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Table 3 Description of the QTL identified in GWAS analyses for the 0/1 or 0/1/2 phenotypes of Normande and Holstein cows

From: Identification of the ABCC4, IER3, and CBFA2T2 candidate genes for resistance to paratuberculosis from sequence-based GWAS in Holstein and Normande dairy cattle

BreedPhenotypeQTLBTAConfidence intervalTOP variant (resistance allele)
Start (bp*)End (bp*)Number of significant variantsNumber of genes−log10(P)IDbp*Freq.EffectSEGeneFunctional annotation
Normande0/112324,804,03425,602,017736.4rs13451743125,575,7320.43− 0.170.03BOLA-DRB2Intron
Normande0/122326,952,21427,814,2321266.4rs11003150926,977,6080.37− 0.150.03NOTCH4Synonymous
Normande0/132328,576,81228,671,569727.0rs20851712428,605,2430.31− 0.170.03TRIM15Intron
Normande0/142332,128,35132,606,3312506.9rs10894202632,551,8690.27− 0.170.03Intergenic
Holstein0/111268,908,05669,745,89126829.4rs37881290369,314,3300.81− 0.160.03Intergenic
Holstein0/121269,774,74671,240,801281110.8rs4316123270,723,0870.88− 0.190.03Intergenic
Holstein0/131272,272,36772,416,27314408.5rs4304734872,351,5830.77− 0.150.03Intergenic
Holstein0/141275,283,61575,380,545607.7rs4310447475,379,7700.90− 0.180.03Intergenic
Holstein0/151276,760,85177,323,51121518.5rs37856858377,285,1890.76− 0.140.02Intergenic
Holstein0/161279,096,88080,067,268617.5rs37948845280,064,1500.84− 0.140.03UBAC2Intron
Holstein0/171363,497,96063,506,53220018.5rs10957020963,502,5660.91− 0.340.04Intergenic
Holstein0/182323,529,49123,976,4323917.1rs21037292623,956,9870.34− 0.110.02PKHD1Intron
Holstein0/192325,115,93325,582,10136038.8rs20918323625,181,6610.66− 0.120.02ELOVL5Intron
Holstein0/1102326,665,22027,629,951114288.2rs47036529326,733,1040.69− 0.170.03ENSBTAG00000023541Intron
Holstein0/1112327,630,24828,817,6101357.4rs10953904328,085,4100.81− 0.130.02IER3Upstream
Holstein0/1/211267,954,91269,097,4273106.9rs11005182168,949,6750.67− 0.210.04Intergenic
Holstein0/1/221269,162,59870,723,08726738.7rs4166708570,127,5190.91− 0.280.05ABCC4Intron
Holstein0/1/231271,239,31771,240,801306.7rs38200773771,240,8010.74− 0.250.05Intergenic
Holstein0/1/241272,272,36772,415,27112507.4rs46364461872,356,3810.95− 0.560.10Intergenic
Holstein0/1/251276,760,85177,323,5116517.0rs38358331677,253,5890.76− 0.170.03Intergenic
Holstein0/1/261363,497,96063,506,53220038.1rs10957020963,502,5660.91− 0.710.05Intergenic
Holstein0/1/272325,119,80825,602,06745638.9rs21065510425,554,2480.83− 0.240.04Intergenic
Holstein0/1/282326,680,41827,629,951345289.0rs47036529326,733,1040.69− 0.260.04ENSBTAG00000023541Intron
Holstein0/1/292327,759,54228,398,451937.4rs20928476228,012,2990.84− 0.210.04Intergenic
  1. * Positions of variants on UMD3.1