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Table 1 Results of a CNV-based case-control association analysis of insect bite hypersensitivity in Friesian horses

From: Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity

       CNV frequency      
       Case Control      
CNVR ID ECAa Start (bp) End (bp) Size (bp) State Gain Loss Total Gain Loss Total P-value Gain P-value Loss P-value ORb Genec
CNVR_1144_1 4 23,383,774 23,505,444 121,671 Gain 1 0 1 9 0 9 0.033   0.0332 0.100.01–0.84  
CNVR_1296_1 4 79,687,222 79,957,793 270,572 Gain 11 0 11 26 0 26 0.009   0.0092 0.360.17–0.78 SPAM1
CNVR_2035_1 8 3,638,239 3,783,874 145,636 Mixed 7 2 9 1 1 2 0.046 0.580 0.0367 5.401.11–26.3 IGLV8–61, ENSECAG00000014327
CNVR_2452_1 10 12,948,489 13,075,518 127,030 Mixed 15 10 25 6 0 6 0.022 0.982 0.0003 5.922.24–15.7 AC011513.3, CEACAM1, CEACAM3-CEACAM8, PSG1-PSG9, PSG11
CNVR_2685_1 11 41,743,465 41,832,225 88,761 Mixed 8 5 13 2 2 4 0.055 0.265 0.0245 3.821.19–12.3  
CNVR_2758_1 12 19,366,263 19,527,441 161,179 Gain 14 0 14 2 0 2 0.004   0.0038 9.862.09–46.5 OR4D10, OR4D11, ENSECAG00000008771
CNVR_2979_1 14 64,375,388 64,516,633 141,246 Gain 3 0 3 11 0 11 0.040   0.0395 0.250.07–0.94  
CNVR_4066 20 20,271 503,862 483,592 Mixed 1 0 1 7 1 8 0.064 0.987 0.0450 0.110.01–0.95  
CNVR_4114_1 20 24,230,088 24,296,409 66,322 Mixed 6 0 6 19 0 19 0.010   0.0100 0.280.10–0.74 BTN3A1, BTN3A2, BTN3A3
CNVR_4120_1 20 26,392,472 26,531,248 138,777 Gain 25 0 25 46 0 46 0.003   0.0034 0.410.23–0.74 ENSECAG00000001951, ENSECAG00000019806, ENSECAG00000002019, ENSECAG00000002140, ENSECAG00000002328, ENSECAG00000000865
CNVR_4132_1 20 29,805,544 29,821,078 15,535 Gain 23 0 23 9 0 9 0.007   0.0074 3.111.36–7.12  
CNVR_4140_1 20 30,493,889 30,523,455 29,567 Mixed 34 8 42 56 4 60 0.003 0.248 0.0159 0.520.30–0.88 MICA, MICB
CNVR_4141_1 20 30,624,048 30,689,273 65,226 Gain 60 0 60 35 0 35 0.001   0.0006 2.651.52–4.61 ENSECAG00000017324, ENSECAG00000002838
CNVR_4142_1 20 30,743,179 30,775,429 32,251 Mixed 14 18 32 11 5 16 0.422 0.008 0.0092 2.451.25–4.79 ENSECAG00000019095
CNVR_4155_1 20 32,467,872 32,582,288 114,417 Mixed 3 10 13 7 19 26 0.231 0.086 0.0285 0.440.21–0.92  
CNVR_4271_1 21 10,784,937 10,861,217 76,281 Mixed 8 1 9 3 0 3 0.077 0.987 0.0464 4.201.02–17.3  
CNVR_4537 23 32,331,580 32,716,916 385,337 Gain 1 0 1 9 0 9 0.034   0.0342 0.110.01–0.85 ENSECAG00000026512, ENSECAG00000009426
CNVR_4747d 26 250,337 434,632 184,296 Mixed 1 8 9 8 8 16 0.048 0.966 0.0332 0.120.01–0.98  
CNVR_4992_1d 28 4428 376,070 371,643 Mixed 3 11 14 12 13 25 0.066 0.620 0.0092 0.210.05–0.83 ENSECAG00000001173, ENSECAG00000003651
  1. Significance level (P-value) based on CNV frequency differences between cases (n = 111) and controls (n = 111) using logistic regression and 1 principal component as covariate, including CNVR identification (CNVR_ID), chromosome, start and end position of CNVR (in base pairs), state (gain, loss or complex), odds ratio (OR) and candidate genes based on Ensembl IDs and human orthologues
  2. aEquus caballus chromosome
  3. bOdds ratio of the CNV with 95% confidence interval in superscript
  4. cSPAM1 = sperm adhesion molecule 1 (OMIM:600930), IGLV8–61 = immunoglobulin lambda variable 8–61 (OMIM:147240), AC011513.3 = ENSG00000267881, CEACAM1 = carcinoembryonic antigen-related cell adhesion molecule 1 (OMIM:109770), CEACAM3 = carcinoembryonic antigen-related cell adhesion molecule 3 (OMIM:609142), CEACAM4 = carcinoembryonic antigen-related cell adhesion molecule 4 (ENSG00000105352), CEACAM5 = carcinoembryonic antigen-related cell adhesion molecule 5 (OMIM:114890), CEACAM6 = carcinoembryonic antigen-related cell adhesion molecule 6 (OMIM:163980), CEACAM7 = carcinoembryonic antigen-related cell adhesion molecule 7 (ENSG00000007306), CEACAM8 = carcinoembryonic antigen-related cell adhesion molecule 8 (OMIM:615747), PSG1 = pregnancy-specific beta-1-glycoprotein 1 (OMIM:176390), PSG2 = pregnancy-specific beta-1-glycoprotein 2 (OMIM:176391), PSG3 = pregnancy-specific beta-1-glycoprotein 3 (OMIM:176392), PSG4 = pregnancy-specific beta-1-glycoprotein 4 (OMIM:176393), PSG5 = pregnancy-specific beta-1-glycoprotein 5 (OMIM:176394), PSG6 = pregnancy-specific beta-1-glycoprotein 6 (OMIM:176395), PSG7 = pregnancy-specific beta-1-glycoprotein 7 (OMIM:176396), PSG8 = pregnancy-specific beta-1-glycoprotein 8 (OMIM:176397), PSG9 = pregnancy-specific beta-1-glycoprotein 9 (OMIM:176398), PSG11 = pregnancy-specific beta-1-glycoprotein 11 (OMIM:176401), OR4D10 = olfactory receptor family 4 subfamily D member 10, OR4D11 = olfactory receptor family 4 subfamily D member 11, BTN3A1 = butyrophilin subfamily 3 member A1 (OMIM:613593), BTN3A2 = butyrophilin subfamily 3 member A2 (OMIM:613594), BTN3A3 = butyrophilin subfamily 3 member A3 (OMIM:613595), MICA = major histocompatibility complex class I chain-related gene A (OMIM:600169), MICB = major histocompatibility complex class I chain-related gene B (OMIM:602436)
  5. dOdds ratio of CNV gain is mentioned