“nominally significant”

However, the M1 protein VGF was only nominally significant at classifying AD in Caucasian AUC = 0.6030 ( p = 0.0406, CI = 0.4887–0.7173), yet highly significant in African Americans AUC = 0.7593 ( p = 5.03e-06, CI = 0.6634–0.8552).

After conditioning on the top variant rs4143332 (LD- r 2 of 0.988 to HLA-B*08:01 ), or complement component 4 ( C4 ) expression levels HLA-C*05:01 remained nominally significant (rs4143332: OR = 0.6869, P = 5.662e −6 , SE = 0.0828; C4 expression: OR = 0.68991SE = 0.0865, P = 1.774e −5 ), indicating partial independence from HLA-B*08:01 and C4 .

5 ) identified an enrichment for rare loss-of-function variants in GRN and indeed, with the second strongest enrichment after GRN ( P = 2.2 × 10 −21 ), we observed a nominally significant enrichment of variants in TET2 in the FTD cohort ( P = 6.4 × 10 −6 ).

For example, TTN has 5 potential functional synonymous mutations in the case group but does not have a nominally significant p value ( p value = 7.11 × 10 − 6 ), owing to the long length of the gene.

We also observed a nominally significant association at ATP5B (OR = 0.19, 95% CI = 0.08–0.43, P = 9.46 × 10 −6 ), but this association was not consistent in the South Korean dataset (Extended Data Fig. 7 ).

2.8 EWAS of physical activity and functional analyses At the nominally significant threshold (defined as p < 1 × 10 −5 ), we identified 7 CpGs associated with %time spent in MVPA (Figure 3a and Table S4a ), and 12 CpGs associated with MET‐Hours (Figure 3b and Table S4b ).

After overlapping the pQTL variants with the nominally significant ( P <1 × 10 -5 ) association signals of the GWAS Catalog, they identified that the CD33 protein-related SNP rs1878047 was also associated with BMI.

Additionally, several of these four disease-transcriptome associations were nominally significant ( p < 10 –5 ) in several other tissues (Supplementary Table 4 ).

However, several nominally significant (p<1.00E-05) variants were identified ( Table 2 ).

In addition, although the PheWAS did not reveal any signals for serious adverse reactions after strict correction, EP300 and P2RY14 show nominally significant associations with traits related to femur shaft bone and caudate nucleus (P < 1 × 10 −5 ), suggesting that their biological effects may not be limited to the intestine.

The numbers of genes or isoform-related genes having effects on eQTL, sQTL, and 3′aQTL in one or more cell conditions were 9775, 10189, and 4087, respectively (nominally significant p < 1 × 10 −5 ).

Replication cohort genotyping, QC and association analysis SNPs determined to have a nominally significant association with a nevirapine hypersensitivity phenotype ( P < 1 × 10 − 5 ) in the discovery cohort were subsequently typed in the replication cohort using either the Sequenom MassArray iPLEX platform (Sequenom Inc., San Diego, CA, USA) or custom TaqMan real-time PCR SNP genotyping assays (Life Technologies, Paisley, UK) according to the manufacturer’s protocols.

To identify independent signals per locus we applied linkage disequilibrium (LD) clumping (‘-clump’ from PLINK 2.0) for all nominally significant single nucleotide polymorphisms passing P < 10 –5 using the corresponding study sample set for calculating LD.

The list of nominally significant CpGs ( p < 1 × 10 −5 ) sorted by their p-value for low and high audiometric frequencies are depicted.

Two of these loci, 3p24.1 and 16q12.1, are nominally significant ( P < 1 × 10 −5 ) in our GWAS meta-analysis, but the remaining three loci (3q29, 17q25.3 and a distinct region at 22q13.1) do not reach nominal significance.

2010 ) to explore to what extent candidate epistatic modifier genes for the Sema‐5c BG2386 and neur BG2391 alleles identified by our GWA analyses form interactive networks, using as input all candidate modifier genes with nominally significant associations at P < 10 −5 (Table S4 and S5).

Of the five genome-wide significant loci in the meta-analysis, rs28971325, rs1042704 and rs2472660 associated with Dupuytren’s disease at the genome-wide significant level, rs17570529 was nominally significant (p = 1x10 -5 ), and rs2472660 did not associate (p = 0.21) ( Table 3 ).

Given the small sample size, nominally significant CpG-smoking associations were defined as having P < 1x10 −5 and were displayed using a ggplot2 boxplot.

The subjects’ own educational attainment showed a nominally significant negative association with F roh ( p = .045), while the contribution of parental education to offspring F roh was highly significant (father: p < 10 -5 ; mother: p = 9×10 -5 ), with more educated parents having offspring with fewer ROHs.

Cross-population transferability of loci Of the nominally significant ( p < 1 × 10 −5 ) loci in the short and long sleep duration analyses in the AFR GWAS, none reached even a nominal significance threshold of p < 0.05 in the EUR analysis, and none demonstrate a lower p-value in the cross-population analysis.

Supplementary Figure S5 shows quantile–quantile (Q-Q) plots of –log 10 P -values and plots of locations of nominally significant ( P < 10 −5 ) variants across the Drosophila genome.

Enrichment for liver-relevant gene sets To provide an easily interpretable enrichment statistic, for liver-relevant pharmacogenetically important gene sets, we used logistic regression to provide natural log odds ratios at the gene level for gene set membership and the presence/absence of a nominally significant cis -eQTL or eGene ( p < 10 –5 ).

In fact, the largest schizophrenia GWAS to date found SNPs in three genes ( CACNA1C , ITPR3 and CYP2D6 ) within the serotonergic synapse pathway reached GWAS significance ( P <5 × 10 −8 ) and SNPs in another 17 genes within this pathway were nominally significant ( P <1 × 10 −5 ). 2 Furthermore, a recent gene-set enrichment analysis of the SZGene database 25 identified 24 pathways significantly enriched for schizophrenia candidate genes among which the serotonin receptor signaling pathway was ranked second. 7 The ubiquitin mediated proteolysis pathway (UPP), a critical system for the removal of damaged/toxic proteins in the cell, has been shown to be dysregulated at the transcript 26 , 27 , 28 , 29 and protein levels 30 in both peripheral and central tissue among individuals with schizophrenia.

Conditioning on the genotype of rs17646946, rs499697 still showed nominally significant association ( P = 1.46e-5) with hair curliness, confirming previous findings.

Notably, we also observed an enrichment for CD56+ NK cell genes among nominally significant underexpressed genes in participants’ class I mutations (FDR p = 1.5 × 10 −5 ) ( Figures S5 A and S5B).