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Table 5 SNPs indicating allelic imbalance in both reciprocal crosses

From: The direction of cross affects obesity after puberty in male but not female offspring

     

Alternative allele1 proportion

 

Chr

SNP-Position

Ref/Alt

Gene symbol

Gene description

patBFMI

matBFMI

Ratio diff.

TFBS2

2

91712576

C/T

Harbi1

harbinger transposase derived 1

48.1

79.7

31.5

Esrra, Esrrb

2

152687856

C/T

Mcts2

malignant T cell amplified sequence 2

88.9

7.2

81.8

-

2

152704657

A/T

H13

histocompatibility 13

18.4

75.9

57.5

-

2

152705549

G/A

H13

 

7.9

100.0

92.1

 

7

6704437

C/T

Peg3

paternally expressed 3 *

93.6

-

-

-

7

6706584

A/G

Peg3

 

100.0

-

-

 

11

22956525

G/A

Commd1

COMM domain containing 1

37.3

57.7

20.3

-

11

22972794

G/T

Commd1

 

98.8

0.0

98.8

 

11

22974882

G/A

Zrsr1

zinc finger (CCCH type), RNA binding motif and serine/arginine rich 1

95.2

4.6

90.7

-

11

109933190

T/C

Abca8b

ATP-binding cassette, sub-family A (ABC1), member 8b

57.6

30.9

26.7

-

11

109933214

C/T

Abca8b

60.8

38.5

22.4

 

11

109974591

A/C

Abca8b

67.7

45.7

22.0

 

12

104081368

A/G

Serpina4-ps1

serine (or cysteine) peptidase inhibitor, clade A, member 4, pseudogene 1

24.6

60.9

36.3

-

12

104081522

G/A

Serpina4-ps1

 

27.2

58.0

30.8

 

17

12380069

G/T

Plg

plasminogen

22.6

71.7

49.1

-

17

78969687

T/C

Prkd3

protein kinase D3

77.5

57.3

20.2

-

  1. Chr – chromosome, matBFMI – F1 males from BFMI mothers, patBFMI – F1 males from BFMI fathers; * Coverage thresholds for ChiSquare based difference calculations in Peg3 were not met in all matBFMI samples. However, variant calling annotates all matBFMI samples as reference (B6) at these positions, confirming the paternal expression. Further ASE gene details are given in Additional file 2: Table S2
  2. 1Alternative allele in these cases is the BFMI allele
  3. 2TFBS - Steroid hormone transcription factor binding sites. Esrra/b – estrogen related receptor a/b, ERE – estrogen response element