Additional file 5: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Genome-Wide Meta-Analysis of Cotinine Levels in Cigarette Smokers Identifies Locus at 4q13.2

Ware, Jennifer
Chen, Xiangning
Vink, Jaqueline
Lyytikäinen, Leo-Pekka
Lehtimäki, Terho
Kähönen, Mika

January 2016

Genome-wide association studies (GWAS) of complex behavioural phenotypes such as cigarette smoking t...

Additional file 2: of Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health

Pei-Chien Tsai (169868)
Craig Glastonbury (5729903)
Melissa Eliot (667253)
Sailalitha Bollepalli (5876465)
Idil Yet (2609974)
Juan Castillo-Fernandez (3861310)
Elena Carnero-Montoro (525376)
Thomas Hardiman (5876474)
Tiphaine Martin (5876480)
Alice Vickers (5876486)
Massimo Mangino (87550)
Kirsten Ward (3417971)
Kirsi PietilĂ¤inen (5876489)
Panos Deloukas (21564)
Tim Spector (153290)
Ana ViĂąuela (5876492)
Eric Loucks (5876495)
Miina Ollikainen (799967)
Karl Kelsey (3398846)
Kerrin Small (174643)
Jordana Bell (667256)

October 2018

Table S1. Four smoking-induced differentially methylated and expressed genes in blood samples. Table...

Additional file 4: Table S3. of DNA methylation and smoking in Korean adults: epigenome-wide association study

Mi Lee (3414719)
Yoonki Hong (3521672)
Sun-Young Kim (24695)
Stephanie London (588804)
Woo Kim (3483326)

September 2016

CpGs differentially methylated in blood DNA in relation to current smoking compared to never smoking...

Additional file 6: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S4. Trans acting methylation quantitative trait loci in the 40 genes highlighted in the EWAS. ...

Additional file 8: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S5. Mediation analysis omnibus P values for the 19 meQTLs associated with serum cotinine level...

Additional file 7: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Figure S3. Mediation analysis to assess whether DNA methylation is a causal mediator to the observed...

Additional file 11: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S8. Results for CIT performed on DILGOM sample replicated CpG sites and SNPs associated with t...

Additional file 3: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S2. SNPs in the 40 top genes significantly associated (FDR pâ<â0.05) with cotinine levels....

Additional file 2: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S1. Gene network (IPA) and pathway analysis (Gene Ontology) of EWAS results. (XLS 3125 kb

Additional file 9: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S6. Transcription factor binding site information for 55 highlighted CpG sites based on ENCODE...

Additional file 1: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Figure S1. Manhattan and QQ plots showing epigenome-wide association results from secondary analysis...

Additional file 10: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S7. CpG sites showing significant (FDR pâ<â0.05) association with cotinine levels in regul...

Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Gupta, Richa
Van Dongen, Jenny
Fu, Yu
Abdellaoui, Abdel
Tyndale, Rachel F.
Velagapudi, Vidya
Boomsma, Dorret I.
Korhonen, Tellervo
Kaprio, Jaakko
Loukola, Anu
Ollikainen, Miina

January 2019

BACKGROUND: DNA methylation alteration extensively associates with smoking and is a plausible link b...

Self-reported smoking, serum cotinine, and blood DNA methylation

Zhang, Y.
Florath, Ines
Saum, K.
Brenner, H.

January 2016

BACKGROUND: Epigenome-wide profiling of DNA methylation pattern with respect to tobacco smoking has ...

Additional file 5: of Genome-wide analysis of DNA methylation in bronchial washings

Sang-Won Um (535627)
Yujin Kim (483088)
Bo Lee (3463586)
Dongho Kim (29790)
Kyung-Jong Lee (5237399)
Hong Kim (101826)
Joungho Han (483091)
Hojoong Kim (535625)
Young Shim (3463580)
Duk-Hwan Kim (483093)

May 2018

Table S3. The correlation between pack-years of smoking and DNA methylation in 53 control groups. (D...

Genome-Wide Meta-Analysis of Cotinine Levels in Cigarette Smokers Identifies Locus at 4q13.2

Ware, Jennifer
Chen, Xiangning
Vink, Jaqueline
Lyytikäinen, Leo-Pekka
Lehtimäki, Terho
Kähönen, Mika

January 2016

Genome-wide association studies (GWAS) of complex behavioural phenotypes such as cigarette smoking t...

Additional file 2: of Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health

Pei-Chien Tsai (169868)
Craig Glastonbury (5729903)
Melissa Eliot (667253)
Sailalitha Bollepalli (5876465)
Idil Yet (2609974)
Juan Castillo-Fernandez (3861310)
Elena Carnero-Montoro (525376)
Thomas Hardiman (5876474)
Tiphaine Martin (5876480)
Alice Vickers (5876486)
Massimo Mangino (87550)
Kirsten Ward (3417971)
Kirsi PietilĂ¤inen (5876489)
Panos Deloukas (21564)
Tim Spector (153290)
Ana ViĂąuela (5876492)
Eric Loucks (5876495)
Miina Ollikainen (799967)
Karl Kelsey (3398846)
Kerrin Small (174643)
Jordana Bell (667256)

October 2018

Table S1. Four smoking-induced differentially methylated and expressed genes in blood samples. Table...

