification and validation of seven new loci showing

Documents