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SUPPLEMENTARY INFORMATION FOR
Exhaustive search for epistatic effects on the human methylome
Authors:
Tobias Egli1,2, Vanja Vukojevic1,2,4, Thierry Sengstag6,7, Martin Jacquot6, Rubén Cabezón6, David
Coynel2,5, Virginie Freytag1,2, Angela Heck1,2,3, Christian Vogler1,2,3, Dominique J.-‐F. de
Quervain2,3,5, Andreas Papassotiropoulos1,2,3,4, Annette Milnik1,2,3,*
Affiliations:
1 Division of Molecular Neuroscience, Department of Psychology, University of Basel, CH-‐4055 Basel, Switzerland
2 Transfaculty Research Platform Molecular and Cognitive Neurosciences, University of Basel, CH-‐4055 Basel, Switzerland
3 Psychiatric University Clinics, University of Basel, CH-‐4055 Basel, Switzerland 4 Department Biozentrum, Life Sciences Training Facility, University of Basel, CH-‐4056
Basel, Switzerland 5 Division of Cognitive Neuroscience, Department of Psychology, University of Basel, CH-‐
4055 Basel, Switzerland 6 sciCORE, Scientific Computing Center, University of Basel, CH-‐4056 7 SIB -‐ Swiss Institute of Bioinformatics
*Corresponding author
Annette Milnik
University of Basel, Division of Molecular Neuroscience
Birmansgasse 8, CH-‐4009 Basel
Phone: + 41 61 267 0267
2
Supplementary Text
Affymetrix SNP 6.0 based genotyping. Genomic DNA concentration was adjusted to 50 ng/μl
in water. Digestion was done with 250 ng of DNA, in parallel with 10 units of Sty I and Nsp I
restriction enzymes (New England Biolabs, Knowl Piece, UK) for 2 hours at 37 °C. Following,
enzyme specific adaptor oligonucleotides were ligated onto the digested ends with T4 DNA
Ligase for 3 hours at 16°C. After adjusting volume to 100 μl with water, 10 μl of the diluted
ligation reactions were subjected to PCR. Three PCR reactions of 100 μl were performed for Sty
digested products and four PCR reactions for Nsp. PCR was performed with Titanium Taq DNA
Polymerase (Clontech, Mountain View, CA) in the presence of 4.5 µM PCR primer 002
(Affymetrix, Santa Clara, CA), 350 µM each dNTP (Clontech), 1M G-‐C Melt (Clontech), and 1 X
Titanium Taq PCR Buffer (Clontech). Following cycling parameters were used: 94 °C, 3 min; 30 x
(94 °C, 30 s; 60 °C, 45 s; 68 °C, 15 s); 68 °C, 7 min. PCR products expected in the range size
between 200-‐1100 bp were verified using 2 % (weight/volume) TBE gel electrophoresis. PCR
products were pooled and purified with the Filter Bottom Plate (Millipore, Billerica, MA; P/N
MDRLN0410) using Agencourt AMPure XP Beads (Beckman Coulter, Fuillerton, CA).
Quantification of purified PCR products was done on a Zenith 200rt microplate reader (Anthos-‐
Labtec, Cambridge, UK), with average yield of 4 to 5 μg/μl per sample. Subsequently, the SNP
Nsp/Sty 5.0/6.0 Assay Kit (Affymetrix) was used. For the fragmentation around 250 μg of
purified PCR products was digested using 0.5 units of DNAse I at 37°C for 35 minutes. Average
size of fragmentation products less than 180 bps was verified using 4 % (weight/volume) TBE
gel electrophoresis. Following, the DNA was end labeled with 105 units of terminal
deoxynucleotidyl transferase at 37 °C for 4 hours. The labeled DNA was then hybridized onto
Genome-‐Wide Human SNP 6.0 Array at 50 °C for 18 hours at 60 rpm. The hybridized array was
washed, stained, and scanned according to the manufacturer’s (Affymetrix) instructions using
Affymetrix GeneChip Command Console (AGCC, version 3.2.0.1515). Generation of SNP calls and
array quality control were performed using the command line programs of the Affymetrix Power
Tools package (version: apt-‐1-‐14.4.1). According to the manufacturer’s recommendation,
3
Contrast QC was chosen as QC metric, using the default value of greater or equal than 0.4. All
samples passing QC criteria were subsequently genotyped using the Birdseed (v2) algorithm.
HumanMethylation Infinium 450K BeadChip based methylation analyses. Samples were
collected using BD Vaccutainer Push Button blood collection set and 10.0 mL BD Vacutainer®
Plus plastic whole blood tube, BD Hemogard™ closure with spray-‐coated K2EDTA (Becton,
Dickinson and Company , New Jersey, NJ). Hematological analysis, including blood cell counts,
was performed at the collection time point with Sysmex pocH-‐100i™ Automated Hematology
Analyzer (Sysmex Co, Kobe, JP.) DNA was isolated from the remaining fraction, upon plasma
removal. The isolation was performed with QIAmp Blood Maxi Kit (Qiagen AG, Hilden, DE), using
the recommended spin protocol.
In order to obtain high purity DNA prior to bisulfite conversion, isolated DNA samples
were additionally re-‐purified. For this purpose, 2 µg of DNA isolated with QIAmp/Oragene
procedure, was incubated overnight at 50 °C with proteinase K (Lysis buffer: 30 mM Tris·Cl; 10
mM EDTA; 1 % SDS, pH 8.0; 150ng/µl Proteinase K), agitated by gentle orbital shaking. Next, the
DNA was purified using Genomic DNA Clean & Concentrate Kit (Zymo Research, Irvine, CA). The
quality and concentration of DNA were assessed using gel electrophoresis, NanoDrop ND-‐ 1000
(Thermo Scientific, Waltham, MA) and fluorometry measurements (Qubit dsDNA BR Assay Kit;
Invitrogen, Carlsbad, CA), respectively.
The bisulfite conversion was performed with 500 ng genomic DNA input using the EZ DNA
Methylation Gold Kit (Zymo Research). A bisulfite conversion quality control on the probes was
performed with DNA qPCR reaction and subsequent melting curve analysis 1. The bisulfite-‐
converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina,
Inc, San Diego, CA), according to the manufacturer's instructions. The BeadChip images were
scanned on the iScan system (performed at ServiceXS B.V., Leiden, Netherlands).
N = 568 subjects of the discovery sample were processed in two batches (2 plates and 4
plates, respectively). For the replication sample, N = 319 subjects were processed within a single
4
batch (4 plates). Within a batch samples were processed with a randomized plate assignment
and with a single bisulfite conversion. Preprocessing was done separately for each batch. Data
were extracted and analyzed from the generated idat files using the R package RnBeads version
0.99.9 2. CpG annotation was based on the manufactures annotation file
(HumanMethylation450_15017482_v.1.2). During preprocessing, the background was
subtracted using the “noob” method in the methylumi package 3, and the signal was further
normalized using the SWAN algorithm 4. The following probe categories were excluded from the
final data sets, based on the annotation provided within the RnBeads package: non-‐CpG context
probes (due to underrepresentation on the 450K array, 0.6 %, 5, functional differences when
compared to CpG context as well as very low abundance of non-‐CpG methylation in somatic
tissues 6; N = 3,091), probes with a SNP mapping directly to the target CpG site, as well as probes
with three and more SNPs mapping within the 50mer probe (MAF threshold was set to 0.01;
N = 18,998 CpGs ), gonosomal probes (N = 11,473 CpGs), non-‐specific probes. Using the
Greedycut algorithm, we iteratively removed the probes and data sets of the highest impurity
(rows and columns in the detection p-‐value table that contain the largest fraction of unreliable
measurements; p < 0.05 2). We performed a cross-‐platform validation of genotyping and
methylation data using the reported sex and the sex-‐predictions based on the arrays data, as
well as matching of all SNPs represented on the Illumina 450K array to the corresponding
Affymetrix SNP 6.0 or imputation derived genotype calls. This crosscheck allowed an
unambiguous assignment of each methylation dataset to the corresponding genetic and
phenotypic dataset.
Affymetrix HTA 2.0 array transcriptome analysis. Total RNA was further isolated with the
PAXgene Blood miRNA Kit (PreAnalytix, Switzerland). Following, a second, additional
purification was performed with the miRNeasy Micro Kit (Qiagen, Germany). The concentration
and quality of the RNA was determined using Nanodrop 2000 (ThermoScientific, USA) and RNA
Nano 6000 Kit on Bioanalyzer 2100 instrument (Agilent, USA). Next, GLOBINclear™-‐Human Kit
(Ambion, USA) was used for a non-‐enzymatic depletion of the alpha and beta globin mRNA
5
starting from 1 µg of total RNA preparations derived from whole blood, following a standard
procedure. The concentration and quality of the “globin-‐free” RNA was assessed as described
above. Following, the alpha and beta globin mRNA depletion was measured by qPCR. In brief: for
reverse transcription, 350 ng of total RNA was denaturized for 8 min at 70 °C followed by ice
incubation in the presence of 25 ng Anchored Oligo(dT)20 Primer (Invitrogen, USA) and 75 ng
Random Decamers Primers (Ambion, USA). In the RT reaction, cDNA was generated in 25 µl
reaction using Super RT kit (HT Biotechnology, Santa Cruz, CA USA). Upon completion of the
reaction, the volume was adjusted to 200 µl in Lambda DNA solution (5 ng/µl final
concentration; Promega, Fitchburg, WI USA). The primers were designed against splice variants
that contain alpha-‐Globin gene: alpha-‐Globin Forward: 5’-‐ GCACGCGCACAAGCT-‐3’, and alpha-‐
Globin Reverse: 5’-‐ GGGTCACCAGCAGGCA-‐3’ (Microsynth, Switzerland). The expression levels
were normalized to RPLPO gene (human large ribosomal protein) using the following primers:
RPLP0-‐Ex3-‐4_FW, 5’-‐CTCTGGAGAAACTGCTGC-‐3’ and RPLP0-‐Ex3-‐4_RV, 5’-‐
CTGATCTCAGTGAGGTCC-‐3’ (Sigma Aldrich, USA). qPCR was performed using the Power SYBR
Green PCR Master Mix (Life Technologies, USA) according to standard recommendations, in
12 µl final volume of reaction, using 2 µl of cDNA template, on RotorGene 6000A instrument
(Corbett Research Pty Ltd, Sydney Australia). Cycling conditions were as follows: 95 °C, 60 s –
40x (95 °C, 3 s – 56 °C, 10s – 72°C, 4 s) followed by a melting curve analysis (61 °C to 95 °C,
rising by 0.7 °C / 3s) to attest amplification specificity. Threshold cycles (crossing point) were
determined using Rotor-‐Gene software version 6.1 (Corbett Research, Australia). RPLPO was
selected as reference gene for normalization after we tested several candidate-‐reference genes,
as had been previously described 7. Expression levels were normalized using a geometric mean
level of expression 7. Fold differences were calculated using the delta-‐delta Ct method 8 with the
help of qBasePlus software (Biogazelle, Ghent, Belgium).
Target synthesis was performed using Ambion® WT Expression Kit (Ambion, Life
Technologies, USA) starting from 250ng of high-‐quality “globin-‐free” RNA, following the
standard procedure. Next, 5.16µg of target cDNA was further labeled and prepared for
hybridization with the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix,
6
USA). The prepared samples were loaded on Affymetrix GeneChip Human Transcriptome Array
2.0 (Cat# 902162) and hybridized for 16 hours (45 °C, 60 rpm) in Hybridization oven 640
(Affymetrix, USA). The arrays were washed and stained on Fluidics Stations 450 (Affymetrix) by
using the Hybridization Wash and Stain Kit (Affymetrix, USA) under FS450_0001 protocol. The
GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, USA).
DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip
Command Control software (Affymetrix, USA). In order to account for technical inter-‐array
variation we performed a full quantile-‐normalization; feature quantification was conducted
using a median-‐polish on transcript-‐level according to the HTA 2.0. lib-‐set-‐version 0.3.
(Affymetrix Power Tools version: 1.16.0). Cross-‐platform validation of genotyping and
expression data was assessed using the MixUpMaper algorithm 9.
7
References
1. Kristensen, L. S., Mikeska, T., Krypuy, M. & Dobrovic, A. Sensitive Melting Analysis after
Real Time-‐ Methylation Specific PCR (SMART-‐MSP): high-‐throughput and probe-‐free
quantitative DNA methylation detection. Nucleic Acids Res. 36, e42 (2008).
2. Assenov, Y. et al. Comprehensive analysis of DNA methylation data with RnBeads. Nat.
Methods 11, 1138–1140 (2014).
3. Davis S, Du P, Bilke S, Triche T Jr & Bootwalla M. methylumi: Handle Illumina methylation
data. R package version 2.12.0. (2014).
4. Maksimovic, J., Gordon, L. & Oshlack, A. SWAN: Subset-‐quantile within array
normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 13,
R44 (2012).
5. Bibikova, M. et al. High density DNA methylation array with single CpG site resolution.
Genomics 98, 288–295 (2011).
6. Ziller, M. J. et al. Genomic distribution and inter-‐sample variation of non-‐CpG methylation
across human cell types. PLoS Genet. 7, e1002389 (2011).
7. Vandesompele, J. et al. Accurate normalization of real-‐time quantitative RT-‐PCR data by
geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034
(2002).
8. Pfaffl, M. W. A new mathematical model for relative quantification in real-‐time RT-‐PCR.
Nucleic Acids Res. 29, e45 (2001).
9. Westra, H.-‐J. et al. MixupMapper: correcting sample mix-‐ups in genome-‐wide datasets
increases power to detect small genetic effects. Bioinformatics 27, 2104–2111 (2011).
8
Supplementary Figures
Supplementary Figure S1. Genetic background. Genetic data from both samples (a, discovery
sample; b, replication sample) is projected on the two first PCA components inferred from
HapMap reference populations (YRI, CEU and CHB-‐JPT populations). Only subjects with
European ancestry (red dots) were included in the analyses.
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−0.04 −0.02 0.00 0.02
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Hapmap Axis 1
Hap
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−0.06 −0.04 −0.02 0.00 0.02 0.04
−0.0
4−0
.02
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0.06
0.08
Hapmap Axis 1
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Replication sampleallincluded
b
9
Supplementary Figure S2. CpG-‐data discovery sample, multidimensional scaling over
samples. Depicted are scatterplots between the first five dimensions. The analysis is based on
40,000 randomly chosen CpGs without missing values.
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V5
10
Supplementary Figure S3. CpG-‐data replication sample, multidimensional scaling over
samples. Depicted are scatterplots between the first five dimensions. The analysis is based on
40,000 randomly chosen CpGs without missing values.
V1
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−40 0 20 60 100−40
020
60100
V5
11
Supplementary Figure S4. Exhaustive search for epistatic effects, sign-‐test for the
interaction term. Results are shown for the N = 4,816 interaction analyses that survived the
initial replication based on a per-‐CpG Bonferroni-‐correction (before sign-‐test and permutation).
We compared the average CpG-‐values of the 9 combined genotype-‐groups between the
screening and replication sample with Pearson’s correlations. The red dashed line corresponds
to r = 0.85, which we used as threshold to determine interaction effects that show the same
direction of effect in both samples.
r
Frequency
−1.0 −0.5 0.0 0.5 1.0
0500
1000
1500
2000
2500
3000
12
Supplementary Figure S5. Distribution of r2-‐values between independent SNPs. In the
discovery sample we determined a sample-‐specific threshold for Linkage Disequilibrium (LD) by
estimating for 10,000 randomly drawn SNPs the association (r2) with 10,000 random SNPs
located on a different chromosome. Based on this result SNP-‐pairs showing values large than
r2 = 0.021 (p < 0.001) were considered as showing LD.
0.00 0.02 0.04 0.06 0.08
0500
1000
1500
r2
Density
13
Supplementary Figures S6. Exhaustive search per-‐CpG models. Shown are the genomic
locations for each of the 174 CpGs and all SNPs that were kept in the final per-‐CpG model. The
top panel depicts information from the knownGene table (hg19) derived from UCSC genome
browser (UCSC-‐GB). The second to panel (grey horizontal bar) depicts transcripts from the
Affymetrix HTA 2.0 array that were significantly associated with the CpG signal in the discover
sample. The next three panels depict information for CpG Islands, transcription factor binding
sites (TFBS) and DNase I hypersensitivity sites (DNase I) derived from UCSC-‐GB. The next panel
(CpG beta discovery sample) shows the average beta-‐values of CpGs and the 5 % -‐ 95 %
percentile in orange. The genomic location of each CpG is depicted with vertical grey lines. Data
is shown for the discovery sample. The next panel shows the CpG (brown dot) and all SNPs
(triangles and rhombi) that were kept in the final per-‐CpG-‐model. Interacting SNPs are shown as
triangles in the same color. Black rhombi describe SNPs with a significant main effect in the full
model. The next two panels (R2 discovery and R2 replication sample) depict the main effects of
each SNP on the CpG signal, independently estimated. The red dashed line shows the variance
explained by the per-‐CpG-‐model including main effects only, whereas the blue dashed line
depicts the variance explained by the full model (including interaction effects). The bottom
panel shows the LD between SNPs, an r2 < 0.021 is shown in white.
