GWAS Details

GWAS Basic Information

GWAS_UNITUS_summer15
Holm-Bonferroni family-wise error rate correction method (HB-FEWER)
1.99E-5
Mixed linear model (MLM)
R/GAPIT
Principal Components of the Genetic Similarity Matrix (PCA-GSM)
First, LDKNNi imputation of missing SNPs with default LD search for KNNi 10Mb, High LD Sites (l) 30 and Number of nearest neighbours (k) of 20. Second, TRADITOM_111K SNPsx1316acc was filtered to have only accession cultivated in UNITUS_summer15. Only SNPs with MAF > 5% were used in the GWAS

GWAS Stat Test, Kinship Algorithm & Reference

t-Test
EMMA
TRADITOM_111K SNPsx1316acc
beta

1) https://doi.org/10.1093/hr/uhac112

Related Study Summary 1

Abbreviation Start Date End Date Location
UNITUS_summer15 UNITUS-DAFNE

Related GWAS Variants Summary 120

Variant Name Alternative Allele MAF Sample Size SNP P Value Adjusted P Value
cirSL2.50ch00V1 c 0.11931818181818 176 9.6603248960707E-7 0.0024228094839345
fse.curvedSL2.50ch00V1 c 0.11931818181818 176 2.3035317968193E-10 5.7772577464228E-7
fse.curvedSL2.50ch00V4 c 0.17045454545454 176 2.9701573792293E-6 0.0024830515690357
fse.curvedSL2.50ch05V2 A 0.076704545454545 176 2.4984675284802E-5 0.015665391403571
fse.curvedSL2.50ch05V3 c 0.088068181818182 176 1.8188537895801E-6 0.0022808426521335
fse.curvedSL2.50ch08V3 g 0.11931818181818 176 3.6826299943904E-5 0.016187705757893
H.curvedSL2.50ch00V2 c 0.11931818181818 176 3.7817091305477E-5 0.094845264994137
dan.macroSL2.50ch00V1 c 0.11931818181818 176 1.9158798028199E-5 0.048050265454722
decSL2.50ch05V1 C 0.082386363636364 176 9.274536938553E-6 0.023260538641891
decSL2.50ch05V2 A 0.076704545454545 176 2.4232069056966E-5 0.030387014597435
dblkSL2.50ch05V1 c 0.053977272727273 176 3.0895086987963E-5 0.077484878165811
desiSL2.50ch05V1 c 0.053977272727273 176 4.7727612368063E-6 0.01197008518191
eccSL2.50ch02V1 g 0.20738636363636 176 2.6735360580633E-5 0.02235076144541
eccSL2.50ch11V1 g 0.4375 176 1.3420950292489E-5 0.016829871666781
eccSL2.50ch11V5 g 0.47727272727273 176 1.0743165167868E-5 0.016829871666781
eccSL2.50ch11V8 c 0.49431818181818 176 3.6287559452384E-5 0.022752299776645
eaiSL2.50ch11V1 g 0.4375 176 3.1226155491561E-6 0.0078315197972834
FEC.orSL2.50ch03V5 c 0.073863636363636 176 3.3373989487145E-6 0.0019710005336815
FEC.orSL2.50ch03V6 t 0.082386363636364 176 5.5011976617905E-6 0.0019710005336815
FEC.orSL2.50ch03V7 g 0.082386363636364 176 5.5011976617905E-6 0.0019710005336815
FEC.orSL2.50ch03V8 t 0.14488636363636 176 4.0402861943924E-6 0.0019710005336815
FEC.orSL2.50ch05V1 a 0.0625 176 6.6165558265477E-6 0.0020742902516227
FEC.orSL2.50ch05V2 c 0.10227272727273 176 2.030903789104E-8 2.5467533515365E-5
FEC.orSL2.50ch05V3 g 0.053977272727273 176 4.8299654684082E-12 1.2113553394768E-8
FEC.pkSL2.50ch08V1 g 0.25568181818182 176 1.8457317752474E-5 0.046290952923205
