Supplement

Supplementary Results
Supplementary Table 1. High- and lower-confidence imprinted gene candidates.

Ensembl ID
173447
184235
131591 (NM 017891)
182839
184163 (Q5EBL5)
131584 (CENTB5)
127054 (NM 017871)
169962 (TAS1R3)
107404 (DVL1)
162576 (NM 032348)
160075 (NM 014188)
178821 (TMEM52)
157916 (RER1)
157911 (PEX10)
157881 (PANK4)
169797
157870 (NM 152371)
177121 (Q8N6L5)
142611 (PRDM16)
162591 (EGFL3)
182956
116213 (WDR8)
183509 (Q8IYL3)
131697 (Q9UFQ2)
130940 (NM 017766)
117154 (NM 032880)
179002 (TAS1R2)
179163 (FUCA1)
142698 (NM 032884)
126070 (EIF2C3)
185668 (POU3F1)
183682 (BMP8)
173935 (NM 182518)
178973 (NM 024547 )
117410 (ATP6V0B)
118473 (SGIP1)
132489 (NM 020948)
117069 (SI7E)
137944 (NM 019610)
162676 (GFI1)
182166
186371 (NDUFA4)
121931 (NM 018372)
116455 (ME50)
179735 (Q8NE92)
184458 (Q86YZ3)
169474 (SPRR1A)
160691 (SHC1)
143620 (EFNA4)
160856 (NM 052939)
132704 (FCRL2)
132703 (APCS)
173110 (HSPA6)
143152 (Q9C074)
117501 (NM 025063)
116147 (TNR)
116703 (PDC)
118194 (TNNT2)
152104 (PTPN14)
152120 (Q9NQI3)
117791 (NM 017898)
185495 (Q9H5Q3)
173419 (Q8IVP0)
081692 (NM 023007 )
124860 (OBSCN)
181203 (HIST3H2BB)
168159 (Q5TA31)
182887
162946 (DISC1)
179397 (NM 173807 )
177356 (Q8NGX0)
035115 (NM 015677 )
172554 (SNTG2)
186170 (TMSL2)
182551 (NM 018269)
134321 (NM 080657 )
115738 (ID2)
138061 (CYP1B1)
152154 (NM 152390)
152518 (ZFP36L2)
181573 (Q96MM2)
112498 (PPP1R11)
Band
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.33
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.32
1p36.31
1p36.22
1p36.13
1p36.13
1p36.11
1p35.1
1p34.3
1p34.3
1p34.3
1p34.2
1p34.2
1p34.1
1p31.2
1p31.2
1p31.1
1p22.2
1p22.1
1p21.2
1p13.3
1p13.3
1p13.2
1q21.1
1q21.3
1q21.3
1q22
1q22
1q23.1
1q23.1
1q23.2
1q23.3
1q24.1
1q24.3
1q25.1
1q31.1
1q32.1
1q32.3
1q41
1q41
1q42.11
1q42.12
1q42.13
1q42.13
1q42.13
1q42.13
1q42.13
1q42.2
1q44
1q44
2p25.3
2p25.3
2p25.3
2p25.2
2p25.2
2p25.1
2p22.2
2p22.1
2p21
6p22.1
6p22.1
Pred.
S
M
S
M
S
M
E
M
E,S
M
S
M
S
M
S
M
E,S
M
S
M
S
M
E,S
P
S
P
E,S
M
S
M
S
M
S
M
E,S
P
E,S
P
S
P
S
M
E,S
M
S
M
S
M
S
M
S
P
S
P
E,S
P
E
P
E
M
S
P
E,S
P
E,S
M
E,S
M
S
M
E
P
E
P
E
P
E,S
M
E,S
P
S
P
E,S
P
S
P
S
P
S
P
S
P
S
M
S
M
S
M
S
P
E
M
S
P
E,S
M
S
M
S
P
S
P
S
P
S
P
E,S
M
S
P
S
P
S
M
S
P
S
P
E,S
P
E,S
M
E
M
E
P
S
M
S
M
E,S
P
S
M
S
P
S
M
S
P
S
P
E
M
E,S
P
S
P
E,S
M
S
P
S
M
Ensembl ID
143921 (ABCG8)
138083 (SIX3)
055813 (Q96PX6)
115507 (OTX1)
116035 (VAX2)
178455
003137 (C26A)
144040 (SFXN5)
135637 (MRPL53)
115325 (DOK1)
116119 (KV2A)
115085 (ZAP70)
135951 (TSGA10)
071082 (RPL31)
169636
183998 (RPL22)
015568 (RANBP2L1)
184764 (RPL22)
184538 (RANBP2L1)
153094 (BCL2L11)
125618 (PAX8)
183300
136720 (HS6ST1)
169822 (NM 030970)
136698 (NM 032545)