2
0.01
1
0.021
0 1R2
cg05117823
Chr1:3046252−3057152R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3047252 3049477 3051702 3053927 3056152
rs2817178
rs2235176●
cg05117823
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PRDM16 uc001akc.3PRDM16 uc001ake.3PRDM16 uc001akf.3knownGene
(UCSC hg19)
2kb
8
0.06
0.62
0.03
0.01
0.56
0.49
0.5
7
0.09
0.36
0.32
0.09
0.03
0.03
6
0.26
0.18
0.91
0.4
0.4
5
0.87
0.25
0.09
0.09
4
0.26
0.11
0.11
3
0.36
0.37
2
0.99
1
0.021
0 1R2
cg24879939
Chr1:3217923−3237041R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3218329 3222757 3227185 3231613 3236041
rs2500283
rs10909924
rs12086132
rs12409315●
cg24879939
rs2483266
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PRDM16 uc001akc.3PRDM16 uc001ake.3PRDM16 uc001akf.3knownGene
(UCSC hg19)
2kb
6
0
0
0
0
0
5
0
0
0.01
0
4
0.99
0
0
3
0
0
2
0.01
1
0.021
0 1R2
cg24196422
Chr1:3713033−3717982 Chr13:76697340−76699340 Chr18:39038714−39040714 Chr21:27102614−27104614R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs7543006●
cg24196422
rs11149021
rs4318293
rs2829887
●CpG
Main effect
No effect
Interaction effect
TC01002136.hg.1 / ENST00000378251
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LRRC47 uc001akx.1ATP5J uc002yls.3ATP5J uc002ylt.3
ATP5J uc002ylu.3 promotor
Exon
knownGene(UCSC hg19)
4kb
11
0.08
0.8
0.11
0.8
0.42
0.1
0.13
0.01
0.33
0.11
10
0.06
0.02
0.07
0.09
0.01
0.19
0
0.03
0.02
9
0.09
0.99
0.57
0.13
0.04
0
0.26
0.09
8
0.09
0.15
0.02
0.08
0.01
0.04
0.79
7
0.57
0.13
0.05
0
0.27
0.09
6
0.11
0.27
0.01
0.45
0.17
5
0.03
0
0.05
0.02
4
0.01
0.24
0.1
3
0.02
0.11
2
0.07
1
0.021
0 1R2
cg20200200
Chr1:18791300−18810896R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
18792300 18796699 18801098 18805497 18809896
rs12144656
rs11261014
rs3007728
rs6665151
rs7528206●
cg20200200
rs2992753
rs2992751
rs2992745
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
KLHDC7A uc001bax.3KLHDC7A uc009vpg.3
promotor
Exon
knownGene(UCSC hg19)
2kb
9
0.06
0.02
0.07
0.09
0.01
0.19
0
0.03
8
0.09
0.99
0.57
0.13
0.04
0
0.26
7
0.09
0.15
0.02
0.08
0.01
0.04
6
0.57
0.13
0.05
0
0.27
5
0.11
0.27
0.01
0.45
4
0.03
0
0.05
3
0.01
0.24
2
0.02
1
0.021
0 1R2
cg13507429
Chr1:18792636−18809711R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
18793636 18797405 18801174 18804943 18808711
rs11261014
rs3007728
rs6665151●
cg13507429
rs2992753
rs2992751
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
KLHDC7A uc001bax.3KLHDC7A uc009vpg.3
promotor
Exon
knownGene(UCSC hg19)
2kb
12
0.12
0.99
0.08
0.03
0.8
0.93
0.93
0.08
0.05
0.36
0.81
11
0.12
0.02
0.29
0.16
0.13
0.13
0.02
0.01
0.31
0.14
10
0.08
0.03
0.81
0.94
0.94
0.08
0.05
0.35
0.82
9
0.01
0.09
0.08
0.08
0.96
0
0.12
0.07
8
0.05
0.03
0.03
0.01
0.01
0.09
0.04
7
0.84
0.85
0.09
0.05
0.38
0.91
6
0.99
0.09
0.01
0.31
0.77
5
0.09
0.01
0.31
0.77
4
0
0.11
0.08
3
0
0.01
2
0.42
1
0.021
0 1R2
cg20432732
Chr1:19404237−19452037R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
19405237 19416687 19428137 19439587 19451037
rs2146866
rs12164540
rs10916957●
cg20432732
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
UBR4 uc001bbi.3UBR4 uc001bbh.3
UBR4 uc001bbk.1knownGene(UCSC hg19)
5kb
0.021
0 1R2
cg24502330
Chr1:20828560−20998340R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
20829560 20871505 20913450 20955395 20997340
rs2641114
rs639400●
cg24502330
rs577042
rs12072405
rs10157351
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MUL1 uc001bdi.4FAM43B uc001bdj.3
CDA uc001bdk.3CDA uc001bdl.3CDA uc009vpv.3
PINK1 uc001bdm.3PINK1 uc001bdn.3
DDOST uc001bdo.1DDOST uc010odd.1DDOST uc010ode.1
KIF17 uc001bdr.4KIF17 uc001bds.4KIF17 uc009vpx.3
promotor
Exon
knownGene(UCSC hg19)
17kb
0.021
0 1R2
cg11070193
Chr1:26503756−26667809R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
26504756 26545270 26585783 26626296 26666809
rs2783631
rs12732022
rs11247870●
cg11070193
rs12145403
rs10902741
●CpG
Main effect
No effect
Interaction effect
TC01000339.hg.1 / ENST00000451429TC01000341.hg.1 / ENST00000270792
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CNKSR1 uc001blm.4CNKSR1 uc001bln.4CNKSR1 uc009vsd.3
CATSPER4 uc009vsf.3CATSPER4 uc010oey.1CATSPER4 uc010oez.2
BC030768 uc001blq.3CEP85 uc001bls.1CEP85 uc010ofa.1
CEP85 uc001blt.1SH3BGRL3 uc001blu.3
UBXN11 uc001bma.3UBXN11 uc001blw.3UBXN11 uc001blx.3
CD52 uc001bmc.3CD52 uc009vsg.1
AIM1L uc001bmd.4AIM1L uc001bmf.3
promotor
Exon
knownGene(UCSC hg19)
17kb
0.021
0 1R2
cg20415053
Chr1:26500044−26693050R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
26501044 26548796 26596547 26644299 26692050
rs2783626
rs2783631
rs11247868
rs12732022
rs6660744
rs11247870●
cg20415053
rs17163749
rs10902741
rs4354529
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC01000341.hg.1 / ENST00000270792TC01000339.hg.1 / ENST00000451429
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CNKSR1 uc001blm.4CNKSR1 uc001bln.4CNKSR1 uc009vsd.3
CATSPER4 uc009vsf.3CATSPER4 uc010oey.1CATSPER4 uc010oez.2
BC030768 uc001blq.3CEP85 uc001bls.1CEP85 uc010ofa.1
CEP85 uc001blt.1SH3BGRL3 uc001blu.3
UBXN11 uc001bma.3UBXN11 uc001blw.3UBXN11 uc001blx.3
CD52 uc001bmc.3CD52 uc009vsg.1
AIM1L uc001bmd.4AIM1L uc001bmf.3
ZNF683 uc001bmg.1ZNF683 uc001bmh.1
ZNF683 uc009vsj.1
promotor
Exon
knownGene(UCSC hg19)
20kb
13
0.09
0.08
0.62
0.09
0.55
0.52
0.32
0.16
0.24
0.08
0.07
0.06
12
0.98
0.05
1
0.04
0.04
0.06
0.14
0.06
0.41
0.13
0.14
11
0.05
0.98
0.04
0.04
0.06
0.13
0.06
0.41
0.13
0.14
10
0.05
0.9
0.8
0.59
0.38
0.16
0.07
0.25
0.24
9
0.04
0.04
0.06
0.14
0.06
0.41
0.13
0.14
8
0.75
0.63
0.36
0.16
0.07
0.22
0.21
7
0.72
0.48
0.19
0.11
0.33
0.32
6
0.53
0.2
0.13
0.23
0.23
5
0.37
0.01
0.06
0.06
4
0.12
0.1
0.1
3
0.38
0.38
2
0.99
1
0.021
0 1R2
cg16585132
Chr1:38232399−38465943R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
38233399 38291285 38349171 38407057 38464943
rs482818
rs1050257
rs10890238●
cg16585132
●CpG
Main effect
No effect
Interaction effect
TC01002530.hg.1 / ENST00000485803TC01002529.hg.1 / ENST00000373019
TC01005411.hg.1 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
MANEAL uc001cbx.2MANEAL uc001cby.2MANEAL uc001cbz.2
YRDC uc001cca.1C1orf122 uc001ccd.2C1orf122 uc010oii.1
MTF1 uc001cce.1MTF1 uc009vvj.1
INPP5B uc001ccg.1INPP5B uc009vvk.1
INPP5B uc001cch.3SNORA63 uc021oln.1
SF3A3 uc001cci.3SF3A3 uc010oik.2
FHL3 uc001cck.3FHL3 uc001ccm.3
FHL3 uc009vvl.2
promotor
Exon
knownGene(UCSC hg19)
24kb
0.021
0 1R2
cg06209491
Chr1:40103461−40194772R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
40104461 40126789 40149117 40171445 40193772
rs784623
rs784595●
cg06209491
rs12039225
rs11579412
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
HEYL uc001cdp.3NT5C1A uc001cdq.1
HPCAL4 uc001cdr.3HPCAL4 uc010oix.2 promotor
Exon
knownGene(UCSC hg19)
9kb
17
0.99
0.17
0.17
0.99
0.06
0.99
0.99
0.04
0.01
0.02
0
0.69
0.48
0
0
0.54
16
0.17
0.17
1
0.06
1
1
0.03
0.01
0.02
0
0.7
0.49
0
0
0.54
15
1
0.17
0.34
0.17
0.17
0.27
0.18
0.19
0.06
0.13
0.02
0.06
0.08
0.03
14
0.17
0.34
0.17
0.17
0.27
0.18
0.19
0.06
0.13
0.02
0.06
0.08
0.03
13
0.06
1
1
0.03
0.01
0.02
0
0.69
0.49
0
0
0.54
12
0.06
0.06
0.71
0.45
0.45
0.16
0.03
0.01
0.14
0.17
0
11
1
0.04
0.01
0.02
0
0.69
0.49
0
0
0.54
10
0.03
0.01
0.02
0
0.69
0.48
0
0
0.54
9
0.68
0.69
0.29
0.04
0.01
0.27
0.3
0.01
8
0.96
0.33
0.03
0.03
0.39
0.34
0.02
7
0.33
0.03
0.02
0.4
0.35
0.02
6
0.07
0.05
0.93
0.93
0
5
0.42
0.07
0.06
0.77
4
0.06
0.06
0.46
3
0.89
0
2
0
1
0.021
0 1R2
cg09408571
Chr1:100942100−101047940R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
100943100 100969258 100995415 101021573 101047730
rs3767832
rs1063302
rs7529081●
cg09408571
rs2809818
rs17402665
●CpG
Main effect
No effect
Interaction effect
TC01000902.hg.1 / ENST00000336454
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CDC14A uc001dtg.4CDC14A uc010oui.1
CDC14A uc009wee.3GPR88 uc001dth.3GPR88 uc021oqq.1
promotor
Exon
knownGene(UCSC hg19)
11kb
0.021
0 1R2
cg06223162
Chr1:100942100−101171999R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
100943100 101000164 101057227 101114291 101171354
rs3767832
rs1063302
rs7529081
rs6702766●
cg06223162
rs2809818
rs17402665
rs11578560
●CpG
Main effect
No effect
Interaction effect
TC01000902.hg.1 / ENST00000336454
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CDC14A uc001dtg.4CDC14A uc010oui.1
CDC14A uc009wee.3GPR88 uc001dth.3GPR88 uc021oqq.1
LOC100128787 uc021oqr.1promotor
Exon
knownGene(UCSC hg19)
23kb
0.021
0 1R2
cg21263664
Chr1:146498296−146581837R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
146499296 146519752 146540207 146560663 146581118
rs2355388
rs12122453
rs12122534
rs11240099
rs575115
rs584107
rs692963●
cg21263664
rs6593732
rs17160790
●CpG
Main effect
No effect
Interaction effect
TC01005785.hg.1TC01003123.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LOC728989 uc001epd.3TRNA_His uc021ovi.1
TRNA_Pseudo uc021ovj.1NBPF13P uc031poj.1 promotor
Exon
knownGene(UCSC hg19)
9kb
0.021
0 1R2
cg03526459
Chr1:146498296−146631916R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
146499296 146532201 146565106 146598011 146630916
rs2355388
rs12122534
rs11240099
rs575115
rs2031481
rs692963●
cg03526459
rs11239930
rs6593732
rs2304893
●CpG
Main effect
No effect
Interaction effect
TC01005785.hg.1TC01003123.hg.1
TC01003124.hg.1 / ENST00000254101 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LOC728989 uc001epd.3TRNA_His uc021ovi.1TRNA_Pseudo uc021ovj.1
NBPF13P uc031poj.1PRKAB2 uc001epe.3PRKAB2 uc010ozm.2PRKAB2 uc010ozn.2
promotor
Exon
knownGene(UCSC hg19)
14kb
0.021
0 1R2
cg00044796
Chr1:146503114−146553390R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
146504114 146516183 146528252 146540321 146552390
rs12122453
rs7514206
rs692963●
cg00044796
●CpG
Main effect
No effect
Interaction effect
TC01003123.hg.1TC01005785.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LOC728989 uc001epd.3TRNA_His uc021ovi.1
TRNA_Pseudo uc021ovj.1 promotor
Exon
knownGene(UCSC hg19)
5kb
0.021
0 1R2
cg08721112
Chr1:146503114−146554807R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
146504114 146516538 146528961 146541384 146553807
rs12122453
rs6657631
rs575115
rs692963●
cg08721112
●CpG
Main effect
No effect
Interaction effect
TC01005785.hg.1TC01003123.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LOC728989 uc001epd.3TRNA_His uc021ovi.1
TRNA_Pseudo uc021ovj.1 promotor
Exon
knownGene(UCSC hg19)
5kb
0.021
0 1R2
cg07796016
Chr1:152738226−152851938R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
152739226 152767154 152795082 152823010 152850938
rs10494277
rs950337
rs6694602
rs6701221
rs877656●
cg07796016
rs7411365
rs1930127
rs3737861
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
LCE1F uc010pdv.2LCE1E uc001fan.3
LCE1E uc021ozg.1LCE1D uc009wnp.3
LCE1D uc021ozh.1LCE1C uc001fap.1
LCE1C uc031ppd.1LCE1C uc021ozi.1
LCE1B uc001faq.3LCE1A uc010pdw.2
LCE6A uc001fas.4LCE6A uc021ozj.1
SMCP uc001fat.3
promotor
Exon
knownGene(UCSC hg19)
12kb
9
0.93
0.93
0.94
0.02
0.93
0.06
0.06
0.69
8
1
1
0.02
1
0.07
0.07
0.76
7
1
0.02
1
0.07
0.07
0.76
6
0.02
1
0.07
0.07
0.76
5
0.03
0.38
0.38
0.03
4
0.07
0.07
0.76
3
0.98
0.08
2
0.08
1
0.021
0 1R2
cg00404053
Chr1:178312656−178453629R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
178313656 178348400 178383143 178417886 178452629●
cg00404053
rs3791025
rs10913560
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RASAL2 uc001glq.3RASAL2 uc009wxb.2
RASAL2 uc001glr.3knownGene(UCSC hg19)
14kb
16
0.01
0.22
0.26
0.22
0.22
0
0
0
0
0.12
0.23
0
0.16
0
0.16
15
0.05
0.03
0.04
0.05
0.01
0
0
0.53
0.01
0.05
0.21
0.03
0.12
0.03
14
0.72
0.66
1
0.08
0.08
0.07
0.1
0.14
0.58
0.05
0.33
0.06
0.34
13
0.91
0.72
0.07
0.08
0.08
0.07
0.11
0.43
0
0.5
0
0.5
12
0.66
0.06
0.09
0.09
0.07
0.09
0.39
0
0.54
0
0.54
11
0.08
0.07
0.07
0.1
0.14
0.58
0.05
0.34
0.06
0.34
10
0
0
0.01
0.01
0.04
0.28
0.05
0.31
0.05
9
0.95
0.01
0.02
0.06
0.27
0.02
0.26
0.02
8
0.01
0.01
0.05
0.25
0.02
0.24
0.02
7
0.03
0.09
0.07
0.05
0.05
0.05
6
0.28
0.05
0.05
0.05
0.05
5
0.18
0.23
0.16
0.23
4
0.14
0.88
0.14
3
0.13
1
2
0.13
1
0.021
0 1R2
cg14159672
Chr1:205753688−205820179R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
205754688 205770811 205786934 205803057 205819179
rs10494874
rs823154
rs823091●
cg14159672
●CpG
Main effect
No effect
Interaction effect
TC01003755.hg.1 / ENST00000367136TC01004974.hg.1
TC01003754.hg.1 / ENST00000367137 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SLC41A1 uc001hdg.1SLC41A1 uc001hdh.1
AX748016 uc001hdi.1PM20D1 uc001hdj.3PM20D1 uc009xbr.3
promotor
Exon
knownGene(UCSC hg19)
7kb
16
0.01
0.22
0.26
0.22
0.22
0
0
0
0
0.12
0.23
0
0.16
0
0.16
15
0.05
0.03
0.04
0.05
0.01
0
0
0.53
0.01
0.05
0.21
0.03
0.12
0.03
14
0.72
0.66
1
0.08
0.08
0.07
0.1
0.14
0.58
0.05
0.33
0.06
0.34
13
0.91
0.72
0.07
0.08
0.08
0.07
0.11
0.43
0
0.5
0
0.5
12
0.66
0.06
0.09
0.09
0.07
0.09
0.39
0
0.54
0
0.54
11
0.08
0.07
0.07
0.1
0.14
0.58
0.05
0.34
0.06
0.34
10
0
0
0.01
0.01
0.04
0.28
0.05
0.31
0.05
9
0.95
0.01
0.02
0.06
0.27
0.02
0.26
0.02
8
0.01
0.01
0.05
0.25
0.02
0.24
0.02
7
0.03
0.09
0.07
0.05
0.05
0.05
6
0.28
0.05
0.05
0.05
0.05
5
0.18
0.23
0.16
0.23
4
0.14
0.88
0.14
3
0.13
1
2
0.13
1
0.021
0 1R2
cg14893161
Chr1:205753688−205820251R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
205754688 205770829 205786970 205803111 205819251
rs10494874
rs823154
rs823088●
cg14893161
●CpG
Main effect
No effect
Interaction effect
TC01003755.hg.1 / ENST00000367136TC01004974.hg.1
TC01003754.hg.1 / ENST00000367137 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SLC41A1 uc001hdg.1SLC41A1 uc001hdh.1
AX748016 uc001hdi.1PM20D1 uc001hdj.3PM20D1 uc009xbr.3
promotor
Exon
knownGene(UCSC hg19)
7kb
16
0.01
0.22
0.26
0.22
0.22
0
0
0
0
0.12
0.23
0
0.16
0
0.16
15
0.05
0.03
0.04
0.05
0.01
0
0
0.53
0.01
0.05
0.21
0.03
0.12
0.03
14
0.72
0.66
1
0.08
0.08
0.07
0.1
0.14
0.58
0.05
0.33
0.06
0.34
13
0.91
0.72
0.07
0.08
0.08
0.07
0.11
0.43
0
0.5
0
0.5
12
0.66
0.06
0.09
0.09
0.07
0.09
0.39
0
0.54
0
0.54
11
0.08
0.07
0.07
0.1
0.14
0.58
0.05
0.34
0.06
0.34
10
0
0
0.01
0.01
0.04
0.28
0.05
0.31
0.05
9
0.95
0.01
0.02
0.06
0.27
0.02
0.26
0.02
8
0.01
0.01
0.05
0.25
0.02
0.24
0.02
7
0.03
0.09
0.07
0.05
0.05
0.05
6
0.28
0.05
0.05
0.05
0.05
5
0.18
0.23
0.16
0.23
4
0.14
0.88
0.14
3
0.13
1
2
0.13
1
0.021
0 1R2
cg24503407
Chr1:205753688−205820492R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
205754688 205770889 205787090 205803291 205819492
rs10494874
rs823154
rs823088●
cg24503407
●CpG
Main effect
No effect
Interaction effect
TC01003755.hg.1 / ENST00000367136TC01004974.hg.1
TC01003754.hg.1 / ENST00000367137 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SLC41A1 uc001hdg.1SLC41A1 uc001hdh.1
AX748016 uc001hdi.1PM20D1 uc001hdj.3PM20D1 uc009xbr.3
promotor
Exon
knownGene(UCSC hg19)
7kb
16
0.01
0.22
0.26
0.22
0.22
0
0
0
0
0.12
0.23
0
0.16
0
0.16
15
0.05
0.03
0.04
0.05
0.01
0
0
0.53
0.01
0.05
0.21
0.03
0.12
0.03
14
0.72
0.66
1
0.08
0.08
0.07
0.1
0.14
0.58
0.05
0.33
0.06
0.34
13
0.91
0.72
0.07
0.08
0.08
0.07
0.11
0.43
0
0.5
0
0.5
12
0.66
0.06
0.09
0.09
0.07
0.09
0.39
0
0.54
0
0.54
11
0.08
0.07
0.07
0.1
0.14
0.58
0.05
0.34
0.06
0.34
10
0
0
0.01
0.01
0.04
0.28
0.05
0.31
0.05
9
0.95
0.01
0.02
0.06
0.27
0.02
0.26
0.02
8
0.01
0.01
0.05
0.25
0.02
0.24
0.02
7
0.03
0.09
0.07
0.05
0.05
0.05
6
0.28
0.05
0.05
0.05
0.05
5
0.18
0.23
0.16
0.23
4
0.14
0.88
0.14
3
0.13
1
2
0.13
1
0.021
0 1R2
cg07157834
Chr1:205753688−205820609R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
205754688 205770919 205787149 205803379 205819609
rs10494874
rs823154
rs823088●
cg07157834
●CpG
Main effect
No effect
Interaction effect
TC01003755.hg.1 / ENST00000367136TC01004974.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SLC41A1 uc001hdg.1SLC41A1 uc001hdh.1
AX748016 uc001hdi.1PM20D1 uc001hdj.3PM20D1 uc009xbr.3
promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg22029157
Chr1:209954848−210028026R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
209955848 209973643 209991437 210009232 210027026
