Table 3 Summary statistics for lead SNPs that reached a significance threshold of p < 1E−06, ordered by p value.

From: Genome-wide association study suggests that variation at the RCOR1 locus is associated with tinnitus in UK Biobank

Chr SNP refA Afreq Beta se p pJ Gene Distance Context CADD GERP PhyloP Global Max
14 rs4906228 A 0.24 0.08 0.014 1.70E−08 1.74E−08 RCOR1 8234 Upstream 4.159 − 1.60 0.5132 0.39 0.49
13 rs7336872 T 0.68 0.072 0.013 5.90E−08 5.94E−08 UBAC2 0 Intron 2.490 0.20 0.2213 0.84 1.00
10 rs118053011 C 0.93 − 0.127 0.024 9.80E−08 9.89E−08 ARID5Ba 6901 Downstream 2.588 0.64 0.5602 0.98 1.00
4 rs113655471 T 0.97 − 0.188 0.036 1.90E−07 1.87E−07 PTPN13 0 Intron 2.531 − 0.79 0.2737 0.99 1.00
5 rs17876046 G 0.98 − 0.288 0.056 2.20E−07 2.18E−07 F12/GRK6 0 Intron 1.698 0.58 0.1065 0.99 1.00
3 rs1532898 A 0.71 − 0.069 0.013 3.20E−07 3.24E−07 TGM4 0 Intron 4.941 0.22 0.2722 0.57 0.88
6 rs553448379 T 0.38 − 0.063 0.013 4.60E−07 4.58E−07 ZNF318a 10,571 Downstream 0.315 0.15 0.0325 n/a n/a
12 rs7314493 A 0.69 − 0.067 0.013 4.80E−07 4.84E−07 E2F7 0 Intron 11.83 1.14 0.3912 0.76 0.93
8 rs4370496 G 0.73 − 0.07 0.014 5.50E−07 5.48E−07 XKR6 0 Intron 0.213 − 0.15 − 0.6709 0.80 0.99
2 2:171146084_CTT_C CTT 0.99 − 0.283 0.057 5.70E−07 5.69E−07 MYO3B 0 Intron n/a n/a n/a 0.99 1.00
3 rs557511691 C 0.64 0.065 0.013 9.70E−07 9.77E−07 MAGI1 0 Intron n/a n/a n/a 0.67 0.83
3 rs72960531 C 0.94 0.125 0.026 9.80E−07 9.80E−07 LINC02016b Intergenic 14.03 2.24 1.3932 0.95 1.00
  1. Bold denotes genome-wide significance at p < 5E−08. Chr, chromosome; SNP, lead SNP; bp, base position; refA, reference allele; beta, effect size from BOLT-LMM approximation to infinitesimal mixed model; se, standard error of the beta; p-value, non-infinitesimal mixed model association test p-value, pJ, joint p-value for variation at loci calculated with GCTA-COJO; Gene, denotes the closest protein coding gene to the variant; Distance, is the distance from the gene (b.p.); Context denotes the consequence of the variant identified by VEP.
  2. aDenotes genes also identified in previous UKBB GWAS of self-reported hearing22.
  3. brs72960531 is in an intergenic region without protein coding genes but is within an intron of the lincRNA LINC02016; Global, global effect allele frequency reported on Ensembl; Max, highest effect allele frequency reported in any group on Ensembl; n/a, data not available.