Skip to main content

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].