rs651141
rs6685182
rs2236909●
cg22029157
rs642961
rs686582
rs684083
rs6689839
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC01003787.hg.1 / ENST00000367021TC01001752.hg.1 / ENST00000491415
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
TRAF3IP3 uc001hhn.3TRAF3IP3 uc001hho.3TRAF3IP3 uc009xcr.3
C1orf74 uc001hhp.1C1orf74 uc021pio.1
IRF6 uc001hhq.2IRF6 uc010psm.2
DIEXF uc001hhr.2DIEXF uc009xcu.2
promotor
Exon
knownGene(UCSC hg19)
8kb
0.021
0 1R2
cg21951975
Chr1:209954848−210025097R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
209955848 209972911 209989973 210007035 210024097
rs651141
rs6685182
rs2013196●
cg21951975
rs11582607
rs684083
rs11119354
●CpG
Main effect
No effect
Interaction effect
TC01003787.hg.1 / ENST00000367021TC01001752.hg.1 / ENST00000491415
TC01001751.hg.1 / ENST00000010338 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
TRAF3IP3 uc001hhn.3TRAF3IP3 uc001hho.3TRAF3IP3 uc009xcr.3
C1orf74 uc001hhp.1C1orf74 uc021pio.1
IRF6 uc001hhq.2IRF6 uc010psm.2
DIEXF uc001hhr.2DIEXF uc009xcu.2
promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg04117972
Chr1:227584983−227637367R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
227585983 227598761 227611538 227624315 227637092
rs6670351
rs6670816●
cg04117972
rs2814091
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
BC039356 uc001hqv.3
promotor
Exon
knownGene(UCSC hg19)
6kb
0.021
0 1R2
cg18126320
Chr1:230895051−230960298R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
230896051 230911958 230927864 230943771 230959677●
cg18126320
rs12059573
rs12027189
rs872504
rs16852607
rs4520425
rs4847021
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CAPN9 uc001htz.1CAPN9 uc001hua.1CAPN9 uc009xfg.1 promotor
Exon
knownGene(UCSC hg19)
7kb
8
0.23
0.2
0.09
0.43
0.46
0.2
0.2
7
0.1
0.33
0.48
0.54
0.1
0.1
6
0.55
0.45
0.41
1
1
5
0.22
0.2
0.55
0.55
4
0.92
0.45
0.45
3
0.41
0.41
2
1
1
0.021
0 1R2
cg04798314
Chr1:246664082−246678397R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
246664131 246667448 246670764 246674081 246677397
rs4654272●
cg04798314
rs10218644
rs10754521
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
SMYD3 uc001ibl.3
promotor
Exon
knownGene(UCSC hg19)
2kb
13
0.02
0.59
0.59
0.09
0.13
0.18
0
0
0.02
0.01
0.08
0.09
12
0.28
0.27
0.11
0.05
0.05
0
0
0.01
0.07
0.01
0.04
11
1
0.02
0
0.32
0.06
0.07
0.02
0.02
0.06
0.12
10
0.03
0
0.31
0.06
0.07
0.02
0.02
0.06
0.12
9
0.05
0.03
0.06
0.06
0.01
0.09
0
0.02
8
0.03
0.2
0.2
0
0.01
0.02
0
7
0.18
0.18
0.02
0.1
0.02
0.21
6
1
0.08
0.12
0.01
0.01
5
0.08
0.12
0.01
0.01
4
0.04
0.06
0.01
3
0.02
0.16
2
0.14
1
0.021
0 1R2
cg27573991
Chr1:247701886−247764857R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
247702886 247718129 247733372 247748615 247763857
rs10925076●
cg27573991
rs3844081
rs12143785
rs12737801
rs4925689
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
GCSAML uc001ida.4GCSAML uc001idb.4GCSAML uc009xgw.3OR2G2 uc010pyy.2 promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg19432688
Chr2:1753932−1774830 Chr18:41775580−42300049R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs1364648
rs10469992●
cg19432688
rs12475777
rs625028
rs3018325
rs4084232
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
BC051727 uc002lax.3SETBP1 uc002lay.3SETBP1 uc010dni.3 promotor
Exon
knownGene(UCSC hg19)
56kb
0.021
0 1R2
cg04846451
Chr2:55339812−55453363R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
55340812 55368700 55396588 55424476 55452363
rs1009555
rs4672024
rs2118284●
cg04846451
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CLHC1 uc002ryh.2CLHC1 uc002ryi.2CLHC1 uc002ryj.2 promotor
Exon
knownGene(UCSC hg19)
12kb
4
0.24
0.31
0.83
3
0.09
0.21
2
0.27
1
0.021
0 1R2
cg23649088
Chr2:200751207−200779866R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
200752207 200758872 200765537 200772202 200778866
rs1509837●
cg23649088
rs166849
●CpG
Main effect
No effect
Interaction effect
TC02005006.hg.1 / ENST00000319974
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
C2orf69 uc010zhb.2
promotor
Exon
knownGene(UCSC hg19)
3kb
0.021
0 1R2
cg03475776
Chr2:240074590−240284334R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
240075590 240127526 240179462 240231398 240283334
rs3791501
rs3791542
rs3791549
rs753302●
cg03475776
rs11693556
rs548717
rs9636379
rs10177607
rs7590833
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
HDAC4 uc002vyk.4HDAC4 uc010fyy.3
HDAC4 uc010fza.2MGC16025 uc010zob.1
MIR4269 uc021vza.1MIR2467 uc021vzb.1
knownGene(UCSC hg19)
21kb
200.08
0.660.15
0.080.08
0.330.07
0.150
0.010.01
0.090.05
0.20.1
0.050.15
0.040.28
190.05
0.010.01
0.010.06
0.010.01
0.120.14
0.140.1
00
0.180
0.040.15
0.01
180.04
0.050.05
0.540.04
0.030.1
0.080.09
0.120.04
0.120.06
0.040.08
0.070.23
170.73
0.720.04
0.70.98
0.270.1
0.10
0.010.05
0.010.01
0.040.01
0.01
160.97
0.050.97
0.750.18
0.060.06
00.01
0.070.02
0.020.06
00.04
150.05
10.74
0.180.06
0.060
0.010.08
0.020.02
0.070.01
0.04
140.05
0.050.16
0.130.14
00.15
0.280.09
0.080.19
0.10.45
130.72
0.170.06
0.060
0.010.07
0.020.03
0.060
0.05
120.27
0.10.1
00.01
0.050.01
0.010.04
0.010.01
110.87
0.870.37
0.030.18
0.530.03
0.130.58
0.05
100.99
0.30.03
0.170.63
0.030.12
0.460.04
90.31
0.030.16
0.640.03
0.120.47
0.04
80.23
0.230.45
0.010.14
0.480.03
70.04
0.020
0.020.02
0.07
60.1
0.240.71
0.120.3
50.02
0.090.7
0.13
40.12
0.020.07
30.14
0.46
20.17
1
0.021
0 1R2
cg01842719
Chr2:241657550−241659550 Chr4:190185162−190311382R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
●
cg01842719
rs11132630
rs10001524
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
KIF1A uc010fzk.3KIF1A uc031rsb.1KIF1A uc002vzx.3 promotor
Exon
knownGene(UCSC hg19)
14kb
0.021
0 1R2
cg27104695
Chr3:15344841−15521639R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
15345841 15389550 15433259 15476968 15520677●
cg27104695
rs9837421
rs2729682
rs2290538
●CpG
Main effect
No effect
Interaction effect
TC03001207.hg.1 / ENST00000253688
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SH3BP5 uc003bzp.2SH3BP5 uc003bzq.2
SH3BP5 uc003bzr.2METTL6 uc003bzs.1METTL6 uc011avp.1
METTL6 uc003bzt.1EAF1 uc003bzu.3EAF1 uc011avq.2
COLQ uc003bzx.3COLQ uc010heo.3COLQ uc003cad.1
promotor
Exon
knownGene(UCSC hg19)
18kb
6
1
0.21
0.15
0.17
0.5
5
0.21
0.15
0.17
0.5
4
0.43
0.01
0
3
0.11
0.05
2
0.33
1
0.021
0 1R2
cg14143723
Chr3:27636962−27652544R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
27637962 27641578 27645194 27648810 27652426
rs2724506●
cg14143723
rs2643823
rs12715123
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
9
0.03
0.77
0.07
0.37
0.59
0.35
0.52
0.02
8
0.04
0.01
0.02
0.01
0.01
0.02
0.06
7
0.03
0.47
0.78
0.45
0.44
0.01
6
0.04
0.03
0.04
0.01
0
5
0.58
0.97
0.76
0.08
4
0.56
0.43
0.06
3
0.77
0.08
2
0.11
1
0.021
0 1R2
cg02071172
Chr3:64423973−64439795R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
64424104 64427777 64431450 64435123 64438795
rs2371526
rs930529●
cg02071172
rs6809391
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
0.021
0 1R2
cg03329597
Chr3:108080217−108161339R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
108081217 108100998 108120778 108140559 108160339
rs3792332
rs4855651
rs13090812
rs17537587●
cg03329597
rs3957543
rs7652606
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
HHLA2 uc003dwy.4HHLA2 uc010hpu.3HHLA2 uc011bhl.2
MYH15 uc003dxa.1 promotor
Exon
knownGene(UCSC hg19)
8kb
0.021
0 1R2
cg17408686
Chr3:126421575−126684166R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
126422575 126487807 126553038 126618269 126683500●
cg17408686
rs16837708
rs6797300
rs4679315
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CHCHD6 uc003ejf.2CHCHD6 uc010hsj.2
knownGene(UCSC hg19)
27kb
12
0.14
0.12
0.16
0.16
0.03
0.03
0.01
0.06
0.06
0.06
0.03
11
0.98
0.79
0.79
0.11
0.11
0.13
0.06
0.06
0.06
0.07
10
0.77
0.76
0.1
0.11
0.12
0.06
0.06
0.06
0.06
9
1
0.09
0.08
0.08
0.01
0.01
0.01
0.04
8
0.09
0.08
0.08
0.01
0.01
0.01
0.04
7
0.83
0.09
0.16
0.17
0.17
0.73
6
0.08
0.24
0.24
0.25
0.88
5
0.16
0.16
0.15
0.08
4
1
0.99
0.18
3
1
0.19
2
0.19
1
0.021
0 1R2
cg12315391
Chr3:157720994−157859930R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
157721994 157756228 157790462 157824696 157858930
rs4317052
rs12631529
rs7642028
rs6810376●
cg12315391
rs7630176
rs4680416
●CpG
Main effect
No effect
Interaction effect
TC03000864.hg.1 / ENST00000295930
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SHOX2 uc003fbr.3SHOX2 uc003fbs.3
SHOX2 uc010hvw.3RSRC1 uc003fbt.4RSRC1 uc003fbu.2RSRC1 uc003fbv.4
promotor
Exon
knownGene(UCSC hg19)
14kb
0.021
0 1R2
cg08697665
Chr3:158346565−158481699R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
158347565 158380849 158414132 158447416 158480699
rs6768636●
cg08697665
rs7617706
●CpG
Main effect
No effect
Interaction effect
TC03001948.hg.1 / ENST00000264265TC03000866.hg.1 / ENST00000264263
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
GFM1 uc003fcd.3GFM1 uc003fce.3GFM1 uc003fcg.3
LXN uc003fch.3LXN uc011bov.1
RARRES1 uc003fci.3RARRES1 uc003fcj.3
AY070437 uc003fck.4
promotor
Exon
knownGene(UCSC hg19)
14kb
14
0.95
0.42
0.94
0.93
0.17
0.69
0.18
0.06
0.72
0.1
0.2
0.01
0.07
13
0.41
0.99
0.98
0.16
0.73
0.17
0.06
0.76
0.12
0.2
0.03
0.07
12
0.4
0.4
0.03
0.39
0.01
0.15
0.4
0.04
0.54
0.08
0.24
11
0.98
0.16
0.73
0.16
0.06
0.76
0.12
0.2
0.03
0.07
10
0.16
0.73
0.16
0.05
0.76
0.11
0.21
0.02
0.07
9
0.09
0.88
0.29
0.09
0.77
0.33
0.2
0.4
8
0.16
0.06
0.96
0.16
0.23
0.06
0.06
7
0.32
0.16
0.83
0.27
0.22
0.42
6
0.06
0.28
0.08
0.81
0.04
5
0.16
0.24
0.06
0.06
4
0.35
0.34
0.43
3
0.11
0.16
2
0.05
1
0.021
0 1R2
cg16975599
Chr3:158932754−158981014R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
158933754 158945364 158956974 158968584 158980193
rs6791853
rs1868414●
cg16975599
rs2621308
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
IQCJ uc003fco.3IQCJ uc003fcp.2IQCJ uc010hvy.2IQCJ−SCHIP1 uc003fcq.2IQCJ−SCHIP1 uc003fcr.2
knownGene(UCSC hg19)
5kb
14
0.31
0.28
0.11
0.1
0.28
0.52
0.1
0.28
0.28
0.11
0.11
0.11
0.23
13
0.93
0.07
0.09
0.91
0.49
0.07
0.91
0.91
0.07
0.07
0.04
0.2
12
0.07
0.08
0.99
0.54
0.07
0.98
0.98
0.08
0.07
0.04
0.19
11
0.02
0.07
0.19
0.89
0.07
0.07
1
0.98
0.01
0.4
10
0.08
0.14
0.02
0.08
0.08
0.02
0.02
0.01
0.42
9
0.55
0.07
0.99
0.99
0.07
0.07
0.04
0.2
8
0.17
0.55
0.55
0.19
0.19
0.07
0
7
0.07
0.07
0.89
0.91
0.01
0.37
6
1
0.07
0.07
0.04
0.19
5
0.07
0.07
0.04
0.19
4
0.98
0.01
0.41
3
0.01
0.4
2
0.02
1
0.021
0 1R2
cg06085579
Chr3:171503273−171522613R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
171504273 171508608 171512943 171517278 171521613
rs4894509
rs1574455●
cg06085579
rs13075194
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PLD1 uc003fhs.3PLD1 uc003fht.3
knownGene(UCSC hg19)
2kb
0.021
0 1R2
cg07777347
Chr3:194360833−194531441R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
194361833 194403985 194446137 194488289 194530441●
cg07777347
rs1773206
rs1471332
rs4558689
●CpG
Main effect
No effect
Interaction effect
TC03002740.hg.1TC03001077.hg.1 / ENST00000329759
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LSG1 uc003fui.3FAM43A uc003fuj.3
LOC100507391 uc021xjd.1 promotor
Exon
knownGene(UCSC hg19)
17kb
9
0.15
0.14
0.24
0.17
0
0.71
0.27
0.04
8
0.95
0.13
0.59
0.28
0.12
0.07
0.21
7
0.13
0.59
0.27
0.12
0.06
0.24
6
0.19
0.5
0.27
0.04
0.07
5
0.4
0.22
0.1
0.2
4
0
0.2
0.13
3
0.24
0.08
2
0.08
1
0.021
0 1R2
cg08644045
Chr4:3472602−3537176R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3473246 3488979 3504711 3520444 3536176
rs13128489●
cg08644045
rs3468
rs3182
rs867246
rs7672287
rs2073503
●CpG
Main effect
No effect
Interaction effect
TC04000983.hg.1 / ENST00000296325TC04002425.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
DOK7 uc003ghd.3DOK7 uc003ghe.3
DOK7 uc003ghg.1LRPAP1 uc003ghh.4 promotor
Exon
knownGene(UCSC hg19)
7kb
10
0
0.2
0.13
0.19
0.2
0.01
0.14
0.12
0.07
9
0.24
0.08
0.25
0.24
0.2
0.15
0.06
0.1
8
0.08
0.99
1
0.1
0.56
0.05
0.04
7
0.08
0.08
0.07
0.05
0.06
0.02
6
0.99
0.1
0.55
0.04
0.04
5
0.1
0.56
0.04
0.04
4
0.22
0.48
0.56
3
0.05
0.11
2
0.29
1
0.021
0 1R2
cg00356499
Chr4:3453454−3517065R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3454304 3469745 3485185 3500625 3516065
rs4690099
rs2344206
rs3468
rs3182●
cg00356499
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DOK7 uc003ghd.3DOK7 uc003ghe.3
DOK7 uc003ghg.1LRPAP1 uc003ghh.4 promotor
Exon
knownGene(UCSC hg19)
7kb
16
0
0.05
0.05
0.02
0.05
0.02
0
0
0
0
0
0
0
0
0
15
0.15
0.14
0.24
0.17
0
0.71
0.27
0.04
0.27
0.27
0.21
0.17
0.05
0.15
14
0.95
0.13
0.59
0.28
0.12
0.07
0.21
0.07
0.07
0.04
0.05
0
0.01
13
0.13
0.59
0.27
0.12
0.06
0.24
0.06
0.06
0.03
0.05
0
0.02
12
0.19
0.5
0.27
0.04
0.07
0.04
0.04
0.08
0.01
0.04
0.17
11
0.4
0.22
0.1
0.2
0.1
0.1
0.06
0.07
0
0
10
0
0.2
0.13
0.19
0.2
0.01
0.14
0.12
0.07
9
0.24
0.08
0.25
0.24
0.2
0.15
0.06
0.1
8
0.08
0.99
1
0.1
0.56
0.05
0.04
7
0.08
0.08
0.07
0.05
0.06
0.02
6
0.99
0.1
0.55
0.04
0.04
5
0.1
0.56
0.04
0.04
4
0.22
0.48
0.56
3
0.05
0.11
2
0.29
1
0.021
0 1R2
cg26401028
Chr4:3453454−3561987R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3454304 3480975 3507646 3534317 3560987
rs4690099
rs13128489
rs3468
rs3182●
cg26401028
rs4037688
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DOK7 uc003ghd.3DOK7 uc003ghe.3
DOK7 uc003ghg.1LRPAP1 uc003ghh.4 promotor
Exon
knownGene(UCSC hg19)
11kb
16
0
0.05
0.05
0.02
0.05
0.02
0
0
0
0
0
0
0
0
0
15
0.15
0.14
0.24
0.17
0
0.71
0.27
0.04
0.27
0.27
0.21
0.17
0.05
0.15
14
0.95
0.13
0.59
0.28
0.12
0.07
0.21
0.07
0.07
0.04
0.05
0
0.01
13
0.13
0.59
0.27
0.12
0.06
0.24
0.06
0.06
0.03
0.05
0
0.02
12
0.19
0.5
0.27
0.04
0.07
0.04
0.04
0.08
0.01
0.04
0.17
11
0.4
0.22
0.1
0.2
0.1
0.1
0.06
0.07
0
0
10
0
0.2
0.13
0.19
0.2
0.01
0.14
0.12
0.07
9
0.24
0.08
0.25
0.24
0.2
0.15
0.06
0.1
8
0.08
0.99
1
0.1
0.56
0.05
0.04
7
0.08
0.08
0.07
0.05
0.06
0.02
6
0.99
0.1
0.55
0.04
0.04
5
0.1
0.56
0.04
0.04
4
0.22
0.48
0.56
3
0.05
0.11
2
0.29
1
0.021
0 1R2
cg04857395
Chr4:3453736−3561987R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
3454304 3480975 3507646 3534317 3560987
rs1203110
rs2344206
rs3468
rs3182●
cg04857395
rs4037688
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DOK7 uc003ghd.3DOK7 uc003ghe.3
DOK7 uc003ghg.1LRPAP1 uc003ghh.4 promotor
Exon
knownGene(UCSC hg19)
11kb
180.03
0.050.48
0.430.03
0.990.01
0.090.49
0.480.5
0.680.35
0.970.16
0.030.07
170
0.070.01
0.010.03
0.450.13
0.070.07
00.11
0.030.02
0.010.01
0.03
160.08
0.020
0.050.01
0.030.07
0.080.05
0.060.03
0.050.01
00
150.23
0.120.47
0.050.56
0.980.97
0.830.67
0.30.49
0.090.04
0.01
140.01
0.440
0.410.23
0.230.27
0.310.76
0.420.01
0.020.01
130.03
00.21
0.130.13
0.150.05
0.020.03
00.51
0.02
120.01
0.090.48
0.480.51
0.680.35
0.970.15
0.030.07
110.08
0.050.05
0.010.07
0.130.01
00
0.01
100.57
0.570.47
0.260.46
0.090.02
0.070.05
90.99
0.850.68
0.310.5
0.090.04
0.01
80.85
0.670.3
0.490.09
0.040.01
70.53
0.170.53
0.10.04
0.01
60.43
0.70.11
0.060.02
50.35
0.010.03
0.01
40.18
0.030.08
30
0.19
20.01
1
0.021
0 1R2
cg24826020
Chr4:38008782−38071998R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
38009782 38025086 38040390 38055694 38070998
rs10517464
rs6833071
rs2052693●
cg24826020
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TBC1D1 uc003gtb.3TBC1D1 uc011byd.2TBC1D1 uc010ifd.3knownGene
(UCSC hg19)
7kb
200.03
0.170.23
0.020.18
0.040.02
0.090.17
0.170.18
00.02
0.050.05
0.030.06
0.140.03
190.01
0.020.03
0.010.09
0.030.01
0.020.02
0.010.01
0.480
0.270.07
00.01
0.06
180.11
0.180.09
0.110.18
0.810.01
0.010.09
0.060
00.02
0.040.01
0.020.04
170.49
0.890.24
0.50.05
0.080.08
0.880.04
0.010.09
00.08
00.11
0.08
160.45
0.511
0.220.12
0.120.44
0.140.02
0.090
0.170
0.160.17
150.23
0.460.11
0.060.06
0.990.04
0.010.08
00.1
00.11
0.1
140.52
0.120.09
0.090.23
0.320.04
0.150
0.270.01
0.310.28
130.22
0.130.12
0.450.14
0.020.1
00.17
00.17
0.18
120.02
0.020.11
0.060
00.01
0.020.02
0.020.03
111
0.060.03
00.02
0.020.08
0.010.05
0.08