ellSL2.50ch11V2 g 0.47727272727273 176 1.5274703580095E-5 0.019154478289439
ellSL2.50ch11V4 c 0.49431818181818 176 1.0511144775671E-5 0.019154478289439
FPS.bpSL2.50ch02V2 c 0.0625 176 1.736542E-7 0.0001083541
FPS.bpSL2.50ch04V1 c 0.08238636 176 6.056272E-8 7.594565E-5
FPS.bpSL2.50ch04V5 t 0.0625 176 3.003411E-12 7.532554E-9
FPS.bpSL2.50ch06V2 g 0.0625 176 4.786722E-6 0.001500637
FPS.bpSL2.50ch06V3 g 0.0625 176 2.160169E-7 0.0001083541
FPS.bpSL2.50ch08V2 c 0.06534091 176 1.291654E-6 0.0004627811
FPS.bpSL2.50ch08V3 g 0.07386364 176 4.497662E-7 0.0001880023
FPS.bpSL2.50ch09V1 c 0.08806818 176 5.519941E-6 0.001538223
FPS.bpSL2.50ch10V1 a 0.08238636 176 1.881625E-7 0.0001083541
FPS.ellSL2.50ch05V1 t 0.1505682 176 6.93393E-6 0.0173903
FPS.flSL2.50ch11V1 g 0.4375 176 2.975306E-5 0.02487356
FPS.flSL2.50ch11V2 t 0.4431818 176 3.602093E-6 0.004517024
FPS.flSL2.50ch11V4 g 0.4772727 176 3.072034E-6 0.004517024
FPS.HtSL2.50ch01V1 t 0.05397727 176 3.941678E-9 9.885728E-6
FPS.HtSL2.50ch01V2 t 0.09090909 176 6.611043E-6 0.003316099
FPS.HtSL2.50ch08V3 g 0.07954545 176 4.415049E-7 0.0002768236
FPS.HtSL2.50ch08V7 t 0.07670455 176 3.357176E-7 0.0002768236
FPS.HtSL2.50ch08V10 g 0.07102273 176 3.417707E-7 0.0002768236
FPS.lgSL2.50ch00V3 c 0.1193182 176 9.913472E-7 0.002486299
FPS.lgSL2.50ch03V2 c 0.2159091 176 3.534269E-5 0.02746723
FPS.lgSL2.50ch08V5 g 0.1193182 176 2.336466E-5 0.02746723
FPS.ovoSL2.50ch02V3 a 0.06818182 176 2.419781E-7 0.000606881
FPS.ovoSL2.50ch03V3 c 0.3039773 176 3.121201E-5 0.01565594
FPS.ovoSL2.50ch08V3 c 0.1022727 176 1.282741E-6 0.001608557
FPS.ovoSL2.50ch08V4 c 0.125 176 1.383955E-5 0.008677396
FPS.ovoSL2.50ch11V1 c 0.1164773 176 1.260451E-5 0.008677396
FPS.oxSL2.50ch01V1 t 0.06818182 176 3.468696E-6 0.001739898
FPS.oxSL2.50ch05V1 g 0.07954545 176 9.391189E-7 0.0006812017
FPS.oxSL2.50ch05V3 c 0.05397727 176 3.642976E-10 9.136584E-7
FPS.oxSL2.50ch05V4 g 0.05113636 176 2.62437E-7 0.000329096
FPS.oxSL2.50ch05V5 g 0.08522727 176 6.273935E-6 0.002622505
FPS.oxSL2.50ch05V7 c 0.07102273 176 2.768078E-5 0.009917628
FPS.oxSL2.50ch05V10 g 0.07670455 176 1.086446E-6 0.0006812017
fasSL2.50ch11V3 t 0.4431818 176 3.089887E-5 0.02583145
fasSL2.50ch11V6 g 0.4772727 176 4.345848E-7 0.0005449694
fasSL2.50ch11V8 c 0.4943182 176 3.081813E-7 0.0005449694
fse.ISL2.50ch00V1 c 0.1193182 176 6.852305E-11 1.718558E-7
fse.ISL2.50ch08V2 g 0.1193182 176 1.531594E-5 0.01920619
fse.IISL2.50ch00V1 c 0.1193182 176 3.007854E-10 7.543699E-7
fse.IISL2.50ch05V2 c 0.08806818 176 2.098921E-5 0.0168372
fse.IISL2.50ch08V2 g 0.1193182 176 2.685358E-5 0.0168372
fse.IISL2.50ch12V1 c 0.07386364 176 1.617684E-5 0.0168372
fsiSL2.50ch00V1 c 0.1193182 176 3.02085E-10 7.576292E-7
fsiSL2.50ch05V2 c 0.08806818 176 2.055407E-5 0.01676828
fsiSL2.50ch08V2 g 0.1193182 176 2.674367E-5 0.01676828
