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

Additional file 1: of Combined genetic influence of the nicotinic receptor gene cluster CHRNA5/A3/B4 on nicotine dependence

Sung-Ha Lee (5990894)
Woo-Young Ahn (442731)
Michał Seweryn (5990897)
Wolfgang Sadee (179657)

November 2018

Table S1. Haplotype of rs6495308 with lead SNPs of bin 1 (rs16969968, G > A) or bin 2 (rs1948, G > A...

Additional file 1: of Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study

Shuai Li (65944)
Ee Wong (3488474)
Minh Bui (659178)
Tuong Nguyen (4664224)
Ji-Hoon Joo (4844136)
Jennifer Stone (3549974)
Gillian Dite (4844133)
Graham Giles (521929)
Richard Saffery (136974)
Melissa Southey (81752)
John Hopper (218871)

February 2018

Table S1. This file includes Table S1: Associations for the 1882 replicated CpGs. (XLSX 156Â kb

Additional file 1: Table S1. of Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Daisuke Nishizawa (259599)
Shinya Kasai (238826)
Junko Hasegawa (259626)
Naomi Sato (3578537)
Hidetaka Yamada (258985)
Fumihiko Tanioka (3578540)
Makoto Nagashima (237138)
Ryoji Katoh (259601)
Yasuo Satoh (259607)
Megumi Tagami (259612)
Hiroshi Ujike (162485)
Norio Ozaki (162512)
Toshiya Inada (40709)
Nakao Iwata (139930)
Ichiro Sora (259637)
Masaomi Iyo (50430)
Mitsuhiko Yamada (113758)
Naoki Kondo (209152)
Moo-Jun Won (3578519)
Nobuya Naruse (3578531)
Kumi Uehara-Aoyama (3578522)
Masanari Itokawa (216595)
Kazutaka Ohi (162471)
Ryota Hashimoto (162478)
Kumpei Tanisawa (3578534)
Tomio Arai (256034)
Seijiro Mori (221879)
Motoji Sawabe (174048)
Makiko Naka-Mieno (3578525)
Yoshiji Yamada (181974)
Miki Yamada (3578528)
Noriko Sato (201880)
Masaaki Muramatsu (222878)
Masashi Tanaka (4571)
Yoko Irukayama-Tomobe (169766)
Yuki Saito (230959)
Takeshi Sakurai (144574)
Masakazu Hayashida (259644)
Haruhiko Sugimura (245172)
Kazutaka Ikeda (142226)

August 2015

Top 51â100 candidate SNPs possibly associated with nicotine dependence (FTND score). (DOC 131 kb

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 5: 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 S3. Cis acting methylation quantitative trait loci in the 40 genes highlighted in the EWAS. (X...

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 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 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 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 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 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...

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...

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...

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 8: Table S7. of Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Daisuke Nishizawa (259599)
Shinya Kasai (238826)
Junko Hasegawa (259626)
Naomi Sato (3578537)
Hidetaka Yamada (258985)
Fumihiko Tanioka (3578540)
Makoto Nagashima (237138)
Ryoji Katoh (259601)
Yasuo Satoh (259607)
Megumi Tagami (259612)
Hiroshi Ujike (162485)
Norio Ozaki (162512)
Toshiya Inada (40709)
Nakao Iwata (139930)
Ichiro Sora (259637)
Masaomi Iyo (50430)
Mitsuhiko Yamada (113758)
Naoki Kondo (209152)
Moo-Jun Won (3578519)
Nobuya Naruse (3578531)
Kumi Uehara-Aoyama (3578522)
Masanari Itokawa (216595)
Kazutaka Ohi (162471)
Ryota Hashimoto (162478)
Kumpei Tanisawa (3578534)
Tomio Arai (256034)
Seijiro Mori (221879)
Motoji Sawabe (174048)
Makiko Naka-Mieno (3578525)
Yoshiji Yamada (181974)
Miki Yamada (3578528)
Noriko Sato (201880)
Masaaki Muramatsu (222878)
Masashi Tanaka (4571)
Yoko Irukayama-Tomobe (169766)
Yuki Saito (230959)
Takeshi Sakurai (144574)
Masakazu Hayashida (259644)
Haruhiko Sugimura (245172)
Kazutaka Ikeda (142226)

August 2015

Demographic variables for subjects included in the SPQ analysis (meanâÂąâSD). (DOC 52 kb

Additional file 1: of Combined genetic influence of the nicotinic receptor gene cluster CHRNA5/A3/B4 on nicotine dependence

Sung-Ha Lee (5990894)
Woo-Young Ahn (442731)
Michał Seweryn (5990897)
Wolfgang Sadee (179657)

November 2018

Table S1. Haplotype of rs6495308 with lead SNPs of bin 1 (rs16969968, G > A) or bin 2 (rs1948, G > A...

Additional file 1: of Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study

Shuai Li (65944)
Ee Wong (3488474)
Minh Bui (659178)
Tuong Nguyen (4664224)
Ji-Hoon Joo (4844136)
Jennifer Stone (3549974)
Gillian Dite (4844133)
Graham Giles (521929)
Richard Saffery (136974)
Melissa Southey (81752)
John Hopper (218871)

February 2018

Table S1. This file includes Table S1: Associations for the 1882 replicated CpGs. (XLSX 156Â kb