100.06
0.030
0.020.02
0.080.01
0.050.08
90.04
0.010.08
00.1
00.11
0.1
80.01
0.260
0.090.01
0.120.09
70
0.220.06
00.01
0.04
60.03
0.280.02
0.550.28
50.28
0.540.02
0.26
40.17
0.540.98
30.01
0.15
20.55
1
0.021
0 1R2
cg03423497
Chr4:39427295−39492521R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
39428176 39444013 39459849 39475685 39491521
rs17431867●
cg03423497
rs2687970
rs10517522
rs2125314
rs2687965
●CpG
Main effect
No effect
Interaction effect
TC04000230.hg.1 / ENST00000261434
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
KLB uc003gua.3KLB uc011byj.2
RPL9 uc003guc.3RPL9 uc011byk.2
RPL9 uc011byl.1LIAS uc003guf.3
LIAS uc003gug.3LIAS uc003gue.4
LOC401127 uc011byn.2
promotor
Exon
knownGene(UCSC hg19)
7kb
200.03
0.170.23
0.020.18
0.040.02
0.090.17
0.170.18
00.02
0.050.05
0.030.06
0.140.03
190.01
0.020.03
0.010.09
0.030.01
0.020.02
0.010.01
0.480
0.270.07
00.01
0.06
180.11
0.180.09
0.110.18
0.810.01
0.010.09
0.060
00.02
0.040.01
0.020.04
170.49
0.890.24
0.50.05
0.080.08
0.880.04
0.010.09
00.08
00.11
0.08
160.45
0.511
0.220.12
0.120.44
0.140.02
0.090
0.170
0.160.17
150.23
0.460.11
0.060.06
0.990.04
0.010.08
00.1
00.11
0.1
140.52
0.120.09
0.090.23
0.320.04
0.150
0.270.01
0.310.28
130.22
0.130.12
0.450.14
0.020.1
00.17
00.17
0.18
120.02
0.020.11
0.060
00.01
0.020.02
0.020.03
111
0.060.03
00.02
0.020.08
0.010.05
0.08
100.06
0.030
0.020.02
0.080.01
0.050.08
90.04
0.010.08
00.1
00.11
0.1
80.01
0.260
0.090.01
0.120.09
70
0.220.06
00.01
0.04
60.03
0.280.02
0.550.28
50.28
0.540.02
0.26
40.17
0.540.98
30.01
0.15
20.55
1
0.021
0 1R2
cg25940248
Chr4:39427295−39492521R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
39428176 39444013 39459849 39475685 39491521
rs17431867●
cg25940248
rs2687970
rs10517522
rs2125314
rs10213304
rs2687965
●CpG
Main effect
No effect
Interaction effect
TC04000230.hg.1 / ENST00000261434
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
KLB uc003gua.3KLB uc011byj.2
RPL9 uc003guc.3RPL9 uc011byk.2
RPL9 uc011byl.1LIAS uc003guf.3
LIAS uc003gug.3LIAS uc003gue.4
LOC401127 uc011byn.2
promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg18401298
Chr4:40872745−40947750R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
40873745 40892094 40910442 40928791 40947139
rs4861321
rs4861322●
cg18401298
rs7685182
rs6814800
rs13139548
rs4861330
rs13110219
rs7680971
rs4327523
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC04001139.hg.1 / ENST00000295974
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
APBB2 uc003gvl.3APBB2 uc003gvm.3APBB2 uc003gvn.3
TRNA_Gln uc021xnu.1knownGene
(UCSC hg19)
8kb
0.021
0 1R2
cg01520956
Chr4:77139733−77199756R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
77140733 77155248 77169762 77184277 77198791
rs10032423
rs1588214●
cg01520956
rs13117238
rs6532316
●CpG
Main effect
No effect
Interaction effect
TC04002602.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
FAM47E uc003hjv.3FAM47E uc003hjx.3FAM47E uc003hjw.2
FAM47E−STBD1 uc003hjy.3FAM47E−STBD1 uc011cbv.2FAM47E−STBD1 uc011cbw.2
knownGene(UCSC hg19)
6kb
17
0
0.02
0.01
0.01
0.02
0.02
0.04
0.04
0.03
0.01
0.05
0
0
0.04
0.55
0.51
16
0.28
0.04
0.04
0.06
0.07
0.08
0.09
0.04
0.02
0.03
0.04
0.12
0
0
0
15
0.5
0.5
0.2
0.26
0.27
0.27
0.1
0.34
0.16
0.02
0.03
0.21
0
0
14
1
0.1
0.13
0.12
0.12
0.04
0.66
0.39
0.13
0.01
0.33
0
0
13
0.1
0.13
0.12
0.12
0.04
0.66
0.39
0.13
0.01
0.33
0
0
12
0.14
0.17
0.17
0.62
0.06
0.02
0.21
0.01
0.03
0.02
0.02
11
0.82
0.81
0.2
0.1
0.14
0.49
0
0.16
0.01
0.01
10
0.99
0.24
0.13
0.06
0.38
0.01
0.08
0.08
0.09
9
0.24
0.13
0.06
0.38
0.01
0.08
0.08
0.09
8
0.11
0.03
0.35
0.01
0.05
0.02
0.03
7
0.52
0.09
0.02
0.44
0.01
0.01
6
0.27
0.02
0.84
0.12
0.11
5
0.01
0.3
0.03
0.02
4
0.05
0
0
3
0.1
0.09
2
0.94
1
0.021
0 1R2
cg05104897
Chr4:120076010−120205550R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
120077010 120108895 120140780 120172665 120204550
rs7668987●
cg05104897
rs13113462
rs17050457
●CpG
Main effect
No effect
Interaction effect
TC04000611.hg.1 / ENST00000274030TC04001498.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
MYOZ2 uc003icp.4AK309988 uc021xre.1
USP53 uc003icr.4USP53 uc003ics.4
USP53 uc003icu.4promotor
Exon
knownGene(UCSC hg19)
13kb
4
0.84
0.07
0.09
3
0.09
0.11
2
0.75
1
0.021
0 1R2
cg16301894
Chr4:129381079−129411425R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
129382079 129389166 129396252 129403339 129410425
rs6534682●
cg16301894
rs2062456
rs11937124
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
AK093416 uc003igh.1
knownGene(UCSC hg19)
3kb
0.021
0 1R2
cg16079430
Chr5:10851242−10924252 Chr20:37858566−37860566Chr21:18829622−18831622R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs11743009
rs4074698●
cg16079430
rs13157531
rs4702742
rs17789197
rs957256
rs1888406
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
10kb
0.021
0 1R2
cg12427317
Chr5:34699704−34796305R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
34700000 34723961 34747921 34771881 34795841
rs11740818
rs16903850●
cg12427317
rs9283739
rs336462
●CpG
Main effect
No effect
Interaction effect
TC05000151.hg.1 / ENST00000265109
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
RAI14 uc003jir.3RAI14 uc010iur.3RAI14 uc011coj.2knownGene
(UCSC hg19)
10kb
6
0.37
0.11
0.07
0.1
0.2
5
0.29
0.15
0.28
0.41
4
0.05
0.97
0.03
3
0.05
0.08
2
0.04
1
0.021
0 1R2
cg19698137
Chr5:35964089−36001608R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
35965089 35973969 35982849 35991729 36000608
rs2161551
rs10040617●
cg19698137
rs11746242
rs10454862
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
UGT3A1 uc003jjy.2UGT3A1 uc003jjw.2
UGT3A1 uc003jjv.2knownGene(UCSC hg19)
4kb
0.021
0 1R2
cg24543939
Chr5:53951507−54019232R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
53951585 53968247 53984909 54001571 54018232●
cg24543939
rs4133308
rs3886214
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
7kb
9
0.02
0.45
0.01
0.39
0.61
0.44
0.39
0.23
8
0.18
0
0.01
0.24
0.19
0.01
0.21
7
0.11
0.17
0.73
0.97
0.17
0.78
6
0.01
0.02
0.11
0
0.15
5
0.23
0.18
0.88
0.2
4
0.74
0.23
0.51
3
0.17
0.77
2
0.24
1
0.021
0 1R2
cg10875794
Chr5:115413612−115427468R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
115414554 115417533 115420511 115423490 115426468
rs1508884
rs7733992●
cg10875794
rs4920905
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
COMMD10 uc003krt.1
promotor
Exon
knownGene(UCSC hg19)
2kb
17
0.43
0.28
0.02
0.33
0.38
0.1
0.03
0.03
0.05
0.07
0.03
0.03
0.14
0.15
0.13
0.15
16
0.63
0.06
0.76
0.88
0.26
0.08
0.08
0.11
0.22
0.07
0.07
0.38
0.39
0.36
0.39
15
0.05
0.73
0.63
0.42
0.05
0.05
0.04
0.35
0.09
0.09
0.58
0.59
0.55
0.59
14
0.08
0.07
0.01
0.3
0.31
0
0.01
0
0
0.01
0.01
0.01
0.01
13
0.85
0.37
0
0
0.02
0.32
0.08
0.08
0.51
0.52
0.48
0.52
12
0.31
0.08
0.08
0.12
0.27
0.07
0.07
0.44
0.45
0.41
0.45
11
0.03
0.03
0.05
0.79
0.04
0.03
0.58
0.58
0.51
0.58
10
1
0.12
0.02
0
0
0.03
0.03
0.03
0.03
9
0.11
0.02
0
0
0.03
0.03
0.03
0.03
8
0.04
0.68
0.67
0.07
0.08
0.09
0.08
7
0.03
0.03
0.56
0.56
0.62
0.56
6
1
0.17
0.18
0.2
0.18
5
0.16
0.17
0.19
0.17
4
1
0.92
1
3
0.92
1
2
0.92
1
0.021
0 1R2
cg14457074
Chr5:180337368−180489943R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
180338368 180376052 180413736 180451420 180489103
rs2276995
rs3733755
rs7724813●
cg14457074
rs10479597
rs11249756
rs12659188
●CpG
Main effect
No effect
Interaction effect
TC05001069.hg.1 / ENST00000342868TC05001070.hg.1
TC05001071.hg.1 / ENST00000327705TC05001067.hg.1 / ENST00000231229 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
BTNL8 uc003mmp.3BTNL8 uc003mmq.3BTNL8 uc010jll.3
BTNL3 uc003mmr.3BTNL3 uc010jlp.3
BTNL9 uc003mmt.3BTNL9 uc011dhi.1
promotor
Exon
knownGene(UCSC hg19)
16kb
9
0.01
0.01
0.13
0.01
0.02
0.16
0.12
0.02
8
0.03
0.08
0.82
0.03
0.1
0.05
0.24
7
0.21
0.02
0.97
0.09
0.07
0.34
6
0.07
0.21
0.26
0.56
0.02
5
0.02
0.12
0.06
0.28
4
0.09
0.06
0.31
3
0.6
0.01
2
0.26
1
0.021
0 1R2
cg25676166
Chr6:6882618−6897853R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
6883618 6886927 6890236 6893545 6896853
rs2182802
rs4960264
rs1887507●
cg25676166
rs13220385
●CpG
Main effect
No effect
Interaction effect
TC06002559.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
9
0.01
0.01
0.13
0.01
0.02
0.16
0.12
0.02
8
0.03
0.08
0.82
0.03
0.1
0.05
0.24
7
0.21
0.02
0.97
0.09
0.07
0.34
6
0.07
0.21
0.26
0.56
0.02
5
0.02
0.12
0.06
0.28
4
0.09
0.06
0.31
3
0.6
0.01
2
0.26
1
0.021
0 1R2
cg02096172
Chr6:6882618−6897853R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
6883618 6886927 6890236 6893545 6896853
rs2182802
rs4960264
rs1887507
rs4246079●
cg02096172
rs2182801
rs13220385
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC06002559.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
0.021
0 1R2
cg08851530
Chr6:27378422−28384589R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
27379409 27630454 27881499 28132544 28383589
rs9368509
rs149946●
cg08851530
rs1150726
rs4412194
●CpG
Main effect
No effect
Interaction effect
TC06000276.hg.1 / ENST00000330236
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ZNF184 uc003nji.3ZNF184 uc003njj.3ZNF184 uc010jqv.3TRNA_Ser uc021ypx.1
TRNA_Ser uc021ypz.1TRNA_Ser uc021yrr.1
TRNA_Asp uc021ypy.1TRNA_Asp uc021yqb.1
TRNA_Asp uc021yql.1TRNA_Gln uc021yqd.1
TRNA_Gln uc021yqh.1TRNA_Gln uc021yrk.1
TRNA_Arg uc021yqj.1TRNA_Arg uc021yqv.1
TRNA_Lys uc021yqk.1TRNA_Lys uc021yqm.1TRNA_Met uc021yqn.1TRNA_Met uc021yri.1
TRNA_Met uc021yrm.1TRNA_Leu uc021yqo.1TRNA_Leu uc021yqp.1
TRNA_Leu uc021yrd.1TRNA_Thr uc021yqq.1
TRNA_Thr uc021yqz.1TRNA_Thr uc021yre.1
TRNA_Ile uc021yqr.1TRNA_Ile uc021yqu.1
TRNA_Ile uc021yra.1TRNA_Val uc021yqy.1
TRNA_Val uc021yqs.1TRNA_Val uc021yrg.1
TRNA_Phe uc021yqt.1LOC100507173 uc021yrb.1LOC100507173 uc021yrc.1LOC100507173 uc003njk.3
LOC100131289 uc021yrh.2HIST1H2BL uc003njl.3HIST1H3H uc003njm.3HIST1H2AJ uc003njn.1
HIST1H2BM uc003njo.3HIST1H4J uc003njp.3
FKSG63 uc003njq.2BC016143 uc021yrl.1HIST1H4K uc003njr.3
HIST1H2AK uc003njs.3
promotor
Exon
knownGene(UCSC hg19)
101kb
3
0
0
2
0.88
1
0.021
0 1R2
cg08049198
Chr3:14658515−14660515 Chr6:32144904−32146904 Chr19:16547375−16549375R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs12495599●
cg08049198
rs10411936
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
AGPAT1 uc003oag.3AGPAT1 uc003oah.3
RNF5 uc003oaj.4RNF5 uc031snv.1
EPS15L1 uc002ndx.4EPS15L1 uc002ndy.4EPS15L1 uc002ndz.2
promotor
Exon
knownGene(UCSC hg19)
3kb
11
0.02
0.24
0.18
0.03
0.16
0.05
0.05
0.1
0.04
0.38
10
0.58
0.64
0.89
0.21
0.06
0.11
0.07
0.01
0.12
9
0.9
0.62
0.1
0.03
0.06
0.11
0.01
0.07
8
0.69
0.11
0.04
0.05
0.09
0.01
0.07
7
0.18
0.07
0.09
0.05
0.02
0.11
6
0.01
0.05
0.04
0.21
0.09
5
0.18
0.17
0.02
0.02
4
0.7
0.11
0.13
3
0.08
0.09
2
0.08
1
0.021
0 1R2
cg12241963
Chr6:33788581−33814971R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
33789581 33795679 33801776 33807874 33813971
rs10947441
rs7761859
rs11753875
rs6901216●
cg12241963
rs4713692
rs6931760
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
3kb
180.41
0.070.04
0.010.01
00.03
0.010.33
0.320.02
0.060.07
0.020.01
0.030.04
170.03
0.080.13
0.040
0.010.04
0.160.16
0.020.1
0.10
00
0.09
160.01
0.010
0.010
0.240.01
0.010.02
0.030.03
0.070.07
0.070.03
150.01
00
00.02
0.020.01
0.190.03
0.020.06
0.060.06
0.02
140
0.270
0.010.02
0.020.11
0.020.02
0.030.03
0.010.01
130.01
00.23
00
0.020.02
0.030.04
0.040.04
0.02
120
0.030.02
0.020.05
0.060.06
0.080.08
0.030.02
110
00.01
0.010
0.010
00
0
100.03
0.030.08
0.10.11
0.180.18
0.170.1
90.93
0.080.15
0.130.09
0.080.09
0.12
80.06
0.150.13
0.070.07
0.110.09
70.02
0.010.01
0.010.01
0.01
60.94
0.450.45
0.330.76
50.47
0.460.34
0.82
40.99
0.830.36
30.84
0.36
20.45
1
0.021
0 1R2
cg13266496
Chr6:110700451−110748068R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
110701451 110712856 110724260 110735664 110747068
rs7748253
rs2235989●
cg13266496
rs9400382
rs9386897
rs7756222
rs9320331
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
METTL24 uc003pub.2DDO uc003puc.3DDO uc003pud.3
SLC22A16 uc003pue.3SLC22A16 uc003puf.3
promotor
Exon
knownGene(UCSC hg19)
5kb
15
0.41
0.07
0.04
0.01
0.01
0
0.03
0.01
0.33
0.32
0.02
0.06
0.07
0.02
14
0.03
0.08
0.13
0.04
0
0.01
0.04
0.16
0.16
0.02
0.1
0.1
0
13
0.01
0.01
0
0.01
0
0.24
0.01
0.01
0.02
0.03
0.03
0.07
12
0.01
0
0
0
0.02
0.02
0.01
0.19
0.03
0.02
0.06
11
0
0.27
0
0.01
0.02
0.02
0.11
0.02
0.02
0.03
10
0.01
0
0.23
0
0
0.02
0.02
0.03
0.04
9
0
0.03
0.02
0.02
0.05
0.06
0.06
0.08
8
0
0
0.01
0.01
0
0.01
0
7
0.03
0.03
0.08
0.1
0.11
0.18
6
0.93
0.08
0.15
0.13
0.09
5
0.06
0.15
0.13
0.07
4
0.02
0.01
0.01
3
0.94
0.45
2
0.47
1
0.021
0 1R2
cg19196401
Chr6:110715252−110748068R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
110716252 110723956 110731660 110739364 110747068
rs11153232●
cg19196401
rs9320328
rs9400382
rs9386897
rs7756222
rs9320331
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
METTL24 uc003pub.2DDO uc003puc.3DDO uc003pud.3
SLC22A16 uc003pue.3SLC22A16 uc003puf.3
promotor
Exon
knownGene(UCSC hg19)
4kb
0.021
0 1R2
cg02662417
Chr6:157154993−157217039R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
157155257 157170493 157185729 157200965 157216200
rs9480394●
cg02662417
rs287899
rs287913
rs9384506
rs6905191
rs287873
rs184074
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ARID1B uc003qqn.3ARID1B uc003qqo.3ARID1B uc003qqp.3knownGene
(UCSC hg19)
7kb
0.021
0 1R2
cg21926612
Chr6:163032350−163160350R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
163033350 163064850 163096350 163127850 163159350
rs13191362
rs1893537●
cg21926612
rs13209100
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PARK2 uc003qtx.4PARK2 uc003qty.4PARK2 uc003qtz.4
PACRG uc003qua.3PACRG uc003qub.3PACRG uc003quc.3
knownGene(UCSC hg19)
13kb
3
0.99
0
2
0
1
0.021
0 1R2
cg23169059
Chr2:47778201−47780201 Chr6:167760204−167762204 Chr11:121120501−121122501R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs12476727●
cg23169059
rs7942167
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MSH2 uc002rvz.4KCNK12 uc002rwb.3
promotor
Exon
knownGene(UCSC hg19)
3kb
15
0.49
0.99
0.99
0.08
0.02
0.98
0.45
0.19
0.71
0.07
0.04
0.04
0.07
0.23
14
0.48
0.48
0.23
0.04
0.48
0.1
0.37
0.33
0.12
0.1
0.1
0.13
0.04
13
0.99
0.08
0.02
0.99
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.24
12
0.08
0.02
0.99
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.23
11
0.01
0.08
0.16
0.08
0.07
0.66
0.03
0.03
0.66
0.11
10
0.02
0.08
0.05
0.01
0.01
0
0
0.01
0.04
9
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.24
8
0.46
0.33
0.13
0.06
0.06
0.13
0.3
7
0.17
0.08
0.02
0.02
0.08
0.14
6
0.08
0.05
0.05
0.07
0.3
5
0.03
0.04
0.97
0.08
4
0.98
0.04
0.23
3
0.04
0.24
2
0.08
1
0.021
0 1R2
cg19087971
Chr7:750233−903394R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
751233 789038 826842 864646 902450●
cg19087971
rs4724821
rs4357190
rs7785252
●CpG
Main effect
No effect
Interaction effect
TC07001075.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
PRKAR1B uc003siw.2PRKAR1B uc021zyk.1PRKAR1B uc021zyj.1
HEATR2 uc003siz.2HEATR2 uc010krz.1
HEATR2 uc003sjb.2SUN1 uc003sjf.3
SUN1 uc021zyl.1SUN1 uc011jvq.2
GET4 uc003sjj.1
promotor
Exon
knownGene(UCSC hg19)
16kb
15
0.49
0.99
0.99
0.08
0.02
0.98
0.45
0.19
0.71
0.07
0.04
0.04
0.07
0.23
14
0.48
0.48
0.23
0.04
0.48
0.1
0.37
0.33
0.12
0.1
0.1
0.13
0.04
13
0.99
0.08
0.02
0.99
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.24
12
0.08
0.02
0.99
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.23
11
0.01
0.08
0.16
0.08
0.07
0.66
0.03
0.03
0.66
0.11
10
0.02
0.08
0.05
0.01
0.01
0
0
0.01
0.04
9
0.46
0.19
0.71
0.07
0.04
0.04
0.07
0.24
8
0.46
0.33
0.13
0.06
0.06
0.13
0.3
7
0.17
0.08
0.02
0.02
0.08
0.14
6
0.08
0.05
0.05
0.07
0.3
5
0.03
0.04
0.97
0.08
4
0.98
0.04
0.23
3
0.04
0.24
2
0.08
1
0.021
0 1R2
cg23605961
Chr7:750331−903394R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
751331 789111 826891 864671 902450●
cg23605961
rs4724821
rs4357190
rs7785252
●CpG
Main effect
