DESCRIPTION:
103 lead SNPs (83 independent loci) for the tobacco use disorder cross-ancestry meta-analysis, including the UK Biobank sample ("TUD-multi+UKBB"). The primary multi-ancestry meta-analysis of 20,801,211 imputed SNPs (lambda λGC=1.141, Figure 2) was performed on seven cohorts from four U.S. biobanks, comprising 653,790 individuals with TUD phecode data available, with 75.71% EUR, 17.50% AA, and 6.79% LA. 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. The summary statistics for TUD in UKBB were downloaded from the GWAS atlas (https://atlas.ctglab.nl/traitDB/3439). In UKBB only, cases were defined as having 1 ICD-10 code for TUD, and controls had none (10,287 cases and 234,603 controls). 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) multi-ancestry reference panel for the multi-ancestry meta-analysis, or the HRC ancestry-appropriate reference panel otherwise. To identify TUD risk loci and lead SNPs, we performed LD clumping in FUMA41 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. From supplementary table 8.
LABEL:
Lead SNP loci TUD-multi+UKBB_pvalue
SCORE TYPE:
P-Value
THRESHOLD:
<= 0.5
GENES IN THRESHOLD:
78
DATE ADDED:
DATE UPDATED:
SPECIES:
AUTHORS:
TITLE:
JOURNAL:
ABSTRACT:
Genes in threshold: 78
| Uploaded As | Gene Symbol | Homology | Score | Priority | LinkOuts | Emphasis |
|---|
GeneWeaver