Additional file 1: Table S1. of Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Daisuke Nishizawa (259599)
Shinya Kasai (238826)
Junko Hasegawa (259626)
Naomi Sato (3578537)
Hidetaka Yamada (258985)
Fumihiko Tanioka (3578540)
Makoto Nagashima (237138)
Ryoji Katoh (259601)
Yasuo Satoh (259607)
Megumi Tagami (259612)
Hiroshi Ujike (162485)
Norio Ozaki (162512)
Toshiya Inada (40709)
Nakao Iwata (139930)
Ichiro Sora (259637)
Masaomi Iyo (50430)
Mitsuhiko Yamada (113758)
Naoki Kondo (209152)
Moo-Jun Won (3578519)
Nobuya Naruse (3578531)
Kumi Uehara-Aoyama (3578522)
Masanari Itokawa (216595)
Kazutaka Ohi (162471)
Ryota Hashimoto (162478)
Kumpei Tanisawa (3578534)
Tomio Arai (256034)
Seijiro Mori (221879)
Motoji Sawabe (174048)
Makiko Naka-Mieno (3578525)
Yoshiji Yamada (181974)
Miki Yamada (3578528)
Noriko Sato (201880)
Masaaki Muramatsu (222878)
Masashi Tanaka (4571)
Yoko Irukayama-Tomobe (169766)
Yuki Saito (230959)
Takeshi Sakurai (144574)
Masakazu Hayashida (259644)
Haruhiko Sugimura (245172)
Kazutaka Ikeda (142226)

August 2015

Top 51â100 candidate SNPs possibly associated with nicotine dependence (FTND score). (DOC 131 kb

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 5: 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 S3. Cis acting methylation quantitative trait loci in the 40 genes highlighted in the EWAS. (X...

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 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 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 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 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 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...

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...

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...

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 8: Table S7. of Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Daisuke Nishizawa (259599)
Shinya Kasai (238826)
Junko Hasegawa (259626)
Naomi Sato (3578537)
Hidetaka Yamada (258985)
Fumihiko Tanioka (3578540)
Makoto Nagashima (237138)
Ryoji Katoh (259601)
Yasuo Satoh (259607)
Megumi Tagami (259612)
Hiroshi Ujike (162485)
Norio Ozaki (162512)
Toshiya Inada (40709)
Nakao Iwata (139930)
Ichiro Sora (259637)
Masaomi Iyo (50430)
Mitsuhiko Yamada (113758)
Naoki Kondo (209152)
Moo-Jun Won (3578519)
Nobuya Naruse (3578531)
Kumi Uehara-Aoyama (3578522)
Masanari Itokawa (216595)
Kazutaka Ohi (162471)
Ryota Hashimoto (162478)
Kumpei Tanisawa (3578534)
Tomio Arai (256034)
Seijiro Mori (221879)
Motoji Sawabe (174048)
Makiko Naka-Mieno (3578525)
Yoshiji Yamada (181974)
Miki Yamada (3578528)
Noriko Sato (201880)
Masaaki Muramatsu (222878)
Masashi Tanaka (4571)
Yoko Irukayama-Tomobe (169766)
Yuki Saito (230959)
Takeshi Sakurai (144574)
Masakazu Hayashida (259644)
Haruhiko Sugimura (245172)
Kazutaka Ikeda (142226)

August 2015

Demographic variables for subjects included in the SPQ analysis (meanâÂąâSD). (DOC 52 kb

Additional file 1: of Combined genetic influence of the nicotinic receptor gene cluster CHRNA5/A3/B4 on nicotine dependence

Sung-Ha Lee (5990894)
Woo-Young Ahn (442731)
Michał Seweryn (5990897)
Wolfgang Sadee (179657)

November 2018

Table S1. Haplotype of rs6495308 with lead SNPs of bin 1 (rs16969968, G > A) or bin 2 (rs1948, G > A...

Additional file 1: of Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study

Shuai Li (65944)
Ee Wong (3488474)
Minh Bui (659178)
Tuong Nguyen (4664224)
Ji-Hoon Joo (4844136)
Jennifer Stone (3549974)
Gillian Dite (4844133)
Graham Giles (521929)
Richard Saffery (136974)
Melissa Southey (81752)
John Hopper (218871)

February 2018

Table S1. This file includes Table S1: Associations for the 1882 replicated CpGs. (XLSX 156Â kb

Additional file 1: Table S1. of Associations between the orexin (hypocretin) receptor 2 gene polymorphism Val308Ile and nicotine dependence in genome-wide and subsequent association studies

Daisuke Nishizawa (259599)
Shinya Kasai (238826)
Junko Hasegawa (259626)
Naomi Sato (3578537)
Hidetaka Yamada (258985)
Fumihiko Tanioka (3578540)
Makoto Nagashima (237138)
Ryoji Katoh (259601)
Yasuo Satoh (259607)
Megumi Tagami (259612)
Hiroshi Ujike (162485)
Norio Ozaki (162512)
Toshiya Inada (40709)
Nakao Iwata (139930)
Ichiro Sora (259637)
Masaomi Iyo (50430)
Mitsuhiko Yamada (113758)
Naoki Kondo (209152)
Moo-Jun Won (3578519)
Nobuya Naruse (3578531)
Kumi Uehara-Aoyama (3578522)
Masanari Itokawa (216595)
Kazutaka Ohi (162471)
Ryota Hashimoto (162478)
Kumpei Tanisawa (3578534)
Tomio Arai (256034)
Seijiro Mori (221879)
Motoji Sawabe (174048)
Makiko Naka-Mieno (3578525)
Yoshiji Yamada (181974)
Miki Yamada (3578528)
Noriko Sato (201880)
Masaaki Muramatsu (222878)
Masashi Tanaka (4571)
Yoko Irukayama-Tomobe (169766)
Yuki Saito (230959)
Takeshi Sakurai (144574)
Masakazu Hayashida (259644)
Haruhiko Sugimura (245172)
Kazutaka Ikeda (142226)

August 2015

Top 51â100 candidate SNPs possibly associated with nicotine dependence (FTND score). (DOC 131 kb

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

Abstract

Extracted data

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

Abstract

Extracted data

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