No effect
Interaction effect
TC07001075.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
PRKAR1B uc003siw.2PRKAR1B uc021zyk.1PRKAR1B uc021zyj.1
HEATR2 uc003siz.2HEATR2 uc010krz.1
HEATR2 uc003sjb.2SUN1 uc003sjf.3
SUN1 uc021zyl.1SUN1 uc011jvq.2
GET4 uc003sjj.1
promotor
Exon
knownGene(UCSC hg19)
16kb
0.021
0 1R2
cg08735705
Chr7:1002645−1217013R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
1003645 1056737 1109829 1162921 1216013●
cg08735705
rs10499317
rs12334290
rs4723801
rs2363286
rs1880297
●CpG
Main effect
No effect
Interaction effect
TC07001080.hg.1 / ENST00000316495TC07001081.hg.1
TC07000019.hg.1TC07003347.hg.1 / ENST00000344111
TC07002098.hg.1−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ADAP1 uc010ksc.3COX19 uc003sjp.1
CYP2W1 uc003sjq.1CYP2W1 uc003sjr.1
C7orf50 uc003sju.2C7orf50 uc011jvt.1C7orf50 uc011jvu.1
MIR339 uc011jvv.1GPR146 uc003sjx.4
GPR146 uc003sjy.1GPER uc010ksd.1
GPER uc003sjz.1GPER uc003ska.1
ZFAND2A uc003skc.3ZFAND2A uc003skd.4AK123998 uc021zyp.1
AK090593 uc003skf.1
knownGene(UCSC hg19)
22kb
0.021
0 1R2
cg12575883
Chr7:1002710−1173518R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
1003710 1045930 1088149 1130369 1172588●
cg12575883
rs2397
rs17227152
rs10499317
rs10256972
rs9655470
rs12112166
rs10265758
●CpG
Main effect
No effect
Interaction effect
TC07003347.hg.1 / ENST00000344111
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ADAP1 uc010ksc.3COX19 uc003sjp.1
CYP2W1 uc003sjq.1CYP2W1 uc003sjr.1
C7orf50 uc003sju.2C7orf50 uc011jvt.1C7orf50 uc011jvu.1
MIR339 uc011jvv.1GPR146 uc003sjx.4
GPR146 uc003sjy.1GPER uc010ksd.1
GPER uc003sjz.1GPER uc003ska.1
knownGene(UCSC hg19)
17kb
0.021
0 1R2
cg07930192
Chr7:984840−1196264R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
985840 1038196 1090552 1142908 1195264
rs7811408●
cg07930192
rs2397
rs10256972
rs4723801
rs12701710
rs10274367
rs7781581
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC07001080.hg.1 / ENST00000316495TC07003347.hg.1 / ENST00000344111
TC07001081.hg.1 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ADAP1 uc003sjo.4ADAP1 uc010ksc.3COX19 uc003sjp.1
CYP2W1 uc003sjq.1CYP2W1 uc003sjr.1
C7orf50 uc003sju.2C7orf50 uc011jvt.1
C7orf50 uc011jvu.1MIR339 uc011jvv.1
GPR146 uc003sjx.4GPR146 uc003sjy.1
GPER uc010ksd.1GPER uc003sjz.1
GPER uc003ska.1ZFAND2A uc003skc.3ZFAND2A uc003skd.4AK123998 uc021zyp.1
promotor
Exon
knownGene(UCSC hg19)
21kb
15
0.26
0.16
0.09
0.36
0.08
0.28
0.34
0.14
0.38
0.37
0.12
0.14
0.09
0.03
14
0.69
0.12
0.13
0.14
0.78
0.12
0.2
0.58
0.12
0.19
0.01
0.02
0.01
13
0.17
0.11
0.2
0.7
0.08
0.18
0.48
0.09
0.08
0.01
0.03
0.02
12
0.04
0.03
0.13
0.05
0.08
0
0.04
0.04
0.06
0.01
0.01
11
0.06
0.16
0.93
0.54
0.19
0.94
0.35
0.54
0.02
0.01
10
0.17
0.06
0.09
0.22
0.06
0.11
0.09
0.21
0.17
9
0.16
0.25
0.74
0.15
0.25
0.02
0.02
0.03
8
0.54
0.21
0.94
0.37
0.54
0.02
0.01
7
0.34
0.58
0.65
0.27
0.03
0.02
6
0.2
0.35
0.04
0.03
0.03
5
0.35
0.53
0.02
0.01
4
0.25
0.05
0.03
3
0.03
0.02
2
0.01
1
0.021
0 1R2
cg09363068
Chr7:1003586−1118436R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
1004523 1032752 1060980 1089208 1117436
rs17227152●
cg09363068
rs10256972
rs4723801
rs2363286
rs10274367
●CpG
Main effect
No effect
Interaction effect
TC07003347.hg.1 / ENST00000344111
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ADAP1 uc010ksc.3COX19 uc003sjp.1
CYP2W1 uc003sjq.1CYP2W1 uc003sjr.1
C7orf50 uc003sju.2C7orf50 uc011jvt.1
C7orf50 uc011jvu.1MIR339 uc011jvv.1
GPR146 uc003sjx.4GPR146 uc003sjy.1
promotor
Exon
knownGene(UCSC hg19)
12kb
3
0
0
2
0
1
0.021
0 1R2
cg12280406
Chr1:82825465−82827465 Chr7:2259901−2261901 Chr17:56281968−56283968 Chr22:47415299−47417299R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs1144283●
cg12280406
rs17174788
rs6009104
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MAD1L1 uc003slf.1MAD1L1 uc003slg.1MAD1L1 uc003slh.1
EPX uc002ivq.3MKS1 uc002ivr.2
MKS1 uc010wnq.2MKS1 uc021uam.1
TBC1D22A uc003bib.3TBC1D22A uc003bie.3TBC1D22A uc010haf.3
promotor
Exon
knownGene(UCSC hg19)
4kb
16
0.2
0.05
0.05
0.1
0.02
0.19
0.21
0.05
0.09
0.46
0.14
0.08
0.29
0.09
0.08
15
0.2
0.09
0.49
0.11
0.01
0.96
0.21
0.48
0
0.38
0.01
0.55
0.5
0.01
14
0.02
0.07
0.02
0.26
0.19
0.97
0.07
0.26
0.07
0.36
0.12
0.05
0.37
13
0.05
0.03
0.22
0.09
0.02
0.05
0.08
0.25
0.06
0.18
0.05
0.06
12
0.06
0.26
0.5
0.07
0.95
0.2
0.22
0.14
0.28
0.89
0.14
11
0.18
0.11
0.02
0.07
0.05
0.23
0.38
0.09
0.07
0.36
10
0.02
0.27
0.26
0
0.25
0.4
0.02
0.22
0.42
9
0.21
0.5
0
0.37
0.01
0.55
0.5
0.01
8
0.07
0.26
0.07
0.36
0.12
0.04
0.37
7
0.22
0.23
0.14
0.29
0.91
0.14
6
0.28
0.03
0.06
0.18
0.03
5
0.03
0.08
0.24
0.03
4
0.29
0.14
0.93
3
0.31
0.26
2
0.15
1
0.021
0 1R2
cg23627948
Chr7:2759692−2815635R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
2760692 2774203 2787713 2801224 2814734●
cg23627948
rs798549
rs7807978
●CpG
Main effect
No effect
Interaction effect
TC07001101.hg.1 / ENST00000275364TC07002113.hg.1
TC07002753.hg.1 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
GNA12 uc003smt.3GNA12 uc003smu.3GNA12 uc011jwb.2knownGene
(UCSC hg19)
6kb
0.021
0 1R2
cg06484146
Chr7:12342463−12496140R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
12342641 12380766 12418891 12457016 12495140
rs12673036
rs1036666
rs1036667
rs848001●
cg06484146
rs17166022
rs17444259
rs9648158
rs864039
●CpG
Main effect
No effect
Interaction effect
TC07001147.hg.1 / ENST00000275358
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
VWDE uc003ssj.2VWDE uc011jxl.1VWDE uc011jxm.1 promotor
Exon
knownGene(UCSC hg19)
16kb
0.021
0 1R2
cg20607287
Chr7:12342463−12496140R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
12342641 12380766 12418891 12457016 12495140
rs12673036
rs1036666
rs1036667
rs848001●
cg20607287
rs17166022
rs17444259
rs9648158
rs864039
●CpG
Main effect
No effect
Interaction effect
TC07001147.hg.1 / ENST00000275358
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
VWDE uc003ssj.2VWDE uc011jxl.1VWDE uc011jxm.1 promotor
Exon
knownGene(UCSC hg19)
16kb
13
0.98
0.08
0.16
0.15
0.01
0.14
0.26
0.26
0.04
0.04
0.04
0.12
12
0.09
0.16
0.15
0.01
0.14
0.26
0.26
0.04
0.04
0.04
0.13
11
0.03
0
0.25
0.05
0.03
0.03
0.02
0.01
0.01
0
10
0.42
0
0.08
0.07
0.06
0.05
0.04
0.11
0.01
9
0.01
0.08
0.05
0.05
0.04
0.08
0.1
0.01
8
0.23
0.02
0.02
0.11
0.08
0.03
0
7
0.55
0.55
0.01
0.01
0.04
0.17
6
1
0.01
0.01
0.12
0.2
5
0.01
0.01
0.12
0.2
4
0.82
0.11
0.16
3
0.11
0.12
2
0.16
1
0.021
0 1R2
cg03226887
Chr7:28573260−28628789R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
28574260 28587746 28601231 28614717 28628202●
cg03226887
rs216721
rs216723
rs2078980
rs11769156
rs216742
rs160337
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CREB5 uc003szo.3CREB5 uc003szq.3CREB5 uc003szr.3knownGene
(UCSC hg19)
6kb
9
0.39
0.51
0.08
0.11
0.05
0.02
0.04
0.03
8
0.64
0.03
0.04
0.02
0.03
0.03
0.18
7
0.18
0.05
0.05
0.04
0.06
0.07
6
0
0.01
0.01
0.01
0.06
5
0
0.01
0
0.02
4
0
0.79
0.18
3
0
0.12
2
0.17
1
0.021
0 1R2
cg10035469
Chr7:83816895−83860120R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
83817895 83828202 83838508 83848814 83859120
rs12707628●
cg10035469
rs1989964
●CpG
Main effect
No effect
Interaction effect
TC07001568.hg.1 / ENST00000265362
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SEMA3A uc003uhz.3
promotor
Exon
knownGene(UCSC hg19)
5kb
0.021
0 1R2
cg15035350
Chr7:83752167−83869694R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
83752883 83781836 83810789 83839742 83868694
rs7808547
rs12707628●
cg15035350
rs1989964
rs10265795
●CpG
Main effect
No effect
Interaction effect
TC07001568.hg.1 / ENST00000265362
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SEMA3A uc003uhz.3
promotor
Exon
knownGene(UCSC hg19)
12kb
0.021
0 1R2
cg05742308
Chr7:83752167−83955266R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
83752883 83803229 83853575 83903921 83954266
rs7808547
rs12707628●
cg05742308
rs594533
rs6467990
●CpG
Main effect
No effect
Interaction effect
TC07001568.hg.1 / ENST00000265362
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SEMA3A uc003uhz.3
promotor
Exon
knownGene(UCSC hg19)
21kb
10
0.26
0.07
0.06
0.42
0.03
0.08
0.08
0.08
0.08
9
0.03
0.03
0.62
0.06
0.04
0.04
0.04
0.04
8
0.64
0.15
0
0.84
0.84
0.84
0.84
7
0.16
0.01
0.81
0.81
0.81
0.81
6
0.07
0.18
0.18
0.18
0.18
5
0.01
0.01
0.01
0.01
4
1
1
1
3
1
1
2
1
1
0.021
0 1R2
cg01198111
Chr7:91907223−92033975R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
91908223 91939411 91970599 92001787 92032975
rs10953067
rs17679665
rs17164519●
cg01198111
●CpG
Main effect
No effect
Interaction effect
TC07000547.hg.1 / ENST00000265742
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ANKIB1 uc003ulw.2ANKIB1 uc010lew.1
knownGene(UCSC hg19)
13kb
0.021
0 1R2
cg15320980
Chr8:553715−656142R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
554715 579822 604929 630036 655142
rs9644289
rs336430
rs336433●
cg15320980
rs89975
rs7004577
●CpG
Main effect
No effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
11kb
0.021
0 1R2
cg23958373
Chr8:576249−658650R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576304 596641 616977 637314 657650
rs12547464
rs89975
rs3735933●
cg23958373
rs1669733
rs336444
rs10092924
rs1616976
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
TC08000881.hg.1 / ENST00000262109−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
9kb
0.021
0 1R2
cg07234876
Chr8:575324−655796R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576209 595943 615676 635409 655142
rs336431
rs12547464
rs89975
rs3735933●
cg07234876
rs1669733
rs336444
rs336441
rs10092924
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
TC08000881.hg.1 / ENST00000262109−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
8kb
0.021
0 1R2
cg02524346
Chr8:548716−932580R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
549716 645182 740648 836114 931580
rs17065159
rs336433
rs12547464
rs89975
rs3735933●
cg02524346
rs1669733
rs336441
rs7003378
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
TC08000881.hg.1 / ENST00000262109 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3ERICH1−AS1 uc003wpj.2
ERICH1−AS1 uc003wpk.3promotor
Exon
knownGene(UCSC hg19)
39kb
0.021
0 1R2
cg07685180
Chr8:586113−658650R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
587113 604748 622382 640016 657650
rs89975
rs3735933●
cg07685180
rs1669733
rs1616976
●CpG
Main effect
No effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
TC08000881.hg.1 / ENST00000262109−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
8kb
13
0.15
0.66
0.12
0.66
0.81
0.06
0.12
0.62
0.28
0.39
0.46
0.28
12
0.04
0.01
0.04
0.1
0.01
0.01
0.02
0.03
0.01
0.05
0.03
11
0.2
0.99
0.57
0.03
0.18
0.55
0.46
0.37
0.74
0.45
10
0.2
0.08
0
0.63
0.07
0.03
0.08
0.09
0.03
9
0.57
0.04
0.18
0.54
0.46
0.37
0.74
0.46
8
0.1
0.15
0.69
0.27
0.37
0.48
0.27
7
0.02
0.1
0.05
0.13
0.07
0.05
6
0.14
0.02
0.07
0.19
0.02
5
0.48
0.54
0.73
0.47
4
0.28
0.64
0.99
3
0.43
0.28
2
0.64
1
0.021
0 1R2
cg26554054
Chr8:576249−607696R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576304 584019 591733 599447 607161
rs12547464
rs89975
rs3735933●
cg26554054
rs1669733
●CpG
Main effect
No effect
Interaction effect
TC08002170.hg.1TC08000882.hg.1
TC08000881.hg.1 / ENST00000262109−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1
promotor
Exon
knownGene(UCSC hg19)
4kb
0.021
0 1R2
cg10396713
Chr8:575209−655796R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576209 595943 615676 635409 655142
rs336430
rs89975●
cg10396713
rs1669733
rs336444
rs10092924
●CpG
Main effect
No effect
Interaction effect
TC08002170.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
8kb
0.021
0 1R2
cg08454824
Chr8:576249−721491R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576304 612351 648398 684445 720491
rs12547464
rs11137016●
cg08454824
rs3735917
rs1703946
rs6559181
●CpG
Main effect
No effect
Interaction effect
TC08000882.hg.1TC08000881.hg.1 / ENST00000262109
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3ERICH1−AS1 uc003wpj.2 promotor
Exon
knownGene(UCSC hg19)
15kb
0.021
0 1R2
cg01053087
Chr8:626181−720043R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
627181 650210 673239 696268 719296
rs4735815
rs11137016
rs336439●
cg01053087
rs3735917
rs4735907
rs12386927
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC08000881.hg.1 / ENST00000262109
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ERICH1 uc003wph.3ERICH1−AS1 uc003wpj.2
promotor
Exon
knownGene(UCSC hg19)
10kb
0.021
0 1R2
cg19002941
Chr8:586113−661575R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
587113 605479 623844 642210 660575
rs89975●
cg19002941
rs732195
rs4735907
●CpG
Main effect
No effect
Interaction effect
TC08002170.hg.1TC08000881.hg.1 / ENST00000262109
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3 promotor
Exon
knownGene(UCSC hg19)
8kb
0.021
0 1R2
cg17179911
Chr8:575304−720043R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
576209 611981 647753 683525 719296
rs4735890
rs4735815
rs9314603
rs1616976●
cg17179911
rs4735916
rs12386927
●CpG
Main effect
No effect
Interaction effect
TC08000881.hg.1 / ENST00000262109TC08000882.hg.1TC08002170.hg.1 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
AK128400 uc003wpf.1ERICH1 uc003wph.3
ERICH1 uc003wpi.3ERICH1−AS1 uc003wpj.2 promotor
Exon
knownGene(UCSC hg19)
15kb
5
0.45
0
0
0
4
0
0
0
3
0.37
0.67
2
0.57
1
0.021
0 1R2
cg19107264
Chr2:168065989−168067989 Chr8:1580598−1582598 Chr10:133923005−133925005R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs11893771●
cg19107264
rs9419204
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
XIRP2 uc002udx.3XIRP2 uc010fpn.3XIRP2 uc010fpo.3
DLGAP2 uc003wpl.4DLGAP2 uc003wpm.4
JAKMIP3 uc001lkx.4promotor
Exon
knownGene(UCSC hg19)
3kb
0.021
0 1R2
cg04912297
Chr8:17916888−17944293R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
17917866 17924223 17930580 17936937 17943293
rs10112857
rs6586684
rs10105871
rs2213909●
cg04912297
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ASAH1 uc003wyn.2ASAH1 uc003wyo.2ASAH1 uc003wyl.2knownGene
(UCSC hg19)
3kb
0.021
0 1R2
cg03562736
Chr8:113682162−114059716 Chr18:23909807−23911807R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs6469434
rs12681949●
cg03562736
rs12954996
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CSMD3 uc003ynu.3CSMD3 uc011lhx.2
CSMD3 uc010mcx.1TAF4B uc002kvs.4TAF4B uc002kvt.4
TAF4B uc002kvu.4
knownGene(UCSC hg19)
39kb
0.021
0 1R2
cg14598338
Chr9:96534966−96624480R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
96535470 96557473 96579475 96601478 96623480
rs7855940
rs10761288
rs7855547
rs10739960●
cg14598338
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MIR4291 uc022bkd.1
promotor
Exon
knownGene(UCSC hg19)
9kb
0.021
0 1R2
cg15550339
Chr10:8444914−8507979R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
8445914 8461181 8476447 8491713 8506979●
cg15550339
rs1002654
rs1361152
rs17469997
rs12416156
rs7090191
rs17143753
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg10616319
Chr10:15324014−15516153R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
15325014 15372631 15420248 15467865 15515482
rs17156509
rs10796289
rs11259651●
cg10616319
rs7896716
rs7079961
rs12263141
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
FAM171A1 uc001iob.3
promotor
Exon
knownGene(UCSC hg19)
20kb
16
0.45
0
0.6
0.03
0.45
0.44
0.58
0.64
0.6
0.04
0
0.02
0
0
0
15
0.48
0.73
0.04
0.99
0.96
0.69
0.72
0.72
0.04
0.02
0.08
0.01
0
0
14
0.16
0.02
0.47
0.46
0.14
0.13
0.15
0
0.04
0.06
0.01
0
0
13
0.04
0.72
0.7
0.94
0.98
0.97
0.09
0.01
0.03
0.01
0
0
12
0.04
0.04
0.04
0.04
0.04
0.38
0.21
0.07
0
0.01
0.05
11
0.96
0.7
0.72
0.71
0.04
0.02
0.08
0.01
0
0
10
0.68
0.69
0.69
0.03
0.02
0.08
0.01
0
0
9
0.96
0.95
0.08
0.01
0.03
0.01
0
0
8
0.99
0.08
0.01
0.03
0.01
0
0
7
0.09
0.01
0.04
0.01
0
0
6
0.38
0.28
0.01
0.02
0.07
5
0.13
0.17
0.05
0.16
4
0.11
0.22
0.22
3
0.03
0.11
2
0.26
1
0.021
0 1R2
cg15115171
