List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term energy expenditure was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Smoking behavior. The EFO term smoking behavior was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
JZ Liu, F Tozzi, DM Waterworth, SG Pillai, P Muglia, L Middleton, W Berrettini, CW Knouff, X Yuan, G Waeber, P Vollenweider, M Preisig, NJ Wareham, JH Zhao, RJ Loos, I Barroso, KT Khaw, S Grundy, P Barter, R Mahley, A Kesaniemi, R McPherson, JB Vincent, J Strauss, JL Kennedy, A Farmer, P McGuffin, R Day, K Matthews, P Bakke, A Gulsvik, S Lucae, M Ising, T Brueckl, S Horstmann, HE Wichmann, R Rawal, N Dahmen, C Lamina, O Polasek, L Zgaga, J Huffman, S Campbell, J Kooner, JC Chambers, MS Burnett, JM Devaney, AD Pichard, KM Kent, L Satler, JM Lindsay, R Waksman, S Epstein, JF Wilson, SH Wild, H Campbell, V Vitart, MP Reilly, M Li, L Qu, R Wilensky, W Matthai, HH Hakonarson, DJ Rader, A Franke, M Wittig, A Schäfer, M Uda, A Terracciano, X Xiao, F Busonero, P Scheet, D Schlessinger, D St Clair, D Rujescu, GR Abecasis, HJ Grabe, A Teumer, H Völzke, A Petersmann, U John, I Rudan, C Hayward, AF Wright, I Kolcic, BJ Wright, JR Thompson, AJ Balmforth, AS Hall, NJ Samani, CA Anderson, T Ahmad, CG Mathew, M Parkes, J Satsangi, M Caulfield, PB Munroe, M Farrall, A Dominiczak, J Worthington, W Thomson, S Eyre, A Barton, V Mooser, C Francks, J Marchini
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Exhaled carbon monoxide levels. The EFO term smoking behavior, carbon monoxide exhalation measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AJ Bloom, SM Hartz, TB Baker, LS Chen, ME Piper, L Fox, M Martinez, D Hatsukami, EO Johnson, CC Laurie, NL Saccone, A Goate, LJ Bierut
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Lung cancer. The EFO term lung carcinoma was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
RJ Hung, JD McKay, V Gaborieau, P Boffetta, M Hashibe, D Zaridze, A Mukeria, N Szeszenia-Dabrowska, J Lissowska, P Rudnai, E Fabianova, D Mates, V Bencko, L Foretova, V Janout, C Chen, G Goodman, JK Field, T Liloglou, G Xinarianos, A Cassidy, J McLaughlin, G Liu, S Narod, HE Krokan, F Skorpen, MB Elvestad, K Hveem, L Vatten, J Linseisen, F Clavel-Chapelon, P Vineis, HB Bueno-de-Mesquita, E Lund, C Martinez, S Bingham, T Rasmuson, P Hainaut, E Riboli, W Ahrens, S Benhamou, P Lagiou, D Trichopoulos, I Holcátová, F Merletti, K Kjaerheim, A Agudo, G Macfarlane, R Talamini, L Simonato, R Lowry, DI Conway, A Znaor, C Healy, D Zelenika, A Boland, M Delepine, M Foglio, D Lechner, F Matsuda, H Blanche, I Gut, S Heath, M Lathrop, P Brennan
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Lung cancer. The EFO term lung carcinoma was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
P Liu, HG Vikis, D Wang, Y Lu, Y Wang, AG Schwartz, SM Pinney, P Yang, M de Andrade, GM Petersen, JS Wiest, PR Fain, A Gazdar, C Gaba, H Rothschild, D Mandal, T Coons, J Lee, E Kupert, D Seminara, J Minna, JE Bailey-Wilson, X Wu, MR Spitz, T Eisen, RS Houlston, CI Amos, MW Anderson, M You
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Chronic obstructive pulmonary disease. The EFO term chronic obstructive pulmonary disease was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
SG Pillai, D Ge, G Zhu, X Kong, KV Shianna, AC Need, S Feng, CP Hersh, P Bakke, A Gulsvik, A Ruppert, KC Lødrup Carlsen, A Roses, W Anderson, SI Rennard, DA Lomas, EK Silverman, DB Goldstein
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Lung cancer. The EFO term lung carcinoma was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
CI Amos, X Wu, P Broderick, IP Gorlov, J Gu, T Eisen, Q Dong, Q Zhang, X Gu, J Vijayakrishnan, K Sullivan, A Matakidou, Y Wang, G Mills, K Doheny, YY Tsai, WV Chen, S Shete, MR Spitz, RS Houlston
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Smoking behavior. The EFO term smoking behavior was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Chronic obstructive pulmonary disease. The EFO term chronic obstructive pulmonary disease was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
MH Cho, PJ Castaldi, ES Wan, M Siedlinski, CP Hersh, DL Demeo, BE Himes, JS Sylvia, BJ Klanderman, JP Ziniti, C Lange, AA Litonjua, D Sparrow, EA Regan, BJ Make, JE Hokanson, T Murray, JB Hetmanski, SG Pillai, X Kong, WH Anderson, R Tal-Singer, DA Lomas, HO Coxson, LD Edwards, W MacNee, J Vestbo, JC Yates, A Agusti, PM Calverley, B Celli, C Crim, S Rennard, E Wouters, P Bakke, A Gulsvik, JD Crapo, TH Beaty, EK Silverman
