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Table 3 CNV association with lung function with P < 0.001 for meta-analysis of 3 adult cohorts with follow up of tag SNPs in replication cohorts

From: Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity

  CNVR CNV results Replicationc
Meta analysis of BHS, B58C & SHIP Best tag SNP SpiroMeta & CHARGE UK BiLEVE UK Biobank Meta-analysisd
N Beta L (SE) Effectb P Genes SNP r2 Beta (SE) P Beta (SE) P Beta (SE) P Beta (SE) Effecte P
FEV1 CNVR1073.1 (2q32.1) 640 bp deletion (2 class) 5560 -0.0467 (0.0135) --. 5.55×10-4 Upstream DNAJC10 rs2696127 0.766 -0.0069 (0.008) 0.38 -0.0073 (0.007)   -0.0061 (0.007) 0.37 0.0068 (0.004) ---- 0.11
CNVR217.1a (1p31.1) 45.7kbp multiallelic (3 class) 7258 0.0268 (0.0078) +++ 5.55×10-4 Upstream NEGR1 rs2568958 1 0.0084 (0.007) 0.24 0.0040 (0.007) 0.56 0.0072 (0.007) 0.27 -0.0065 (0.004) ++++ 0.10
CNVR4222.1a (9p21.2) 4.01kbp deletion (2 class) 7284 -0.0868 (0.0263) --- 9.78×10-4 Intronic LINGO2 rs10968307 0.980 0.0067 (0.031) 0.83 -0.0129 (0.026) 0.61 0.0084 (0.024) 0.73 0.0003 (0.015) - + -+ 0.99
FVC CNVR4742.1 (10q21.1) 1.35kbp deletion (3 class) 5528 0.0599 (0.0174) ++. 5.65×10-4 intergenic rs1903969 0.995 0.0020 (0.005) 0.72 0.0082 (0.010) 0.40 0.0048 (0.009) 0.61   ++++ 0.32
CNVR4222.1a (9p21.2) 4.01kbp deletion (2 class) 7284 -0.1126 (0.0329) --- 6.30×10-4 Intronic LINGO2 rs10968307 0.980 0.0342 (0.106) 0.75 -0.0150 (0.026) 0.56 -0.0126 (0.024) 0.60   - + -- 0.65
CNVR6854.1a (16q24.2) 3.25kbp deletion (3 class) 7281 0.0389 (0.0116) +++ 7.72×10-4 Downstream BANP rs7501378 0.940 0.0111 (0.005) 0.017 0.0232 (0.008) 0.0037 -0.0021 (0.008) 0.79   +++- 0.0038
CNVR7142.1a (17q22) 2.62kbp deletion (3 class) 5519 -0.0454 (0.0136) --. 8.20×10-4 Downstream SCPEP1 rs880266 0.766 -0.0021 (0.006) 0.73 -0.0048 (0.008) 0.53 0.0108 (0.007) 0.14   ---+ 0.77
FEV1 / FVC CNVR94.3a (1p36.13) 14.5kbp deletion (3 class) 4800 0.0061 (0.0016) +.- 1.96×10-4 Upstream CROCC rs696095 0.263          
CNVR94.5 (1p36.13) 51.3kbp deletion (4 class) 3005 0.0045 (0.0012) +.. 2.08×10-4 Exonic CROCC rs696095 0.169          
CNVR94.4 (1p36.13) 106kbp multiallelic (4 class) 2951 0.0046 (0.0013) +.. 2.69×10-4 Exonic CROCC rs696095 0.169          
CNVR3585.1 (7q34) 560 bp multiallelic (4 class) 3082 -0.0052 (0.0014) -.. 2.89×10-4 Intronic MGAM rs62477625 0.644          
CNVR7927.1a (20q13.33) 880 bp gain (3 class) 5548 0.0056 (0.0016) ++. 5.98×10-4 upstream HAR1A; downstream HAR1B; downstream LOC63930 rs4809276 0.818 -0.0037 (0.010) 0.71 0.0083 (0.008) 0.30 0.0056 (0.008) 0.47 -0.0044 (0.005) +-++ 0.37
  1. FEV 1 Forced Expiratory Volume in 1 second, FVC Forced Vital Capacity (FVC). aCNVR class frequencies consistent with independent cohort (Additional file 1: Table S1). bEffect direction: BHS/B58C/SHIP (a dot signifies no result). r2 correlation coefficient between CNVR copy number and SNP genotype in BHS. Replication was performed where there was a tag SNP with r2 > 0.7. cLung function traits are rank inverse-normalised apart from FVC in SpiroMeta & CHARGE which is untransformed mL. dInverse-variance weighted meta-analysis for FEV1 and FEV1/FVC; Z-score meta-analysis for FVC. eEffect direction: CNVR/SpiroMeta & CHARGE/UK BiLEVE/UK Biobank. Gene annotations provided by ANNOVAR [30]