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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
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