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Table 4 The ASE pattern of genes reaching statistical significance (Illumina Assay).

From: High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

rsID

Name

Chr

Imprinting status

Average intensity >11.25

Number of hets

Number of hets with p < 0.01

Pattern of ASE

Alleles

rs1802710

DLK1

14

control

13.57

15

14

imprinting

 

rs8100247

ZNF331

19

control

12.61

13

12

imprinting

 

rs2075745

H19

11

control

14.01

12

12

imprinting

 

rs2839702

H19

11

control

13.48

11

11

imprinting

 

rs1082

PHACTR2

6

candidate

12.09

14

10

partial imprinting

 

rs12982082

ZNF331

19

control

12.27

12

10

imprinting

 

rs13073

PEG10

7

control

12.09

11

10

imprinting

 

rs1055359

PEG3

19

control

11.8

10

10

imprinting

 

rs9373409

PLAGL1

6

control

12.48

11

9

imprinting

 

rs1860565

PEG3

19

control

13.63

9

9

imprinting

 

rs2309428

TJP2

9

candidate

12.86

9

8

random ASE

 

rs178077

SNAP29

22

candidate

11.95

10

7

random ASE

 

rs1003483

IGF2AS

11

control

11.32

8

7

imprinting

 

rs8585

UBE2V1

20

candidate

12.36

13

6

preferential

A>G

rs1130663

CD151

11

candidate

12.44

18

5

random ASE

 

rs4664114

FMNL2

2

candidate

11.51

14

5

random ASE

 

rs4944960

XRRA1

11

candidate

12.43

12

5

preferential

G>C

rs2282336

TJP2

9

candidate

12.32

9

5

random ASE

 

rs6633

CDK2AP1

12

candidate

11.34

8

5

random ASE

 

rs4614

VPS11

11

candidate

13.09

13

4

random ASE

 

rs3817672

TFRC

3

candidate

12.07

13

4

* preferential

T>C

rs2905

C14orf130

14

candidate

11.33

12

4

random ASE

 

rs12190287

TCF21

6

candidate

12.88

10

4

random ASE

 

rs3809865

ITGB3

17

candidate

12.09

10

4

random ASE

 

rs10863

MEST

7

control

12.32

4

4

imprinting

 

rs915894

NOTCH4

6

candidate

13.44

16

3

* preferential

A>C

rs754615

CAST

5

candidate

13.71

14

3

preferential

G>C

rs838896

SCARB1

12

candidate

12.62

10

3

random ASE

 

rs5758651

TCF20

22

candidate

12.4

10

3

random ASE

 

rs11699879

NCOA3

20

candidate

12.68

9

3

random ASE

 

rs838891

SCARB1

12

candidate

11.85

9

3

random ASE

 

rs2425009

MYH7B

20

candidate

11.68

9

3

random ASE

 

rs9749449

ZNF211

19

candidate

11.71

6

3

random ASE

 

rs4797

SQSTM1

5

candidate

14.48

18

2

preferential

G>A

rs1128933

MAN2C1

15

candidate

12.71

16

2

preferential

C>T

rs10277

SQSTM1

5

candidate

11.78

16

2

preferential

G>A

rs2249057

NM_006031

21

candidate

13.31

13

2

* preferential

C>A

rs7226091

MGC16597

17

candidate

11.83

13

2

* preferential

C>G

rs1043618

HSPA1A

6

candidate

13.6

12

2

random ASE

 

rs17085249

ELL2

5

candidate

12.98

12

2

random ASE

 

rs2255255

CRNKL1

20

candidate

12.86

12

2

random ASE

 

rs2013162

IRF6

1

candidate

12.64

12

2

* preferential

C>A

rs11121567

PGD

1

candidate

12.03

12

2

* preferential

A>G

rs3780473

ACO1

9

candidate

11.67

12

2

random ASE

 

rs4669

TGFBI

5

candidate

13.27

11

2

random ASE

 

rs7242

SERPINE1

7

candidate

13.01

11

2

random ASE

 

rs2788478

FLJ10300

7

candidate

13.04

10

2

random ASE

 

rs2271108

DOCK5

8

candidate

12.85

10

2

random ASE

 

rs552282

PPFIA1

11

candidate

11.58

10

2

* preferential

C>T

rs1044116

NOTCH3

19

candidate

12.21

9

2

random ASE

 

rs7204628

MGC24665

16

candidate

11.84

9

2

random ASE

 

rs844

FCGR2B

1

candidate

13.05

8

2

* preferential

C>T

rs11156878

KIAA0391

14

candidate

12.15

5

2

random ASE

 

rs12780

PRDM8

4

candidate

12.02

5

2

random ASE

 

rs5919

ITGB3

17

candidate

11.55

4

2

random ASE

 

rs13390

PHLDA2

11

control

12.33

2

2

imprinting

 
  1. All SNPs had an average intensity above 11.25 and all or a subset of heterozygous samples had a significant statistical ASE test (p < 0.01). For each SNP, the ASE pattern (see text for details) was subjectively determined by examination of the bar charts, designed as in Figure 4, for all heterozygous samples. In case of preferential expression, the allele that was more expressed is indicated in the last column. *For these SNPs, the preferential bias is weaker.