Bonferroni-significant results (p<2.63E-06) of gene-based association analyses (MAGMA) for TUD-EUR. We conducted independent GWAS of TUD cases and controls in individuals of European (EUR) ancestry across four U.S. biobanks (PsycheMERGE sites (BioVU, MGBB, PMBB, and MVP)) and performed a GWAS meta-analysis. We defined cases as patients who received at least two TUD ICD-9 or −10 codes (corresponding to the phecode definition) in their medical records, and controls as patients who had no TUD diagnosis codes. TUD-EUR included 11,422,241 imputed SNPs in a cohort of 163,734 TUD cases and 331,271 controls, which is 8.5 times larger than the total sample size of previous nicotine dependence GWAS. Genome-wide significant (GWS) loci were defined as those with p<5.00E-08 with LD r2>0.1, within a 1MB window, based on the structure of the Haplotype Reference Consortium (HRC) ancestry-appropriate reference panel. To identify TUD risk loci and lead SNPs, we performed LD clumping in FUMA using a range of 3 Mb, r2 >0.1, and the respective ancestry 1000 Genome reference panel. Genomic risk loci that were located <1Mb apart were incorporated into a single locus. For loci that harbored multiple variants, we used conditional & joint association analysis using GWAS summary statistics (COJO) in Genome-wide Complex Trait Analysis (GCTA) software to define independent variants by conditioning them on the most significant variant within each locus. Following conditioning, significant variants (p<5.00E-08) were considered independent. To further our biological interpretation of the TUD-EUR GWAS results and prioritize potential candidate genes and proteins, we performed multiple in silico downstream analyses. We conducted gene-based analyses via MAGMA v1.0841, which; Supplementary Table 15). SNPs were mapped to 19,532 protein-coding genes from Ensembl (build 85). We applied a Bonferroni correction based on the total number of genes tested (p<2.63E−06). Gene sets were obtained from Msigdb v7.0 (“Curated gene sets”, “GO terms”). The MAGMA analysis mapped SNP-level associations to 91 significant genes (p<2.63E-06), 20 (21.62%) of which replicated genes near or in GWS loci (e.g., CHRNA3, CHRNA4, KDM4A, DBH). P-values were 2-sided. The following geneset contains the results of MAGMA from the TUD-EUR analysis. From supplementary table 15.
Authors:
Sylvanus Toikumo, Mariela V Jennings, Benjamin K Pham, Hyunjoon Lee, Travis T Mallard, Sevim B Bianchi, John J Meredith, Laura Vilar-Ribó, Heng Xu, Alexander S Hatoum, Emma C Johnson, Vanessa K Pazdernik, Zeal Jinwala, Shreya R Pakala, Brittany S Leger, Maria Niarchou, Michael Ehinmowo, , Greg D Jenkins, Anthony Batzler, Richard Pendegraft, Abraham A Palmer, Hang Zhou, Joanna M Biernacka, Brandon J Coombes, Joel Gelernter, Ke Xu, Dana B Hancock, Nancy J Cox, Jordan W Smoller, Lea K Davis, Amy C Justice, Henry R Kranzler, Rachel L Kember, Sandra Sanchez-Roige
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Smoking cessation in chronic obstructive pulmonary disease. The EFO term chronic obstructive pulmonary disease, smoking cessation was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
M Siedlinski, MH Cho, P Bakke, A Gulsvik, DA Lomas, W Anderson, X Kong, SI Rennard, TH Beaty, JE Hokanson, JD Crapo, EK Silverman
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Current cigarettes per day in chronic obstructive pulmonary disease. The EFO term chronic obstructive pulmonary disease, smoking behaviour measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
M Siedlinski, MH Cho, P Bakke, A Gulsvik, DA Lomas, W Anderson, X Kong, SI Rennard, TH Beaty, JE Hokanson, JD Crapo, EK Silverman
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Age at smoking initiation in chronic obstructive pulmonary disease. The EFO term chronic obstructive pulmonary disease, smoking initiation was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
M Siedlinski, MH Cho, P Bakke, A Gulsvik, DA Lomas, W Anderson, X Kong, SI Rennard, TH Beaty, JE Hokanson, JD Crapo, EK Silverman
GWAS: triglyceride measurement, high density lipoprotein cholesterol measurement
Description:
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term triglyceride measurement, high density lipoprotein cholesterol measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term fasting blood glucose measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term homocysteine measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term gestational age was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term birth weight was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term IGF-1 measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term triglyceride measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term transforming growth factor beta measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term hip circumference was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term body weight was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term heart rate was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Obesity-related traits. The EFO term waist height ratio was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
AG Comuzzie, SA Cole, SL Laston, VS Voruganti, K Haack, RA Gibbs, NF Butte
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