Table 1 Genes with cis-eQTL detected in the population of 140 natural A. thaliana accessions (SCHMITZ-data) contributing to the accession specific presence or absence of transcripts and earlier reported biological function
LocusGeneSNPaMAFbLog odds ratio ± SEcP-valuedReplicatedeReference
AT2G21045HAC1chr2_90286850.144.84 ± 0.761.75 × 10−10Yes-GBFChao et al. 2014
AT5G59340WOX2chr5_239352240.432.82 ± 0.541.83 × 10−7YesLie et al. 2012
AT1G77235MIR402chr1_290074640.467.07 ± 1.025.18 × 10−12No.eKim et al. 2010
AT2G38220APD3chr2_160170430.290.37 ± 0.073.64 × 10−7No.eLuo et al. 2012
AT1G13430ATST4Cchr1_46017620.510.36 ± 0.063.87 × 10−10NoMarsolais et al. 2007
AT1G66600WRKY63chr1_242177980.060.14 ± 0.023.22 × 10−10NoVan Aken et al. 2013
AT2G19500ATCKX2chr2_81685120.070.18 ± 0.036.13 × 10−9Novon Schwartzenberg et al. 2007
AT3G27620AOX1Cchr3_102304730.390.4 ± 0.076.45 × 10−8NoWang et al. 2012
AT3G57270BG1chr3_220317710.060.15 ± 0.021.09 × 10−9NoZavaliev et al. 2013
AT4G01420CBL5chr4_5834220.120.2 ± 0.037.48 × 10−12NoCheong et al. 2010
AT4G02850DAAR1chr4_5973730.060.15 ± 0.021.41 × 10−9NoStrauch et al. 2015
AT4G29340PRF4chr4_146399840.210.36 ± 0.072.32 × 10−7NoDeeks et al. 2005
  • a Top SNP in association analysis.

  • b Minor allele frequency of the top associated SNP in the SCHMITZ-data.

  • c Log odds ratio of the top associated SNP ± SE.

  • d Nominal P-value for the top associated SNP.

  • e Could the original association in the SCHMITZ-data be replicated in the DUBIN-data: Yes-GBF, Replicated at Genome Wide Bonferroni threshold; Yes, replicated at Bonferroni threshold correcting for number of markers in ± 1 Mb window of the peak SNP in Dubin-data; No.e, not expressed in DUBIN-data so could not be tested for replication; No, nonsignificant in replication analysis.