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Table 2 Ten phenotypes whose expression level is significantly regulated by both cis- and trans-acting determinants

From: Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans

   Cis-Association analysis (Step 1) Linkage analysis of residuals (Step 2) – Signals at cis-SNPs Association analysis under linkage peaks (Step 3)
Gene Symbol Location p-value for cis-SNP with peak LOD score Variation explained (R2%) cis-SNP with peak LOD score Peak (cis) LOD score (R2%) No. of SNPs in model
PARP4a 13q11 0.023 3.3 rs735770 6.21 80.2 4
VAMP8b 2p12-p11.2 0.003 1.2 rs1432265 7.8 99.9 3
ITGB1BP1 2p25.2 0.051 2.4 rs1003653 10.56 55.3 5
TPP2 13q32-q33 0.693 0.2 rs1412953 6.01 99.3 3
GSTM2b 1p13.3 0.001 8.9 rs559479 9.22 86.8 4
GSTM1a, b 1p13.3 0.024 7.1 rs15864 6.53 32.3 8
IRF5a, b 7q32 0.606 0.2 rs754386 6.1 98.9 5
DDX17b 22q13.1 0.01 19.3 rs2064088 10.89 70.8 6
CHI3L2b 1p13.3 0.086 10.1 rs1264898 9.48 64.9 2
PEX6 6p21.1 0.004 11.6 rs1537638 7.2 66.7 5
  1. This table shows the result from the cis-SNP association analysis (step 1) that corresponds to the largest cis-LOD score in step 2, as well as the total variance explained from step 3, for each of these expression measures.
  2. aRegions of these genes show copy number variation http://projects.tcag.ca/variation/.
  3. bThese genes were also identified by Morley et al. [1] and are shown in Table 1 of Cheung et al. [2].