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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