Skip to main content

Table 1 High-confidence imprinted genes identified in LCLs and whole blood

From: RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting

 

Gene name

Chr

Start (hg19)

End (hg19)

Cytogenetic band

Strand

Pat ratio (LCLS/LCLU/WB)

Preferentially expressed allele

Confidence (LCL/WB)

1

PER3

1

7844380

7905237

p36.23

+

0.61/0.65/0.68

Paternal

HC/LC

2

RP3-467L1.4

1

7870302

7887402

p36.23

–

0.81/0.69/0.62

Paternal

HC/−

3

PPIEL

1

39997510

40024379

p34.3

–

0.78/0.78/0.90

Paternal

HC/HC

4

ZDBF2

2

207139387

207179148

q33.3

+

0.94/0.94/0.95

Paternal

HC/HC

5

ADAM23

2

207308263

207485851

q33.3

+

0.71/0.70/0.63

Paternal

HC/−

6

AC069277.2

3

6532166

6777816

p26.1

+

0.79/0.79/0.80

Paternal

HC/−

7

NAP1L5

4

89617066

89619386

q22.1

–

0.97/0.95/0.93

Paternal

HC/LC

8

PXDC1

6

3722848

3752260

p25.2

–

0.65/0.64/0.68

Paternal

HC/LC

9

FAM50B

6

3849620

3851551

p25.2

+

0.94/0.94/1.00

Paternal

HC/HC

10

GRB10

7

50657760

50861159

p12.1

–

0.57/0.57/0.29

Maternal

−/HC

11

SGCE

7

94214542

94285521

q21.3

–

0.83/0.83/0.53

Paternal

HC/−

12

PEG10

7

94285637

94299007

q21.3

+

0.97/0.97/1.00

Paternal

HC/LC

13

RP11-134O21.1

8

2523591

2585991

p23.2

–

0.70/0.68/0.78

Paternal

HC/−

14

GS1-57L11.1

8

2584858

2680004

p23.2

+

0.73/0.73/0.91

Paternal

HC/−

15

H19

11

2016406

2022700

p15.5

–

0.10/0.26/0.00

Maternal

HC/HC

16

KCNQ1

11

2465914

2870339

p15.5

+

0.18/0.36/0.46

Maternal

HC/HC

17

KCNQ1OT1

11

2629558

2721224

p15.5

–

0.96/0.94/0.74

Paternal

HC/HC

18

RB1

13

48877887

49056122

q14.2

+

0.39/0.39/0.54

Maternal

HC/−

19

LPAR6

13

48963707

49018840

q14.2

–

0.87/0.39/0.60

Paternal

HC/LC

20

MEG3

14

101245747

101327368

q32.2

+

0.21/0.24/0.02

Maternal

LC/HC

21

MKRN3

15

23810454

23873064

q11.2

+

0.90/0.90/1.00

Paternal

HC/LC

22

SNRPN

15

25068794

25223870

q11.2

+

0.98/0.98/1.00

Paternal

HC/HC

23

SNURF

15

25200181

25245423

q11.2

+

0.98/0.98/1.00

Paternal

HC/HC

24

SNHG14

15

25223730

25664609

q11.2

+

0.98/0.89/0.88

Paternal

HC/HC

25

IGF1R

15

99192200

99507759

q26.3

+

0.56/0.56/0.50

Paternal

HC/−

26

PRR25

16

855443

863861

p13.3

+

0.69/0.67/0.66

Paternal

HC/−

27

ZNF597

16

3486104

3493542

p13.3

–

0.04/0.06/0.05

Maternal

HC/HC

28

NAA60

16

3493611

3536963

p13.3

+

0.06/0.05/0.03

Maternal

HC/HC

29

ZNF714

19

21264965

21308073

p12

+

0.62/0.62/0.63

Paternal

HC/−

30

ZNF613

19

52430400

52452012

q13.41

+

0.50/0.50/0.67

Paternal

−/HC

31

ZNF331

19

54024235

54083523

q13.42

+

0.81/0.81/0.70

Paternal

HC/HC

32

PEG3

19

57321445

57352096

q13.43

–

0.98/0.98/1.00

Paternal

HC/−

33

HM13

20

30102231

30157370

q11.21

+

0.57/0.58/0.63

Paternal

HC/HC

34

L3MBTL1

20

42136320

42179590

q13.12

+

0.96/0.96/0.97

Paternal

HC/HC

35

SGK2

20

42187608

42216877

q13.12

+

0.92/0.91/0.93

Paternal

HC/HC

36

GNAS-AS1

20

57393974

57425958

q13.32

–

0.96/0.96/0.98

Paternal

HC/HC

37

NHP2L1

22

42069934

42086508

q13.2

–

0.57/0.57/0.62

Paternal

HC/HC

  1. High-confidence imprinted genes were classified as those transcripts showing significant evidence of parental expression bias (at 10% FDR) by both statistical tests used in at least one of the two cohorts studied. LCLs and LCLu indicate the results from LCL stranded and unstranded data, respectively. For genes with multiple UGFs (Additional file 3), we report paternal ratios for the UGF with the most significant p value
Back to article page

BMC Biology

ISSN: 1741-7007

Contact us