fsiSL2.50ch12V1 c 0.07386364 176 1.575753E-5 0.01676828
triSL2.50ch05V1 c 0.05397727 176 1.860929E-5 0.04667211
FWSL2.50ch11V11 g 0.4772727 176 3.74031E-5 0.09380697
GHSL2.50ch02V1 t 0.05397727 176 6.721734E-6 0.01460324
GHSL2.50ch02V2 a 0.05965909 176 1.746799E-5 0.01460324
GHSL2.50ch02V3 t 0.05965909 176 1.746799E-5 0.01460324
H.midSL2.50ch00V2 c 0.1193182 176 1.217717E-5 0.03054034
lcnSL2.50ch11V2 t 0.4431818 176 1.788601E-10 1.49527E-7
lcnSL2.50ch11V5 g 0.4772727 176 2.430079E-11 6.094639E-8
lcnSL2.50ch11V11 c 0.4943182 176 8.715293E-11 1.092898E-7
LSh.plSL2.50ch01V1 t 0.09943182 176 7.733671E-7 0.0009698023
LSh.plSL2.50ch04V1 g 0.09375 176 2.524193E-8 6.330677E-5
LSh.plSL2.50ch06V1 t 0.05681818 176 9.917404E-6 0.004145475
LSh.plSL2.50ch06V2 g 0.1079545 176 2.635525E-5 0.00815457
LSh.plSL2.50ch06V4 a 0.05965909 176 2.926281E-5 0.00815457
LSh.plSL2.50ch06V5 g 0.07386364 176 2.868957E-5 0.00815457
LSh.plSL2.50ch06V6 t 0.06818182 176 8.766157E-6 0.004145475
LSh.plSL2.50ch06V7 t 0.05397727 176 3.733349E-6 0.00234081
LSh.plSL2.50ch10V1 g 0.08522727 176 1.634721E-6 0.001366627
LSh.rlSL2.50ch01V1 t 0.09943182 176 7.733671E-7 0.0009698023
LSh.rlSL2.50ch04V1 g 0.09375 176 2.524193E-8 6.330677E-5
LSh.rlSL2.50ch06V1 t 0.05681818 176 9.917404E-6 0.004145475
LSh.rlSL2.50ch06V2 g 0.1079545 176 2.635525E-5 0.00815457
LSh.rlSL2.50ch06V3 a 0.05965909 176 2.926281E-5 0.00815457
LSh.rlSL2.50ch06V4 g 0.07386364 176 2.868957E-5 0.00815457
LSh.rlSL2.50ch06V5 t 0.06818182 176 8.766157E-6 0.004145475
LSh.rlSL2.50ch06V6 t 0.05397727 176 3.733349E-6 0.00234081
LSh.rlSL2.50ch10V1 g 0.08522727 176 1.634721E-6 0.001366627
H.maxSL2.50ch00V2 c 0.1193182 176 1.730404E-5 0.04339852
osiSL2.50ch11V4 c 0.1164773 176 2.999484E-5 0.07522707
pan.macroSL2.50ch00V1 c 0.1193182 176 8.61507E-7 0.002160659
pblkSL2.50ch02V1 a 0.06818182 176 1.420354E-5 0.03562248
recSL2.50ch02V2 a 0.06818182 176 2.438907E-6 0.00611678
RCESL2.50ch11V5 g 0.4795322 171 3.080804E-5 0.07726656
pshSL2.50ch11V1 t 0.4431818 176 1.426475E-5 0.02005783
pshSL2.50ch11V3 g 0.4772727 176 1.599508E-5 0.02005783
SkCSL2.50ch08V1 g 0.2556818 176 1.845732E-5 0.04629095
SPS.dtSL2.50ch11V4 g 0.4795322 171 1.441045E-6 0.003614142
SPS.dtSL2.50ch11V5 c 0.497076 171 3.763584E-6 0.004719534
SPS.lnSL2.50ch01V1 t 0.07017544 171 1.358185E-5 0.009858539
SPS.lnSL2.50ch05V7 c 0.06140351 171 7.086575E-6 0.008886565
SPS.lnSL2.50ch05V14 g 0.06725146 171 1.572335E-5 0.009858539
SPS.lnSL2.50ch05V15 g 0.05263158 171 6.395395E-10 1.603965E-6
SPS.stSL2.50ch03V1 t 0.05555556 171 1.530084E-5 0.03837451
parSL2.50ch11V1 g 0.4772727 176 2.3314E-6 0.005847152
par.RSL2.50ch04V1 c 0.05681818 176 3.801183E-6 0.009533367
ptkSL2.50ch11V1 g 0.4772727 176 7.998893E-6 0.02006122
WwSL2.50ch00V1 c 0.1193182 176 1.277726E-6 0.003204537