Chr10:17595121−17760871R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
17596121 17637059 17677996 17718934 17759871
rs6602203●
cg15115171
rs17141324
rs7073625
rs7097801
rs7912011
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PTPLA uc001ipg.3PTPLA uc001iph.1
PTPLA uc001ipi.3STAM uc001ipj.2
STAM uc010qcf.2STAM uc009xjw.2
promotor
Exon
knownGene(UCSC hg19)
17kb
0.021
0 1R2
cg07356745
Chr10:86078877−86314427R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
86079877 86138323 86196768 86255213 86313658
rs12251522
rs17719302●
cg07356745
rs7077085
●CpG
Main effect
No effect
Interaction effect
TC10000596.hg.1 / ENST00000224756
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CCSER2 uc001kdh.1CCSER2 uc010qmd.1
CCSER2 uc001kdi.2DD413707 uc021pvn.1
knownGene(UCSC hg19)
24kb
14
0.97
0
0
0
0
0
0.01
0
0
0
0.01
0
0
13
0
0
0
0.01
0.01
0.01
0
0
0
0.01
0
0
12
0.01
0.01
0
0
0
0
0
0
0.01
0
0
11
1
0
0
0
0
0
0
0
0
0
10
0
0
0
0
0
0
0
0
0
9
0.39
0.01
0.02
0.02
0.05
0.01
0.05
0
8
0.16
0.39
0.37
0.03
0.01
0.03
0
7
0.39
0.4
0.01
0.17
0.01
0
6
0.96
0
0.05
0
0
5
0
0.06
0
0
4
0.08
0.99
0
3
0.08
0
2
0
1
0.021
0 1R2
cg00257187
Chr4:169499402−169501402 Chr5:78758026−78844271 Chr9:81166146−81168146Chr10:91400349−91402349R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs17650886
rs7733509
rs10805927
rs7871063●
cg00257187
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PALLD uc003iru.3PALLD uc011cjx.2
HOMER1 uc003kfy.4HOMER1 uc010jab.4HOMER1 uc010jac.4
PANK1 uc001kgp.2PANK1 uc001kgn.2PANK1 uc001kgo.2
promotor
Exon
knownGene(UCSC hg19)
13kb
4
0.08
0.18
0
3
0.03
0.09
2
0.1
1
0.021
0 1R2
cg20615879
Chr10:102883730−102898868R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
102884730 102888015 102891299 102894584 102897868
rs964236●
cg20615879
rs2742042
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TLX1NB uc001ksv.3TLX1 uc001ksw.3TLX1 uc021pxd.1 promotor
Exon
knownGene(UCSC hg19)
2kb
180.13
11
0.130.13
0.070.19
0.010.34
0.010.71
0.330.71
0.710.01
0.010.71
170.13
0.131
10.16
0.350.2
0.40.2
0.110.39
0.110.11
0.190.19
0.11
161
0.130.13
0.070.19
0.010.34
0.010.71
0.330.71
0.710.01
0.010.71
150.13
0.130.07
0.190.01
0.340.01
0.710.33
0.710.71
0.010.01
0.71
141
0.160.35
0.20.4
0.190.11
0.390.11
0.110.19
0.190.11
130.16
0.350.2
0.40.2
0.110.39
0.110.11
0.190.19
0.11
120.44
0.090.18
0.090.05
0.180.05
0.050.08
0.080.05
110.2
00.2
0.310
0.310.31
0.190.19
0.31
100.44
0.980.07
0.420.07
0.070.97
0.960.07
90.45
0.30.97
0.30.3
0.440.43
0.3
80.06
0.440.06
0.060.99
0.980.06
70.29
11
0.070.07
1
60.29
0.30.44
0.440.29
51
0.070.07
1
40.07
0.071
30.99
0.07
20.07
1
0.021
0 1R2
cg17283857
Chr10:102988315−102990315 Chr19:21673962−21778082R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
●
cg17283857
rs2246914
rs11085468
rs939301
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
LBX1 uc001ksx.3FLJ41350 uc010qpy.2
LINC00664 uc002nqa.3LINC00664 uc002nqb.3
LINC00664 uc002nqc.3ZNF429 uc002nqd.1ZNF429 uc010ecu.2
AX748435 uc002nqf.1BC033373 uc002nqg.3
promotor
Exon
knownGene(UCSC hg19)
12kb
0.021
0 1R2
cg22633036
Chr10:123197332−123356576R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
123197653 123237134 123276615 123316096 123355576
rs2162543
rs4752559
rs7918550
rs6585737●
cg22633036
●CpG
Main effect
No effect
Interaction effect
TC10001711.hg.1 / ENST00000346997
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
FGFR2 uc001lfn.5FGFR2 uc010qtl.2
FGFR2 uc010qtm.2 promotor
Exon
knownGene(UCSC hg19)
16kb
0.021
0 1R2
cg17389077
Chr10:128808645−128856597R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
128809541 128821055 128832569 128844083 128855597
rs4751179
rs1340242●
cg17389077
rs2066161
rs2066160
rs17698492
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DOCK1 uc001ljt.3DOCK1 uc010qun.2
DOCK1 uc031pxq.1knownGene(UCSC hg19)
5kb
10
0.46
0.74
0.47
0.32
0.3
0.16
0.22
0.17
0.01
9
0.51
0.58
0.64
0.63
0.31
0.32
0.25
0.02
8
0.25
0.47
0.42
0.12
0.18
0.13
0.01
7
0.61
0.61
0.42
0.37
0.28
0.03
6
0.89
0.38
0.32
0.24
0.03
5
0.39
0.33
0.25
0.04
4
0.55
0.41
0.05
3
0.74
0.04
2
0.02
1
0.021
0 1R2
cg16259904
Chr10:134070848−134165341R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
134071848 134094972 134118095 134141218 134164341
rs2814191●
cg16259904
rs2474334
rs2698779
rs2497644
●CpG
Main effect
No effect
Interaction effect
TC10000942.hg.1 / ENST00000344079TC10002376.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
STK32C uc010quu.1STK32C uc001lle.1
STK32C uc009ybd.1LRRC27 uc001llg.2
LRRC27 uc010quw.1LRRC27 uc001lli.2
knownGene(UCSC hg19)
10kb
15
0.38
0.38
0.6
0.09
0.36
0.8
0.51
0.44
0.63
0.65
0.32
0.32
0.24
0.01
14
0.93
0.38
0
0.15
0.29
0.11
0.3
0.25
0.26
0.29
0.22
0.15
0.04
13
0.39
0
0.15
0.29
0.11
0.3
0.24
0.26
0.3
0.22
0.15
0.03
12
0.13
0.59
0.75
0.33
0.77
0.46
0.46
0.38
0.38
0.3
0.02
11
0.21
0.11
0.16
0.11
0.07
0.07
0.16
0.11
0.13
0.04
10
0.46
0.74
0.47
0.32
0.3
0.16
0.22
0.17
0.01
9
0.51
0.58
0.64
0.63
0.31
0.32
0.25
0.02
8
0.25
0.47
0.42
0.12
0.18
0.13
0.01
7
0.61
0.61
0.42
0.37
0.28
0.03
6
0.89
0.38
0.32
0.24
0.03
5
0.39
0.33
0.25
0.04
4
0.55
0.41
0.05
3
0.74
0.04
2
0.02
1
0.021
0 1R2
cg23771949
Chr10:134070848−134191734R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
134071848 134101570 134131291 134161013 134190734
rs2814191
rs7075670
rs2474334
rs2698779●
cg23771949
rs2474338
rs7079070
rs4481949
●CpG
Main effect
No effect
Interaction effect
TC10002376.hg.1TC10000942.hg.1 / ENST00000344079
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
STK32C uc010quu.1STK32C uc001lle.1
STK32C uc009ybd.1LRRC27 uc001llg.2
LRRC27 uc010quw.1LRRC27 uc001lli.2
promotor
Exon
knownGene(UCSC hg19)
12kb
7
0.01
0.01
0.15
0.22
0.42
0.14
6
0.98
0.3
0.47
0.14
0.31
5
0.31
0.46
0.14
0.31
4
0.04
0.02
0.97
3
0.08
0.04
2
0.03
1
0.021
0 1R2
cg24668570
Chr10:134965154−134983123R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
134965295 134969502 134973709 134977916 134982123
rs12768641
rs4284331●
cg24668570
rs3008304
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
KNDC1 uc001llz.1KNDC1 uc001lma.1
promotor
Exon
knownGene(UCSC hg19)
2kb
190.17
0.010.01
00.01
0.30.06
0.30.31
0.480.3
0.290.3
0.110.11
0.020.11
0.09
180.1
0.110.1
0.10.37
0.030.38
0.370.22
0.380.06
0.370.02
0.020.04
0.660
170.94
0.950.97
00.22
00
0.040
0.350
0.080.08
0.410.11
0.22
160.97
0.910
0.20
00.03
00.37
00.11
0.110.43
0.110.19
150.92
00.2
00
0.030
0.350
0.10.11
0.440.11
0.18
140
0.210
00.04
00.36
00.08
0.080.43
0.120.2
130.05
0.990.99
0.610.99
0.130.98
0.410.4
0.030.35
0
120.05
0.050.1
0.050.07
0.050.02
0.020.09
0.030.08
111
0.621
0.130.99
0.40.4
0.030.34
0
100.61
10.13
0.990.4
0.390.03
0.340
90.62
0.230.61
0.250.24
00.21
0.02
80.13
0.990.4
0.40.03
0.340
70.13
0.040.03
0.170.05
0.33
60.42
0.410.03
0.340
50.99
0.250.01
0.01
40.24
0.010.01
30.06
0.08
20
1
0.021
0 1R2
cg09068031
Chr11:11489764−11508157R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
11489894 11494210 11498526 11502842 11507157
rs11021865
rs901549●
cg09068031
rs7117475
rs4910362
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
GALNT18 uc001mjo.2
knownGene(UCSC hg19)
2kb
6
1
0.01
0
0
0
5
0.01
0
0
0
4
0.01
0
0
3
0
0
2
0.52
1
0.021
0 1R2
cg11063328
Chr1:18267405−18269405 Chr1:167621119−167623119 Chr4:127087140−127089140 Chr11:18342203−18344203 Chr16:10990988−10992988R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs652234
rs12067995
rs523306●
cg11063328
rs8048002
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RCSD1 uc001gem.3RCSD1 uc010pli.2
HPS5 uc001mod.1HPS5 uc001moe.1HPS5 uc001mof.1
GTF2H1 uc001moh.2GTF2H1 uc001moi.2
GTF2H1 uc009yhm.2CIITA uc002dai.4CIITA uc002daj.4
CIITA uc002dak.4
promotor
Exon
knownGene(UCSC hg19)
5kb
0.021
0 1R2
cg03447554
Chr11:43007961−43162203R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
43008961 43047022 43085082 43123143 43161203
rs1565251
rs10838000
rs1425853
rs10501294●
cg03447554
rs11037263
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
16kb
0.021
0 1R2
cg13308137
Chr11:47418663−47874883R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
47419663 47533218 47646773 47760328 47873883
rs1534576
rs4237544●
cg13308137
rs7120548
rs10838739
rs7930612
rs6485788
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC11001737.hg.1 / ENST00000527426TC11000407.hg.1 / ENST00000354884
TC11001746.hg.1 / ENST00000302503 −1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SLC39A13 uc001nfd.3SLC39A13 uc001nfe.1SLC39A13 uc001nff.4
PSMC3 uc001nfh.2RAPSN uc001nfi.2RAPSN uc001nfj.2RAPSN uc009yls.1
CELF1 uc001nfn.3CELF1 uc001nfp.3
CELF1 uc001nfk.2PTPMT1 uc001nfs.4PTPMT1 uc001nfu.4PTPMT1 uc001nfv.4NDUFS3 uc001nft.3
NDUFS3 uc001nga.2NDUFS3 uc010rhn.1
KBTBD4 uc001nfy.3KBTBD4 uc001nfz.3KBTBD4 uc001nfx.3
FAM180B uc001ngb.2C1QTNF4 uc001ngc.2
C1QTNF4 uc021qit.1MTCH2 uc010rho.2MTCH2 uc010rhp.2
AGBL2 uc001ngg.3AGBL2 uc001ngf.3
AGBL2 uc010rhq.1FNBP4 uc001ngj.3FNBP4 uc009ylv.3
FNBP4 uc001ngl.2NUP160 uc001ngm.3NUP160 uc009ylw.3NUP160 uc021qiu.1
Y_RNA uc021qiv.1
promotor
Exon
knownGene(UCSC hg19)
46kb
17
0.57
0.01
0.73
0.63
0.29
0.07
0.17
0.05
0.06
0.56
0.09
0.01
0.05
0.06
0.12
0.47
16
0.27
0.38
0.33
0.54
0.14
0.02
0.09
0.1
0.27
0.03
0
0.11
0.1
0.07
0.23
15
0.06
0.05
0.19
0.05
0.15
0.5
0.53
0.05
0.33
0.04
0.05
0.03
0.01
0.04
14
0.86
0.21
0.1
0.17
0.06
0.06
0.62
0.08
0.01
0.08
0.02
0.14
0.53
13
0.28
0.12
0.12
0.02
0.03
0.64
0.05
0.01
0.1
0.02
0.17
0.56
12
0.25
0
0.09
0.08
0.29
0.12
0.05
0.27
0.18
0.08
0.24
11
0.43
0.08
0.07
0.1
0.08
0.02
0.86
0.13
0.05
0.08
10
0.21
0.2
0.18
0.25
0.04
0.39
0.27
0.02
0.16
9
0.89
0.04
0.54
0.01
0.07
0.03
0
0.04
8
0.07
0.61
0
0.07
0.04
0.01
0.07
7
0.1
0.01
0.13
0.06
0.23
0.87
6
0.01
0.11
0.08
0.01
0.05
5
0.01
0.01
0
0.02
4
0.12
0.05
0.13
3
0.01
0.06
2
0.22
1
0.021
0 1R2
cg04046629
Chr11:60759971−60826022R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
60760530 60776718 60792905 60809092 60825279
rs929230
rs2283263
rs7929471●
cg04046629
rs4939493
rs175112
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CD6 uc001nqq.3CD6 uc001nqr.3CD6 uc001nqs.3
TRNA_Pseudo uc021qkd.1 promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg15531562
Chr11:65576516−65986168R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
65577516 65679429 65781342 65883255 65985168
rs10896050
rs7102454●
cg15531562
rs630303
rs659824
rs512421
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC11000645.hg.1 / ENST00000307886TC11003210.hg.1TC11001946.hg.1 / ENST00000307998
TC11001950.hg.1 / ENST00000312234TC11000650.hg.1 / ENST00000312175
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
SNX32 uc001ofr.3SNX32 uc009yqt.3SNX32 uc010rop.1
CFL1 uc001ofs.3CFL1 uc001oft.3
MUS81 uc001ofv.4MUS81 uc001ofx.4
EFEMP2 uc001ofy.4EFEMP2 uc001ofz.3
CTSW uc001ogc.1FIBP uc001ogd.3FIBP uc001oge.3FIBP uc010roq.1CCDC85B uc001ogf.3
FOSL1 uc001ogg.1FOSL1 uc010ros.1
C11orf68 uc001ogi.3C11orf68 uc009yqv.3
DRAP1 uc001ogj.2TSGA10IP uc001ogk.1TSGA10IP uc009yqw.1TSGA10IP uc009yqx.1
SART1 uc001ogl.3SART1 uc009yqy.1SART1 uc010rot.1
EIF1AD uc001ogm.2EIF1AD uc001ogn.2
EIF1AD uc021qlr.1BANF1 uc001ogo.3BANF1 uc001ogp.3AX747517 uc001ogq.1AX747517 uc001ogs.1
CST6 uc001ogr.3CATSPER1 uc001ogt.3
AX746604 uc001ogu.1GAL3ST3 uc001ogv.3GAL3ST3 uc001ogw.3
SF3B2 uc001ogx.1SF3B2 uc001ogy.1SF3B2 uc031qbn.1
PACS1 uc001ogz.1PACS1 uc001oha.2
promotor
Exon
knownGene(UCSC hg19)
41kb
0.021
0 1R2
cg04592747
Chr8:70008214−70113933 Chr11:66034942−66036942R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs2912524
rs4348505
rs485219
rs683567
rs13267697●
cg04592747
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
LOC100505718 uc003xyc.1TRNA_Pseudo uc022avp.1
KLC2 uc010rov.1KLC2 uc010row.1KLC2 uc001ohb.2
RAB1B uc001ohf.3promotor
Exon
knownGene(UCSC hg19)
12kb
11
0
0.14
0
0.2
0.04
0.03
0.08
0.12
0.01
0.01
10
0
0.18
0.04
0.01
0.01
0.07
0.07
0.08
0.08
9
0.24
0.08
0.01
0.01
0.07
0.11
0.02
0.05
8
0.1
0.06
0.06
0.29
0.04
0.11
0.08
7
0.08
0.08
0.35
0.18
0.18
0.16
6
0.76
0
0.04
0.01
0.01
5
0.01
0.07
0.02
0.03
4
0.51
0.59
0.57
3
0.25
0.22
2
0.91
1
0.021
0 1R2
cg04827223
Chr11:72373037−72461155R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
72373496 72395161 72416826 72438491 72460155
rs11235559
rs341053
rs10898868
rs10898869●
cg04827223
rs7124056
rs4943997
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PDE2A uc010rrc.2PDE2A uc010rrd.2PDE2A uc001osq.3
ARAP1 uc001osv.3ARAP1 uc001osu.3ARAP1 uc001oss.3
BC150585 uc009yti.1
promotor
Exon
knownGene(UCSC hg19)
9kb
190.04
0.040.34
0.970.34
0.010.09
0.010.01
00.68
0.010.04
0.050.06
0.040.04
0.06
180.98
0.280.04
0.290.02
0.010.02
0.060.06
0.020.03
0.040.08
0.090.04
0.180.01
170.29
0.040.29
0.020.01
0.020.06
0.060.02
0.030.04
0.070.08
0.050.18
0.01
160.33
0.980.08
0.020.07
0.080.08
0.250.05
0.180.03
0.030
0.010.12
150.34
0.010.09
0.010.01
00.7
0.020.03
0.060.05
0.050.04
0.04
140.08
0.020.07
0.080.08
0.260.05
0.170.02
0.030
0.010.11
130
0.970.01
00.01
0.860.06
0.090.09
0.020.02
0.04
120
0.10.11
0.010
0.010.03
0.030.02
0.010
110.01
0.010.01
0.880.06
0.090.09
0.020.02
0.04
100.96
0.040.01
0.120.18
0.190.2
0.020.03
90.04
0.010.11
0.170.18
0.190.03
0.03
80.01
0.020.12
0.120.09
0.030.11
70.05
0.080.08
0.020.02
0.03
60.62
0.630.43
0.040.09
50.96
0.70.11
0
40.69
0.110
30.24
0
20
1
0.021
0 1R2
cg25314284
Chr11:80997251−81046482R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
80998251 81010059 81021867 81033675 81045482●
cg25314284
rs17141868
rs11232607
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
5kb
190.76
0.450.29
0.450.02
0.080.97
0.010.21
0.270.51
0.410.49
0.410
0.060.24
0.01
180.59
0.220.59
0.120.11
0.740.01
0.230.33
0.640.46
0.380.36
0.060.04
0.170.07
170.14
0.990.07
0.120.43
0.070.43
0.550.76
0.260.22
0.230.04
0.020.1
0.12
160.14
00.02
0.290.02
0.250.1
0.140.38
0.460.15
00
0.010
150.07
0.120.44
0.070.43
0.560.78
0.260.22
0.240.04
0.020.11
0.12
140.01
0.020.01
0.010.02
0.060.02
0.010
0.280
0.010.5
130.08
0.080.07
0.070.02
0.060.04
0.030.01
0.010.02
0.01
120.01
0.190.26
0.510.38
0.480.43
0.010.05
0.260.02
110.03
0.040
0.050.07
0.050
0.220.02
0.01
100.29
0.510.64
0.530.03
0.080.06
0.060.07
90.52
0.170.15
0.580.02
0.020.08
0.07
80.35
0.290.2
0.050.03
0.150.14
70.83
0.140.13
0.10.04
0.02
60.24
00.1
0.030.01
50.04
0.020.14
0.01
40
00.4
30
0
20.01
1
0.021
0 1R2
cg01663953
Chr11:86122041−86184632R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
86123041 86138244 86153447 86168650 86183853
rs11234643●
cg01663953
rs4944580
rs2511082
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
CCDC81 uc001pbw.2CCDC81 uc001pbx.2CCDC81 uc001pby.2
ME3 uc009yvk.3ME3 uc001pca.3
ME3 uc010rtr.1promotor
Exon
knownGene(UCSC hg19)
7kb
0.021
0 1R2
cg25724515
Chr11:131925464−131985267R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
131926464 131940987 131955509 131970031 131984553●
cg25724515
rs1547895
rs11533200
rs12223742
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
NTM uc001qgm.3NTM uc010sch.2NTM uc010sci.2knownGene
(UCSC hg19)
6kb
180.07
0.040.03
0.370.01
0.010.02
0.020.01
0.010.02
0.010.01
0.010.02
0.060.05
170.03
0.040.57
0.050.12
0.140.14
0.040.11
0.140.1
0.110.09
0.150.02
0.03
160.36
0.290.01
0.620.09
0.090.01
0.620.09
0.630.62
0.670.09
0.360.32
150.34
0.170.69
0.010.01
0.050.69
0.010.67
0.690.62
0.020.32
0.37
140.05
0.460.11
0.110.03
0.450.11
0.440.45
0.40.11
0.270.31
130.12
0.350.35
00.12
0.350.11
0.120.13
0.360.18
0.17
120.26
0.260.04
0.980.26
0.970.98
0.910.26
0.620.67
111
0.010.26
0.990.24
0.260.27
0.970.41
0.38
100.01
0.260.99
0.240.26
0.270.97
0.410.38
90.03
0.010.04
0.030
0.010
0.05
80.27
0.981
0.920.26
0.630.69
70.25
0.270.28
0.980.41
0.38
60.98
0.910.24
0.620.67
50.92
0.260.63
0.69
40.27
0.680.6
30.42
0.39
20.92
1
0.021
0 1R2
cg12020590
Chr11:134502242−134533846R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
134503242 134510768 134518293 134525819 134533344
rs3019643
rs3019665●
cg12020590
rs1944876
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
4kb
10
0.22
0.33
0.33
0.23
0.03
0.04
0.55