Additional file 4: Table S3. of DNA methylation and smoking in Korean adults: epigenome-wide association study

Mi Lee (3414719)
Yoonki Hong (3521672)
Sun-Young Kim (24695)
Stephanie London (588804)
Woo Kim (3483326)

September 2016

CpGs differentially methylated in blood DNA in relation to current smoking compared to never smoking...

Additional file 6: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S4. Trans acting methylation quantitative trait loci in the 40 genes highlighted in the EWAS. ...

Additional file 8: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S5. Mediation analysis omnibus P values for the 19 meQTLs associated with serum cotinine level...

Additional file 7: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Figure S3. Mediation analysis to assess whether DNA methylation is a causal mediator to the observed...

Additional file 11: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S8. Results for CIT performed on DILGOM sample replicated CpG sites and SNPs associated with t...

Additional file 3: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S2. SNPs in the 40 top genes significantly associated (FDR pâ<â0.05) with cotinine levels....

Additional file 2: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S1. Gene network (IPA) and pathway analysis (Gene Ontology) of EWAS results. (XLS 3125 kb

Additional file 9: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S6. Transcription factor binding site information for 55 highlighted CpG sites based on ENCODE...

Additional file 1: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Figure S1. Manhattan and QQ plots showing epigenome-wide association results from secondary analysis...

Additional file 10: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Richa Gupta (365179)
Jenny Dongen (6177455)
Yu Fu (16582)
Abdel Abdellaoui (109742)
Rachel Tyndale (3437195)
Vidya Velagapudi (152739)
Dorret Boomsma (39586)
Tellervo Korhonen (577826)
Jaakko Kaprio (43154)
Anu Loukola (253094)
Miina Ollikainen (799967)

January 2019

Table S7. CpG sites showing significant (FDR pâ<â0.05) association with cotinine levels in regul...

Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Gupta, Richa
Van Dongen, Jenny
Fu, Yu
Abdellaoui, Abdel
Tyndale, Rachel F.
Velagapudi, Vidya
Boomsma, Dorret I.
Korhonen, Tellervo
Kaprio, Jaakko
Loukola, Anu
Ollikainen, Miina

January 2019

BACKGROUND: DNA methylation alteration extensively associates with smoking and is a plausible link b...

Self-reported smoking, serum cotinine, and blood DNA methylation

Zhang, Y.
Florath, Ines
Saum, K.
Brenner, H.

January 2016

BACKGROUND: Epigenome-wide profiling of DNA methylation pattern with respect to tobacco smoking has ...

Additional file 5: of Genome-wide analysis of DNA methylation in bronchial washings

Sang-Won Um (535627)
Yujin Kim (483088)
Bo Lee (3463586)
Dongho Kim (29790)
Kyung-Jong Lee (5237399)
Hong Kim (101826)
Joungho Han (483091)
Hojoong Kim (535625)
Young Shim (3463580)
Duk-Hwan Kim (483093)

May 2018

Table S3. The correlation between pack-years of smoking and DNA methylation in 53 control groups. (D...

Genome-Wide Meta-Analysis of Cotinine Levels in Cigarette Smokers Identifies Locus at 4q13.2

Ware, Jennifer
Chen, Xiangning
Vink, Jaqueline
Lyytikäinen, Leo-Pekka
Lehtimäki, Terho
Kähönen, Mika

January 2016

Genome-wide association studies (GWAS) of complex behavioural phenotypes such as cigarette smoking t...

Additional file 2: of Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health

Pei-Chien Tsai (169868)
Craig Glastonbury (5729903)
Melissa Eliot (667253)
Sailalitha Bollepalli (5876465)
Idil Yet (2609974)
Juan Castillo-Fernandez (3861310)
Elena Carnero-Montoro (525376)
Thomas Hardiman (5876474)
Tiphaine Martin (5876480)
Alice Vickers (5876486)
Massimo Mangino (87550)
Kirsten Ward (3417971)
Kirsi PietilĂ¤inen (5876489)
Panos Deloukas (21564)
Tim Spector (153290)
Ana ViĂąuela (5876492)
Eric Loucks (5876495)
Miina Ollikainen (799967)
Karl Kelsey (3398846)
Kerrin Small (174643)
Jordana Bell (667256)

October 2018

Table S1. Four smoking-induced differentially methylated and expressed genes in blood samples. Table...

Additional file 4: Table S3. of DNA methylation and smoking in Korean adults: epigenome-wide association study

Mi Lee (3414719)
Yoonki Hong (3521672)
Sun-Young Kim (24695)
Stephanie London (588804)
Woo Kim (3483326)

September 2016

CpGs differentially methylated in blood DNA in relation to current smoking compared to never smoking...

Additional file 5: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Abstract

Extracted data

Additional file 5: of Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci

Abstract

Extracted data

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