0.34
0.27
9
0.13
0.13
0.09
0.01
0.02
0.2
0.01
0.1
8
0.99
0.56
0.21
0.12
0.33
0.23
0.63
7
0.56
0.21
0.12
0.33
0.23
0.62
6
0.15
0.07
0.45
0.2
0.66
5
0.77
0.07
0.02
0.18
4
0.09
0.03
0.23
3
0.41
0.48
2
0.21
1
0.021
0 1R2
cg04012082
Chr12:1877392−1913526R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
1878154 1886747 1895340 1903933 1912526
rs12821401
rs12828908●
cg04012082
rs12823985
rs7300241
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ADIPOR2 uc001qjm.3ADIPOR2 uc001qjn.3
CACNA2D4 uc021qsx.1CACNA2D4 uc009zds.2CACNA2D4 uc009zdr.2
promotor
Exon
knownGene(UCSC hg19)
4kb
0.021
0 1R2
cg21224286
Chr12:1802521−1913526R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
1803521 1830773 1858024 1885275 1912526
rs2058035
rs11061935
rs11061962
rs4766415
rs12821401
rs12828908●
cg21224286
rs12823985
rs7300241
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ADIPOR2 uc001qjm.3ADIPOR2 uc001qjn.3
CACNA2D4 uc021qsx.1CACNA2D4 uc009zds.2CACNA2D4 uc009zdr.2
knownGene(UCSC hg19)
11kb
10
0.63
0.45
0.28
0.06
0.07
0.03
0.03
0.03
0.18
9
0.17
0.05
0.12
0.13
0.06
0.06
0.06
0.22
8
0.69
0.08
0.08
0.07
0.07
0.07
0.36
7
0.08
0.07
0.06
0.06
0.06
0.22
6
0.98
0.73
0.72
0.73
0.02
5
0.74
0.73
0.74
0.02
4
0.99
1
0.07
3
0.99
0.07
2
0.06
1
0.021
0 1R2
cg10980102
Chr12:6152514−6170733R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
6153514 6157569 6161624 6165679 6169733
rs1063857
rs7954351●
cg10980102
rs10744696
rs4764482
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
VWF uc001qnn.1VWF uc010set.1
knownGene(UCSC hg19)
2kb
0.021
0 1R2
cg02873991
Chr12:25106130−25163703R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
25107130 25121024 25134917 25148810 25162703
rs10842439
rs1497262
rs2352739●
cg02873991
rs859145
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
C12orf77 uc001rgf.3C12orf77 uc031qgr.1
promotor
Exon
knownGene(UCSC hg19)
6kb
17
0.82
1
0.52
0.38
0.51
0.18
0.17
0.92
0.04
0.83
0.84
0.17
0.11
0.18
0.36
0.91
16
0.82
0.42
0.54
0.41
0.2
0.13
0.78
0
0.87
0.87
0.13
0.1
0.13
0.44
0.79
15
0.51
0.38
0.51
0.18
0.17
0.91
0.04
0.82
0.83
0.17
0.11
0.18
0.36
0.9
14
0.09
1
0.45
0.21
0.52
0.04
0.44
0.45
0.22
0.12
0.22
0.1
0.51
13
0.09
0.39
0.09
0.38
0.03
0.48
0.47
0.09
0.15
0.09
0.84
0.39
12
0.45
0.21
0.52
0.04
0.44
0.44
0.22
0.12
0.22
0.1
0.51
11
0.06
0.2
0
0.23
0.23
0.06
0.11
0.06
0.45
0.22
10
0.18
0.02
0.14
0.14
0.97
0.01
0.98
0.13
0.17
9
0.07
0.85
0.85
0.17
0.12
0.18
0.37
0.97
8
0.02
0.01
0.02
0
0.02
0.05
0.05
7
0.99
0.14
0.1
0.14
0.51
0.86
6
0.14
0.1
0.15
0.51
0.87
5
0.02
0.99
0.13
0.17
4
0.02
0.16
0.11
3
0.13
0.17
2
0.39
1
0.021
0 1R2
cg03550075
Chr12:132191836−132279530R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
132192836 132214260 132235683 132257107 132278530
rs10444602
rs11246770
rs4964986
rs10794425
rs6598153●
cg03550075
rs10902450
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
SFSWAP uc001uja.2SFSWAP uc010tbn.2SFSWAP uc001ujb.1knownGene
(UCSC hg19)
9kb
16
0.8
0.67
0.8
0.54
0.28
0.53
0.21
0.12
0.79
0.06
0.68
0.68
0.13
0.07
0.13
15
0.82
1
0.52
0.38
0.51
0.18
0.17
0.92
0.04
0.83
0.84
0.17
0.11
0.18
14
0.82
0.42
0.54
0.41
0.2
0.13
0.78
0
0.87
0.87
0.13
0.1
0.13
13
0.51
0.38
0.51
0.18
0.17
0.91
0.04
0.82
0.83
0.17
0.11
0.18
12
0.09
1
0.45
0.21
0.52
0.04
0.44
0.45
0.22
0.12
0.22
11
0.09
0.39
0.09
0.38
0.03
0.48
0.47
0.09
0.15
0.09
10
0.45
0.21
0.52
0.04
0.44
0.44
0.22
0.12
0.22
9
0.06
0.2
0
0.23
0.23
0.06
0.11
0.06
8
0.18
0.02
0.14
0.14
0.97
0.01
0.98
7
0.07
0.85
0.85
0.17
0.12
0.18
6
0.02
0.01
0.02
0
0.02
5
0.99
0.14
0.1
0.14
4
0.14
0.1
0.15
3
0.02
0.99
2
0.02
1
0.021
0 1R2
cg08693745
Chr12:132206534−132292061R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
132207135 132228117 132249098 132270080 132291061
rs11246771
rs1051219
rs6598153●
cg08693745
rs10751695
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
SFSWAP uc001uja.2SFSWAP uc010tbn.2
SFSWAP uc001ujb.1knownGene(UCSC hg19)
9kb
0.021
0 1R2
cg20293942
Chr13:50442558−50722117R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
50443527 50512925 50582322 50651720 50721117
rs9526614●
cg20293942
rs2066593
●CpG
Main effect
No effect
Interaction effect
TC13000202.hg.1 / ENST00000298772TC13001088.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CTAGE10P uc001vdk.2SPRYD7 uc001vdl.2SPRYD7 uc001vdm.2SPRYD7 uc010tgm.1DLEU2 uc001vdn.1DLEU2 uc001vdo.1
DLEU2 uc001vdx.3MIR3613 uc021rjp.1TRIM13 uc001vdp.1TRIM13 uc001vdq.1TRIM13 uc001vdr.1
KCNRG uc001vdt.3KCNRG uc001vdu.3
MIR16−1 uc001vea.1DM119508 uc021rjr.1
DLEU1 uc001veg.1DLEU1 uc001vei.1
DLEU1 uc010ado.1
promotor
Exon
knownGene(UCSC hg19)
28kb
2
0
1
0.021
0 1R2
cg00843117
Chr4:130599622−130601622 Chr5:115774542−115776542 Chr13:50801085−50803085R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs7691964
rs26592●
cg00843117
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DLEU1 uc001veg.1DLEU1 uc001vei.1
DLEU1 uc010ado.1BCMS uc001vem.1
BCMS uc001vel.1BCMS uc001ven.1
promotor
Exon
knownGene(UCSC hg19)
3kb
8
0.31
0.31
0.11
0.31
0.09
0.03
0.05
7
0.99
0.04
0.02
0.42
0.32
0.3
6
0.04
0.02
0.42
0.31
0.3
5
0.02
0.01
0.05
0.01
4
0.35
0.13
0.15
3
0.14
0.58
2
0.23
1
0.021
0 1R2
cg11462099
Chr13:113512682−113541512R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
113513306 113520108 113526909 113533711 113540512
rs10492684
rs4907464
rs1278769●
cg11462099
●CpG
Main effect
No effect
Interaction effect
TC13000413.hg.1TC13001312.hg.1
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
ATP11A uc001vsi.4ATP11A uc001vsj.4ATP11A uc010ago.3
AK025511 uc021rmp.1knownGene
(UCSC hg19)
3kb
7
0.08
0.18
0.08
0
0.3
0.31
6
0.4
0.92
0.13
0.16
0.18
5
0.41
0.34
0.01
0.01
4
0.14
0.19
0.2
3
0.02
0.02
2
0.98
1
0.021
0 1R2
cg12537329
Chr13:113672695−113695840R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
113673695 113678982 113684268 113689554 113694840
rs2993300●
cg12537329
rs2993312
rs1537025
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MCF2L uc010tjr.2MCF2L uc031qnk.1MCF2L uc010tjs.2knownGene
(UCSC hg19)
3kb
13
0.12
0.08
0.07
0.1
0.25
0.08
0.44
0.24
0.24
0.14
0.02
0.01
12
0.72
0.02
0.02
0.08
0.66
0.03
0.01
0.01
0.04
0.07
0
11
0.02
0.02
0.14
0.91
0.09
0.01
0.01
0.04
0.15
0
10
0.83
0.02
0.02
0.09
0.01
0.01
0
0.04
0.05
9
0.03
0.02
0.09
0.01
0.02
0
0.06
0.06
8
0.16
0.19
0.43
0.44
0.07
0.08
0
7
0.09
0.01
0.01
0.03
0.16
0
6
0.22
0.22
0.22
0.04
0.06
5
0.98
0.02
0.07
0.06
4
0.03
0.07
0.06
3
0.1
0.23
2
0.15
1
0.021
0 1R2
cg16512163
Chr13:114872205−114938294R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
114873205 114889228 114905250 114921272 114937294
rs9314891●
cg16512163
rs2183244
rs2149773
rs6560933
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RASA3 uc001vui.3RASA3 uc001vuj.3RASA3 uc010tkl.1 promotor
Exon
knownGene(UCSC hg19)
7kb
6
0.05
0.82
0.24
0.19
0.06
5
0.06
0.08
0.01
0.11
4
0.27
0.2
0.07
3
0.27
0.6
2
0.45
1
0.021
0 1R2
cg26146732
Chr14:70689454−70748906R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
70690454 70704973 70719492 70734011 70748530●
cg26146732
rs9323533
rs10145919
rs12880065
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ADAM21P1 uc010ttg.2
promotor
Exon
knownGene(UCSC hg19)
6kb
10
0.05
0.82
0.24
0.19
0.06
0.01
0.17
0.04
0.06
9
0.06
0.08
0.01
0.11
0.01
0
0.29
0.1
8
0.27
0.2
0.07
0
0.18
0.05
0.08
7
0.27
0.6
0.02
0.27
0.11
0.58
6
0.45
0.11
0.88
0.11
0.41
5
0.04
0.4
0.17
0.9
4
0.11
0.02
0.04
3
0.09
0.47
2
0.18
1
0.021
0 1R2
cg21484985
Chr14:70657939−70748906R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
70658044 70680666 70703287 70725909 70748530
rs2332272●
cg21484985
rs9323533
rs10145919
rs12880065
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ADAM21P1 uc010ttg.2
promotor
Exon
knownGene(UCSC hg19)
10kb
0.021
0 1R2
cg08322580
Chr14:70657939−70846363R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
70658044 70705002 70751959 70798917 70845874
rs2332272
rs1559714●
cg08322580
rs9323533
rs12880065
rs17566989
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ADAM21P1 uc010ttg.2COX16 uc001xmb.3
COX16 uc021rvl.1SYNJ2BP−COX16 uc021rvm.1SYNJ2BP−COX16 uc021rvn.1SYNJ2BP−COX16 uc021rvo.1
U2 uc021rvp.1SYNJ2BP uc001xmc.4
promotor
Exon
knownGene(UCSC hg19)
19kb
13
0.01
0.32
0.23
0.01
0.02
0.31
0.13
0.15
0.33
0.02
0.02
0.03
12
0.03
0.03
0.72
0.02
0.04
0.13
0.15
0
0.04
0.15
0.12
11
0.67
0.03
0.56
0.98
0
0.01
0.1
0.02
0.01
0.01
10
0.03
0.36
0.66
0.05
0
0.07
0
0.02
0
9
0.02
0.03
0.11
0.13
0
0.02
0.1
0.08
8
0.55
0.06
0.05
0.01
0
0.05
0
7
0
0.01
0.12
0.02
0.01
0.01
6
0.7
0.03
0.05
0.41
0.01
5
0.05
0.16
0.57
0.04
4
0.02
0.02
0.01
3
0.18
0.34
2
0.08
1
0.021
0 1R2
cg23950756
Chr14:90972750−91055072R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
90973750 90993831 91013911 91033992 91054072
rs1297787
rs1294540●
cg23950756
rs1294564
rs1006117
rs1286474
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TTC7B uc001xyo.3TTC7B uc001xyp.3TTC7B uc010ats.3 promotor
Exon
knownGene(UCSC hg19)
9kb
9
0.11
0.11
0.05
0.05
0.05
0.01
0.02
0.02
8
0.99
0.34
0.34
0.34
0.01
0.25
0.16
7
0.34
0.34
0.34
0.01
0.25
0.16
6
1
0.98
0.01
0.66
0.56
5
0.99
0.01
0.67
0.56
4
0.01
0.66
0.55
3
0.01
0.01
2
0.73
1
0.021
0 1R2
cg18416503
Chr14:93437821−93495030R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
93438821 93452741 93466661 93480581 93494500
rs4905017
rs8005216
rs4905030●
cg18416503
rs12587868
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ITPK1 uc001ybe.2ITPK1 uc001ybg.3ITPK1 uc001ybh.3knownGene
(UCSC hg19)
6kb
6
0.96
0.06
0.15
0.18
0.15
5
0.06
0.16
0.2
0.15
4
0.02
0.05
0.02
3
0.18
0.62
2
0.22
1
0.021
0 1R2
cg13019568
Chr14:95819298−95836758R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
95820298 95824322 95828345 95832368 95836391
rs8010752●
cg13019568
rs8017312
rs1187718
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
6
0.96
0.06
0.15
0.18
0.15
5
0.06
0.16
0.2
0.15
4
0.02
0.05
0.02
3
0.18
0.62
2
0.22
1
0.021
0 1R2
cg05369327
Chr14:95819298−95836758R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
95820298 95824322 95828345 95832368 95836391
rs8010752●
cg05369327
rs8017312
rs1187718
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
6
0.96
0.06
0.15
0.18
0.15
5
0.06
0.16
0.2
0.15
4
0.02
0.05
0.02
3
0.18
0.62
2
0.22
1
0.021
0 1R2
cg14228933
Chr14:95819298−95838865R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
95820298 95824690 95829082 95833474 95837865
rs8010752
rs8017312
rs1187718●
cg14228933
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
2kb
10
0.17
0.16
0.16
0.05
0.16
0
0
0.01
0
9
0.98
0.98
0.3
0.98
0.01
0.01
0.01
0
8
1
0.31
1
0.01
0.01
0.01
0
7
0.31
1
0.01
0.01
0.01
0
6
0.31
0.01
0.01
0.01
0
5
0.01
0.01
0.01
0
4
1
0
0
3
0
0
2
0
1
0.021
0 1R2
cg10784720
Chr2:115984658−115986658Chr7:7249449−7251449Chr12:20650594−20652594 Chr14:106915597−106989024R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs12991531
rs7780273
rs6487097●
cg10784720
rs12885997
rs11847718
rs41480349
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
DPP10 uc002tla.2DPP10 uc002tlb.2DPP10 uc002tlc.2
C1GALT1 uc003srb.3C1GALT1 uc010ktm.1
PDE3A uc001reh.2abParts uc031qqx.1
LINC00221 uc001ysy.2
promotor
Exon
knownGene(UCSC hg19)
11kb
13
0.99
0.99
0.7
0.17
0.17
0.06
0.17
0.05
0.04
0.04
0.17
0.06
12
1
0.72
0.18
0.18
0.07
0.18
0.05
0.04
0.04
0.18
0.07
11
0.72
0.18
0.18
0.07
0.18
0.05
0.04
0.04
0.18
0.07
10
0.22
0.21
0.11
0.22
0.08
0.08
0.08
0.23
0.06
9
0.99
0.43
0.98
0.33
0.2
0.2
0.01
0.13
8
0.44
0.97
0.33
0.2
0.2
0.01
0.13
7
0.43
0.73
0.51
0.51
0.28
0.03
6
0.34
0.2
0.2
0.01
0.14
5
0.69
0.68
0.21
0.14
4
0.98
0.33
0.14
3
0.34
0.14
2
0.26
1
0.021
0 1R2
cg02313495
Chr15:40386971−40479577R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
40387971 40410623 40433274 40455926 40478577
rs11637681
rs11858141●
cg02313495
rs537455
rs11634065
rs3759843
rs12148261
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
BMF uc001zku.4BMF uc001zkw.4
BMF uc001zkv.4BUB1B uc001zkx.4
BUB1B uc010ucl.1promotor
Exon
knownGene(UCSC hg19)
10kb
0.021
0 1R2
cg17728600
Chr15:77390603−77853897R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
77391603 77506927 77622250 77737574 77852897
rs12899474
rs12910419
rs12911362
rs17394732●
cg17728600
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PEAK1 uc021sqy.1PEAK1 uc002bcn.2AX747193 uc021sqz.1
LINC00597 uc002bcp.4HMG20A uc002bcq.1HMG20A uc002bcr.3HMG20A uc002bcs.3
AK025664 uc021sra.1
promotor
Exon
knownGene(UCSC hg19)
47kb
0.021
0 1R2
cg02196730
Chr15:80106090−80200249R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
80107090 80130130 80153170 80176210 80199249
rs16971376
rs16971450●
cg02196730
rs8030396
●CpG
Main effect
No effect
Interaction effect
TC15002781.hg.1 / ENST00000478497
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
U6 uc021sro.1MTHFS uc002bex.4MTHFS uc021srp.1MTHFS uc021srq.1
ST20−MTHFS uc021srr.1AK054972 uc002bey.3
ST20 uc002bfa.4ST20 uc021sru.1ST20 uc021srs.1
promotor
Exon
knownGene(UCSC hg19)
10kb
0.021
0 1R2
cg25846076
Chr15:86232851−86333964R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
86233009 86257998 86282987 86307976 86332964
rs338553
rs12913266
rs2614658
rs8041288●
cg25846076
rs2946365
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
AKAP13 uc002blu.2AKAP13 uc002blv.2AKAP13 uc031qtl.1
KLHL25 uc002bly.3KLHL25 uc021stw.1
MIR1276 uc021stx.1promotor
Exon
knownGene(UCSC hg19)
10kb
12
0.09
0.27
0
0.01
0.03
0.05
0.03
0
0.03
0.03
0.06
11
0.01
0.01
0.01
0.01
0
0.01
0.06
0
0.02
0.03
10
0
0.02
0.02
0.13
0.11
0.01
0.03
0.02
0.04
9
0
0.01
0
0
0
0
0
0.01
8
0.12
0.09
0.2
0.03
0.05
0
0.06
7
0.38
0.3
0.11
0.53
0.55
0.39
6
0
0.04
0.26
0.28
0.11
5
0.06
0.22
0.16
0.07
4
0.06
0.09
0.06
3
0.44
0.33
2
0.73
1
0.021
0 1R2
cg00101154
Chr16:359303−512183R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
360303 398023 435743 473463 511183
rs3842949
rs7195617
rs11649268
rs3848368●
cg00101154
rs743961
rs3743898
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC16000727.hg.1 / ENST00000250930TC16000726.hg.1 / ENST00000389675
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LUC7L uc021szo.1AXIN1 uc002cgp.2AXIN1 uc002cgq.2
MRPL28 uc002cgs.2TMEM8A uc002cgu.4TMEM8A uc002cgv.4
LOC100134368 uc002cgw.1RPL2B uc002cgx.3
NME4 uc021szp.1NME4 uc002cgz.3
DECR2 uc002chb.3DECR2 uc002chc.3DECR2 uc002chd.3
RAB11FIP3 uc002chf.3
promotor
Exon
knownGene(UCSC hg19)
16kb
11
0.09
0.27
0
0.01
0.03
0.05
0.03
0
0.03
0.03
10
0.01
0.01
0.01
0.01
0
0.01
0.06
0
0.02
9
0
0.02
0.02
0.13
0.11
0.01
0.03
0.02
8
0
0.01
0
0
0
0
0
7
0.12
0.09
0.2
0.03
0.05
0
6
0.38
0.3
0.11
0.53
0.55
5
0
0.04
0.26
0.28
4
0.06
0.22
0.16
3
0.06
0.09
2
0.44
1
0.021
0 1R2
cg12437481
Chr16:368413−512183R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
369413 404856 440298 475741 511183
rs8064205
rs7195617
rs2885415
rs11649268
rs3848368●
cg12437481
rs743961
rs3743898
●CpG
Main effect
No effect
Interaction effect
Interaction effect
TC16000726.hg.1 / ENST00000389675TC16000727.hg.1 / ENST00000250930
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
LUC7L uc021szo.1AXIN1 uc002cgp.2AXIN1 uc002cgq.2
MRPL28 uc002cgs.2TMEM8A uc002cgu.4TMEM8A uc002cgv.4
LOC100134368 uc002cgw.1RPL2B uc002cgx.3
NME4 uc021szp.1NME4 uc002cgz.3
DECR2 uc002chb.3DECR2 uc002chc.3DECR2 uc002chd.3
RAB11FIP3 uc002chf.3
promotor
Exon
knownGene(UCSC hg19)
15kb
180.04
0.10.04
0.080.02
0.130.06
00.07
0.130.02
0.020.06
0.020
0.050.02
170.3
0.020.04
0.020
0.010.01
0.020.04
0.070.07
0.030.03
0.040.01
0.03
160.03
0.010.03
00.02
00.03
00.04
0.040.01
0.030.01
0.020
150.1
0.020.02
0.010.01
0.020.05
0.020.02
0.020
0.010.01
0.01
140.15
0.180.11
0.030.09
0.390.21
0.210.1
0.090.3
0.080.13
130.05
0.030
0.020.09
0.060.06
0.030.45
0.270.02
0.02
120.59
0.010.28
0.310.09
0.090.23
0.080.11
0.510.03
110.01
0.010.17
0.250.25
0.460.05
0.060.86
0.02
100
0.010.01
0.010.01
0.010.01
0.010
90.09
0.030.03
0.020.01
0.010.01
0.01
80.64
0.640.39
0.010.01
0.150.22
71
0.390
0.010.24
0.22
60.39
00.01
0.240.22
50.02
0.040.41
0.01
40.25
0.050.05
30.07
0.35
20.02
1
0.021
0 1R2
cg07957035
Chr16:49601130−49657098R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
49601768 49615351 49628933 49642516 49656098
rs11640355
rs7187662
rs12923113
rs1420683●
cg07957035
rs4490001
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
ZNF423 uc010vgn.3ZNF423 uc031qwd.1ZNF423 uc031qwe.1knownGene
(UCSC hg19)
6kb
13
0.4
0.18
0.43
0.09
0.01
0.03
0.19
0
0.24
0.07
0.43
0.31
12
0.51
0.95
0.06
0.25
0.03
0.08
0.24
0.12
0.1
0.16
0.19
11
0.53
0.09
0.52
0.02
0.11
0.5
0.22
0.13
0
0
10
0.06
0.27
0.03
0.08
0.26
0.12
0.09
0.2
0.23
9
0.02
0
0.01
0.02
0.37
0.01
0.18
0.14
8
0.01
0.06
0.95
0.07
0.27
0.09
0.15
7
0.01
0.01
0
0
0.01
0.08
6
0.07
0.02
0.01
0.44
0.3
5
0.07
0.26
0.1
0.15
4
0.03
0.21
0.25
3
0.03
0.04
2
0.7
1
0.021
0 1R2
cg04811706
Chr16:55681999−55707499R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
55682999 55689063 55695127 55701191 55707254
rs11645905●
cg04811706
rs17247999
rs13333066
rs187714
●CpG
Main effect
No effect
Interaction effect
Interaction effect
Associatedtranscripts (HTA 2.0)
SLC6A2 uc021tio.1SLC6A2 uc002eif.3
SLC6A2 uc002eig.3 promotor
Exon
knownGene(UCSC hg19)
3kb
3
0.97
0.96
2
0.98
1
0.021
0 1R2
cg00158530
Chr16:69958988−69969367R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
69959988 69962083 69964178 69966273 69968367
rs904807●
cg00158530
rs8048590
●CpG
Main effect
No effect
Interaction effect
TC16000571.hg.1 / ENST00000356003
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
WWP2 uc002exu.2WWP2 uc002exv.2WWP2 uc010vlm.2
MIR140 uc002exx.1knownGene
(UCSC hg19)
2kb
0.021
0 1R2
cg00443946
Chr16:86369962−86396647R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
86370962 86377362 86383762 86390162 86396562●
cg00443946
rs2581300
rs2581303
rs1687632
rs41362847
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
LINC00917 uc002fjj.2LINC00917 uc010chr.2
LINC00917 uc010von.1 promotor
Exon
knownGene(UCSC hg19)
3kb
11
0.1
0.77
0.07
0.04
0.04
0.13
0.02
0.02
0.02
0.01
10
0.11
0.52
0.55
0.44
0.57
0.06
0.01
0.05
0.01
9
0.09
0.04
0.04
0.16
0.02
0.03
0.05
0.01
8
0.47
0.25
0.25
0.2
0.1
0.15
0
7
0.58
0.35
0.1
0.04
0.12
0
6
0.27
0.02
0
0.16
0
5
0.08
0.06
0.02
0
4
0.48
0.02
0
3
0.04
0
2
0.13
1
0.021
0 1R2
cg10330187
Chr16:88608326−88676177R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
88609326 88625793 88642260 88658727 88675194
rs899737
rs11076678
rs9935402●
cg10330187
rs9932685
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
C16orf85 uc010vox.1ZC3H18 uc002fky.3ZC3H18 uc010voz.2ZC3H18 uc010voy.1 promotor
Exon
knownGene(UCSC hg19)
7kb
4
0.72
0.11
0.02
3
0.01
0.09
2
0.21
1
0.021
0 1R2
cg26955290
Chr17:6981444−7023290R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
6982444 6992406 7002367 7012329 7022290
rs444207
rs10521152●
cg26955290
rs12951306
rs4796383
●CpG
Main effect
No effect
Interaction effect
TC17001075.hg.1 / ENST00000254850
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
CLEC10A uc002gej.3CLEC10A uc002gek.3CLEC10A uc010clv.2
ASGR2 uc002geo.2ASGR2 uc002gep.3
ASGR2 uc010vtl.1promotor
Exon
knownGene(UCSC hg19)
4kb
2
0
1
0.021
0 1R2
cg19437868
Chr4:140828147−140830147 Chr12:77696923−77698923 Chr17:7975285−7977285R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs17051003
rs10858665●
cg19437868
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MAML3 uc011chd.1MAML3 uc021xsg.1
ALOX12B uc002gjy.1 promotor
Exon
knownGene(UCSC hg19)
3kb
0.021
0 1R2
cg01787735
Chr17:16689169−16691169 Chr17:18108328−18563720R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
●
cg01787735
rs2124370
rs8065874
rs7222009
rs4441330
●CpG
Main effect
No effect
Interaction effect
TC17002871.hg.1TC17002079.hg.1
TC17001223.hg.1 / ENST00000392176TC17002892.hg.1 / ENST00000285176
TC17002532.hg.1TC17001201.hg.1 / ENST00000316694
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
USP32P1 uc010cpj.1USP32P1 uc010cpk.1USP32P1 uc010vwq.1
ALKBH5 uc010cpw.3LLGL1 uc002gsp.3
FLII uc002gsr.2FLII uc010vxn.2FLII uc010vxo.2
DQ596932 uc010vxp.1SMCR7 uc002gst.3SMCR7 uc002gsu.3SMCR7 uc010vxq.2
TOP3A uc002gsx.1TOP3A uc010vxs.1
TOP3A uc010cqa.1SMCR8 uc002gsy.4
SHMT1 uc002gta.3SHMT1 uc002gtb.3SHMT1 uc010vxt.2
AX747021 uc002gtc.1EVPLL uc002gte.3DQ571055 uc021trn.1DQ570768 uc021tro.1DQ576083 uc002gtg.1DQ585755 uc002gth.2DQ595911 uc002gti.3
DQ578124 uc010vxv.2DQ579248 uc002gtj.3DQ592713 uc002gtk.1DQ586114 uc021trp.1DQ595299 uc021trq.1DQ585853 uc021trr.1DQ593368 uc021trs.1DQ578661 uc021trt.1
DQ573130 uc002gto.3DQ579174 uc021tru.1DQ572309 uc002gtp.3DQ592578 uc021trv.1DQ586004 uc021trw.1DQ584883 uc010vxx.1
AX748015 uc002gtt.1BC040601 uc010vxy.2LOC339240 uc002gtv.3
AK296148 uc010vxz.2
promotor
Exon
knownGene(UCSC hg19)
47kb
16
0.01
0.4
0.01
0.32
0.02
0.31
0.01
0.01
0.01
0.01
0.03
0.01
0.22
0.01
0.01
15
0
0.01
0.05
0
0.02
0.01
0.01
0
0.01
0.26
0.01
0.02
0.01
0
14
0.01
0.76
0.06
0.18
0
0
0.06
0
0.01
0
0.24
0
0.06
13
0.04
0
0.04
0.11
0.11
0.01
0.1
0.01
0.1
0.05
0.1
0.01
12
0.07
0.22
0.01
0.01
0.06
0.01
0.04
0.01
0.29
0.01
0.06
11
0.05
0.02
0.02
0.01
0.02
0.01
0.02
0.06
0.02
0
10
0.43
0.43
0.02
0.42
0.09
0.39
0.78
0.38
0.01
9
1
0.01
0.97
0.04
0.93
0.37
0.93
0.01
8
0.01
0.97
0.04
0.93
0.37
0.93
0.01
7
0.01
0
0.01
0.06
0.01
0.95
6
0.04
0.96
0.36
0.95
0.01
5
0.04
0.1
0.04
0.01
4
0.38
0.99
0.01
3
0.38
0.06
2
0.01
1
0.021
0 1R2
cg08471713
Chr17:41702554−41758610R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
41703554 41717179 41730803 41744427 41758051
rs8064916
rs16940067
rs8081000●
cg08471713
rs8070993
rs16940093
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
MEOX1 uc002idz.3MEOX1 uc002iea.3MEOX1 uc002ieb.3 promotor
Exon
knownGene(UCSC hg19)
6kb
0.021
0 1R2
cg08496953
Chr17:42732527−42968295R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
42733527 42791969 42850411 42908853 42967295●
cg08496953
rs4369727
rs17745948
rs7210042
●CpG
Main effect
No effect
Interaction effect
TC17002227.hg.1TC17000573.hg.1 / ENST00000315005
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
C17orf104 uc002iha.3C17orf104 uc010wja.1
C17orf104 uc002igz.3CCDC43 uc002ihc.2CCDC43 uc010czw.1
CCDC43 uc021tye.1DBF4B uc002ihf.3
DBF4B uc010wjc.2DBF4B uc002ihe.3
ADAM11 uc002ihh.3ADAM11 uc010wjd.2
ADAM11 uc002ihi.3GJC1 uc002ihl.3GJC1 uc002ihk.3GJC1 uc002ihj.3
HIGD1B uc031rau.1HIGD1B uc002ihm.4
EFTUD2 uc002ihn.2EFTUD2 uc010wje.1EFTUD2 uc010wjf.1
promotor
Exon
knownGene(UCSC hg19)
24kb
7
0.19
0.41
0.04
0.4
0.04
0
6
0.08
0.12
0.09
0.1
0
5
0.08
0.86
0.07
0
4
0.07
0.98
0
3
0.08
0
2
0
1
0.021
0 1R2
cg27123423
Chr17:62970335−62982333 Chr17:66252095−66273177R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
●
cg27123423
rs17685439
rs7105
rs2362727
rs7210814
rs8080714
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
AMZ2P1 uc002jfa.3AMZ2P1 uc002jfb.3AMZ2P1 uc010del.2
AMZ2 uc002jgr.1AMZ2 uc002jgs.1AMZ2 uc002jgt.1
ARSG uc002jhc.2SLC16A6 uc002jgz.2SLC16A6 uc002jha.2
promotor
Exon
knownGene(UCSC hg19)
5kb
4
0
0
0
3
0
0
2
0
1
0.021
0 1R2
cg25442652
Chr2:76099564−76101564 Chr4:112437430−112439430 Chr14:99811577−99813577 Chr17:80620718−80622718R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs6755718
rs10004952
rs906933●
cg25442652
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RAB40B uc002kfs.3RAB40B uc002kft.3
promotor
Exon
knownGene(UCSC hg19)
4kb
16
0.12
0.43
0.13
0.47
0.47
0.47
0.22
0.13
0.06
0.02
0.23
0.23
0.05
0.37
0.34
15
0.3
0.17
0.26
0.26
0.26
0.01
0.17
0.09
0.1
0.02
0.02
0.43
0.01
0
14
0.28
0.93
0.93
0.92
0.56
0.28
0.22
0.04
0.58
0.57
0.15
0.15
0.19
13
0.27
0.28
0.27
0.48
0.97
0.04
0.01
0.48
0.48
0.06
0.26
0.29
12
0.98
0.97
0.52
0.27
0.16
0.04
0.55
0.54
0.13
0.17
0.16
11
0.98
0.54
0.28
0.16
0.04
0.54
0.54
0.13
0.18
0.16
10
0.53
0.28
0.15
0.04
0.54
0.54
0.13
0.19
0.17
9
0.5
0.13
0.08
0.97
0.95
0.22
0.48
0.52
8
0.05
0.01
0.5
0.49
0.06
0.27
0.3
7
0.01
0.13
0.13
0.05
0.1
0.06
6
0.08
0.08
0.22
0.05
0.05
5
0.98
0.23
0.49
0.55
4
0.22
0.51
0.56
3
0.1
0.12
2
0.92
1
0.021
0 1R2
cg10935494
Chr17:80714054−80835447R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
80714899 80744786 80774673 80804560 80834447
rs2451214●
cg10935494
rs12945629
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TBCD uc002kfx.1TBCD uc002kfy.1TBCD uc002kfz.3
ZNF750 uc002kga.3knownGene
(UCSC hg19)
12kb
10
0.06
0.23
0.75
0.36
0.37
0.02
0.35
0.09
0.83
9
0.19
0.05
0.2
0.21
0.43
0.2
0.08
0.03
8
0.26
0.03
0.03
0.08
0.02
0.47
0.21
7
0.5
0.5
0.02
0.48
0.12
0.71
6
0.99
0.11
0.96
0.3
0.45
5
0.11
0.96
0.29
0.45
4
0.11
0.05
0.02
3
0.3
0.43
2
0.12
1
0.021
0 1R2
cg25413575
Chr17:80833447−80903411R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
80834447 80851438 80868429 80885420 80902411
rs12945629●
cg25413575
rs1127986
rs12940475
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TBCD uc002kfz.3TBCD uc002kfy.1
TBCD uc002kgd.3B3GNTL1 uc002kge.1
B3GNTL1 uc002kgf.1B3GNTL1 uc002kgg.1
knownGene(UCSC hg19)
7kb
13
0.06
0.17
0.6
0.26
0.59
0.07
0.17
0.02
0.06
0.01
0.13
0.14
12
0.05
0.05
0
0.05
0.05
0
0.38
0.06
0
0.04
0
11
0.08
0
0.08
0.08
0
0.03
0.07
0.01
0.01
0.02
10
0.54
0.98
0.07
0.34
0.03
0.06
0.03
0.32
0.19
9
0.53
0.13
0.49
0.05
0.13
0.01
0.16
0.07
8
0.07
0.34
0.03
0.07
0.03
0.32
0.18
7
0.12
0.01
0.91
0.01
0.02
0.05
6
0.01
0.11
0.07
0.2
0.05
5
0.01
0
0.01
0.01
4
0.01
0.03
0.03
3
0.02
0.13
2
0.1
1
0.021
0 1R2
cg24258439
Chr18:60030184−60058341R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
60030587 60037276 60043964 60050653 60057341
rs17069901
rs8089829
rs4426449●
cg24258439
rs17665435
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
TNFRSF11A uc002lin.4TNFRSF11A uc010dpv.4TNFRSF11A uc031rim.1knownGene
(UCSC hg19)
3kb
6
0.99
0.07
0.03
0.14
0.16
5
0.07
0.03
0.14
0.16
4
0.1
0.03
0.16
3
0.07
0.55
2
0.19
1
0.021
0 1R2
cg19560656
Chr19:14409014−14452948R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
14410014 14420498 14430981 14441465 14451948
rs11672794
rs8108124●
cg19560656
rs4926111
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
BC011648 uc002myk.3
promotor
Exon
knownGene(UCSC hg19)
5kb
16
0.04
0.58
0.05
0.01
0.05
0.03
0.05
0.09
0.05
0.01
0.09
0.06
0.06
0.06
0.07
15
0.06
0.05
0.22
0.05
0.01
0.05
0
0.01
0.01
0.01
0.07
0.07
0.07
0.01
14
0.08
0.01
0.08
0.03
0.08
0.15
0.08
0.01
0.11
0.04
0.04
0.04
0.06
13
0.01
1
0.03
1
0.5
0.55
0.02
0
0.03
0.03
0.03
0.04
12
0.01
0.01
0.01
0.03
0.01
0.01
0
0.03
0.03
0.03
0.01
11
0.03
1
0.5
0.55
0.03
0
0.03
0.03
0.03
0.04
10
0.03
0.11
0.02
0.09
0.01
0.02
0.02
0.03
0.02
9
0.49
0.55
0.02
0
0.03
0.03
0.03
0.04
8
0.61
0.06
0.01
0.02
0.02
0.02
0.01
7
0.03
0.05
0.12
0.12
0.12
0.06
6
0.03
0.07
0.07
0.07
0.05
5
0.45
0.45
0.45
0.32
4
1
0.99
0.79
3
1
0.79
2
0.79
1
0.021
0 1R2
cg08551532
Chr19:39913748−40062294R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
39914748 39951385 39988021 40024658 40061294
rs31726
rs4803238●
cg08551532
rs4802035
rs1433110
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PLEKHG2 uc010xuz.2PLEKHG2 uc010xuy.2
PLEKHG2 uc010xva.2RPS16 uc002olk.3RPS16 uc002oll.3RPS16 uc002olm.3
SUPT5H uc002oln.4SUPT5H uc002olo.4SUPT5H uc002olp.4
TIMM50 uc002olt.2TIMM50 uc002olu.1
TIMM50 uc002olv.1DLL3 uc002olw.2DLL3 uc002olx.2
DLL3 uc010egq.3SELV uc021uum.1
EID2B uc002olz.1EID2 uc002oma.3
promotor
Exon
knownGene(UCSC hg19)
15kb
16
0.04
0.58
0.05
0.01
0.05
0.03
0.05
0.09
0.05
0.01
0.09
0.06
0.06
0.06
0.07
15
0.06
0.05
0.22
0.05
0.01
0.05
0
0.01
0.01
0.01
0.07
0.07
0.07
0.01
14
0.08
0.01
0.08
0.03
0.08
0.15
0.08
0.01
0.11
0.04
0.04
0.04
0.06
13
0.01
1
0.03
1
0.5
0.55
0.02
0
0.03
0.03
0.03
0.04
12
0.01
0.01
0.01
0.03
0.01
0.01
0
0.03
0.03
0.03
0.01
11
0.03
1
0.5
0.55
0.03
0
0.03
0.03
0.03
0.04
10
0.03
0.11
0.02
0.09
0.01
0.02
0.02
0.03
0.02
9
0.49
0.55
0.02
0
0.03
0.03
0.03
0.04
8
0.61
0.06
0.01
0.02
0.02
0.02
0.01
7
0.03
0.05
0.12
0.12
0.12
0.06
6
0.03
0.07
0.07
0.07
0.05
5
0.45
0.45
0.45
0.32
4
1
0.99
0.79
3
1
0.79
2
0.79
1
0.021
0 1R2
cg03807316
Chr19:39913748−40062294R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
39914748 39951385 39988021 40024658 40061294
rs31726
rs4803238●
cg03807316
rs4802035
rs1433110
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
PLEKHG2 uc010xuz.2PLEKHG2 uc010xuy.2
PLEKHG2 uc010xva.2RPS16 uc002olk.3RPS16 uc002oll.3RPS16 uc002olm.3
SUPT5H uc002oln.4SUPT5H uc002olo.4SUPT5H uc002olp.4
TIMM50 uc002olt.2TIMM50 uc002olu.1
TIMM50 uc002olv.1DLL3 uc002olw.2DLL3 uc002olx.2
DLL3 uc010egq.3SELV uc021uum.1
EID2B uc002olz.1EID2 uc002oma.3
promotor
Exon
knownGene(UCSC hg19)
15kb
8
0
0
0
0.03
0.17
0.18
0.14
7
1
1
0.02
0.02
0.02
0.03
6
1
0.02
0.02
0.02
0.03
5
0.02
0.02
0.02
0.03
4
0.07
0.07
0.16
3
0.97
0.71
2
0.73
1
0.021
0 1R2
cg26466157
Chr19:46925667−46960007R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
46926667 46934752 46942837 46950922 46959007
rs11083825●
cg26466157
rs371657
rs4803953
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
knownGene(UCSC hg19)
4kb
13
0.25
0.24
0.25
0.19
0.18
0.2
0.19
0.19
0.34
0.19
0.18
0.17
12
0.06
0.24
0.1
0.11
0.11
0.11
0.11
0.01
0.12
0.11
0.11
11
0.06
0.05
0.05
0.05
0.05
0.05
0.09
0.05
0.05
0.04
10
0.01
0.01
0.01
0.01
0.01
0.22
0.01
0.01
0.01
9
0.91
0.94
0.91
0.9
0.47
0.93
0.88
0.76
8
0.94
0.91
0.9
0.46
0.95
0.9
0.79
7
0.94
0.93
0.5
0.97
0.91
0.78
6
0.99
0.52
0.96
0.96
0.78
5
0.52
0.95
0.95
0.78
4
0.5
0.49
0.41
3
0.93
0.81
2
0.79
1
0.021
0 1R2
cg15028160
Chr9:136875021−136930046 Chr19:49621717−49623717R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
rs441233
rs465724
rs736902●
cg15028160
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
LINC00094 uc004ceu.3BRD3 uc004cew.3
BRD3 uc004cex.2LIN7B uc002pmp.3
C19orf73 uc002pmq.4PPFIA3 uc002pmr.3PPFIA3 uc010yai.2
promotor
Exon
knownGene(UCSC hg19)
7kb
10
0.99
0.16
0.04
0.1
0.1
0.27
0.01
0.04
0.5
9
0.16
0.04
0.1
0.1
0.27
0.01
0.04
0.5
8
0.38
0.45
0.45
0.33
0.54
0.39
0.01
7
0.02
0.02
0.16
0.39
1
0.04
6
1
0.12
0.11
0.02
0
5
0.12
0.11
0.02
0
4
0.33
0.16
0.27
3
0.4
0.14
2
0.04
1
0.021
0 1R2
cg16140273
Chr21:30389557−30471512R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
30390557 30410546 30430535 30450524 30470512
rs11700764
rs2832153●
cg16140273
rs1571680
rs2832173
●CpG
Main effect
No effect
Interaction effect
TC21000353.hg.1 / ENST00000286788TC21000352.hg.1 / ENST00000486719
−1 0 1
r expression
Associatedtranscripts (HTA 2.0)
RWDD2B uc002yms.3USP16 uc002ymw.3USP16 uc002ymx.3USP16 uc002ymy.3
CCT8 uc002ynb.3CCT8 uc011acq.2CCT8 uc002yna.3
MAP3K7CL uc002ynd.3MAP3K7CL uc002yne.3MAP3K7CL uc010gln.3
promotor
Exon
knownGene(UCSC hg19)
8kb
7
0.58
0.04
0.04
0.02
0.48
0.19
6
0.29
0.29
0.25
0.85
0.11
5
0.99
0.01
0.32
0.36
4
0.01
0.31
0.36
3
0.31
0.09
2
0.12
1
0.021
0 1R2
cg18120111
Chr21:43897112−43953568R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
43898112 43911726 43925340 43938954 43952568
rs12482483●
cg18120111
rs228050
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RSPH1 uc002zbg.3SLC37A1 uc002zbi.3
SLC37A1 uc002zbj.3 promotor
Exon
knownGene(UCSC hg19)
6kb
10
0.35
0.35
0.67
0.38
0.09
0.09
0.07
0.36
0.26
9
1
0.24
0.12
0.11
0.11
0.39
0.11
0.05
8
0.24
0.12
0.11
0.11
0.39
0.11
0.05
7
0.58
0.04
0.04
0.02
0.48
0.19
6
0.29
0.29
0.25
0.85
0.11
5
0.99
0.01
0.32
0.36
4
0.01
0.31
0.36
3
0.31
0.09
2
0.12
1
0.021
0 1R2
cg20460554
Chr21:43897112−43961219R2 full model
R2 main effects only
0.00
0.25
0.50
0.75
1.00
R2 re
plic
atio
n
0.00
0.25
0.50
0.75
1.00
R2 d
isco
very
0.00
0.25
0.50
0.75
1.00
CpG
βdi
scov
ery
CpG Island
DNase I
TFBS
43898112 43913639 43929166 43944693 43960219
rs12482483●
cg20460554
rs228068
●CpG
Main effect
No effect
Interaction effect
Associatedtranscripts (HTA 2.0)
RSPH1 uc002zbg.3SLC37A1 uc002zbi.3
SLC37A1 uc002zbj.3 promotor
Exon
knownGene(UCSC hg19)
7kb
![Plasmids - static-content.springer.com10.1038...pCAG ZNF91 [1-11]. pCAG ZNF91 was digested with XmaI and NotI and religated resulting in the removal of the C-terminal 12-36 domains](https://img.pdfslide.us/doc/110x75/5fa4ab19cfca06359b78d836/plasmids-static-101038-pcag-znf91-1-11-pcag-znf91-was-digested-with-xmai.jpg)