179843 (RAB6C)
183840 (GPR39)
136539 (NM 014880)
174470 (Q96M44)
128714 (HOXD13)
128713 (HOXD11)
128709 (HOXD9)
170166 (HOXD4)
171567 (TIGD1)
157985 (CENTG2)
144485 (HES6)
132326 (PER2)
186540 (Q9Y419)
178580 (Q8WXC7 )
172428 (MYEOV2)
178602 (NM 148961)
063660 (GPC1)
142327 (RNPEPL1)
115687 (PASK )
132170 (PPARG)
131374 (TBC1D5)
060971 (ACAA1)
010282 (KB73)
178055 (NM 182702)
068028 (RASSF1)
145050 (ARMET )
114841 (NM 015512)
010322 (NISCH)
168268 (NM 022908)
144741 (NM 173471)
183185 (Q9UIV9)
184804
185565 (LSAMP)
144908 (FTHFD)
114626 (ABTB1)
179348 (GATA2)
004399 (PLXND1)
174640 (SLC21A2)
144872
181882
168875 (SOX14)
114120 (NM 018155)
175685 (Q9BZ57 )
174963 (ZIC4)
152977 (ZIC1)
175726
174948 (Q86SP6)
151967 (SCHIP1)
181501
163882 (POLR2H)
114315 (HES1)
169020 (ATP5I)
145214 (DGKQ)
127418 (FGFRL1)
176836
120896 (VINE)
179388 (EGR3)
Band
2p21
2p21
2p16.1
2p15
2p13.3
2p13.2
2p13.2
2p13.2
2p13.1
2p13.1
2p11.2
2q11.2
2q11.2
2q11.2
2q12.3
2q13
2q13
2q13
2q13
2q13
2q13
2q14.3
2q14.3
2q14.3
2q21.1
2q21.1
2q21.2
2q24.2
2q24.2
2q31.1
2q31.1
2q31.1
2q31.1
2q37.1
2q37.2
2q37.3
2q37.3
2q37.3
2q37.3
2q37.3
2q37.3
2q37.3
2q37.3
2q37.3
3p25.2
3p24.3
3p22.3
3p22.1
3p21.31
3p21.31
3p21.31
3p21.1
3p21.1
3p21.1
3p14.1
3q12.1
3q13.12
3q13.31
3q21.3
3q21.3
3q21.3
3q22.1
3q22.1
3q22.2
3q22.3
3q22.3
3q23
3q24
3q24
3q24
3q25.1
3q25.2
3q25.32
3q26.33
3q27.1
3q29
4p16.3
4p16.3
4p16.3
4p16.3
8p21.3
8p21.3
Pred.
E,S
M
S
P
E,S
P
E,S
M
E,S
M
S
P
S
P
S
P
S
M
S
M
S
P
S
P
E
P
S
P
E,S
P
E
P
S
P
E,S
P
S
P
S
P
S
M
S
P
S
P
S
P
S
M
S
M
E
M
S
P
S
M
S
M
S
M
S
M
E
M
E,S
P
E
M
S
M
S
M
E,S
M
S
P
E,S
P
S
P
S
M
S
M
E
M
S
P
E
M
S
P
S
P
S
M
S
M
S
P
S
M
S
M
S
M
S
P
S
P
E
M
S
M
E,S
M
S
P
S
M
S
P
S
P
S
P
E,S
P
S
M
S
M
S
P
S
M
E,S
M
S
M
S
M
S
P
E
M
S
M
E,S
P
S
M
S
M
E,S
M
S
P
S
M
S
M
Ensembl ID
159674 (SPON2)
163945 (NP 065945.1)
174141 (Q15270)
068078 (FGFR3)
163956 (LRPAP1)
183190
182739 (GRINL1B)
153851 (Q9NYI9)
153852 (Q9NYJ6)
180769 (Q8N507 )
138821 (NM 022154)
168743 (NP 001028219.1)
164093 (PITX2)
177826
170153 (Q9ULK6)
180519
151615 (POU4F2)
172799
145431 (PDGFC)
038295 (TLL1)
056050 (NM 017867 )
168322 (NM 030970)
177310 (NM 153008)
186158
186147 (DUX2)
066230 (SLC9A3)
185486
125063 (NM 017808)
112877 (NM 018140)
145506 (NKD2)
113504 (SLC12A7 )
174358
153395 (Q8NF37 )
113430 (IRX4)
170561 (IRX2)
170549 (IRX1)
145536 (ADAMTS16)
164236 (XP 293937.5)
133357 (NM 030970)
145526 (CDH18)
132404
113492 (AGXT2)
168621 (GDNF )
016082 (ISL1)
164258 (NDUFS4)
164283 (ESM1)
152929 (Q9BXE3)
145645 (Q9P193)
171540 (OTP)
131730 (CKMT2)
131732 (NM 032280)
153922 (CHD1)
174132 (Q8TBP5)
181751 (NM 033211)
176857
080709 (KCNN2)
113396 (SLC27A6)
164400 (CSF2)
069011 (PITX1)
174313
081818 (PCDHB4)
177895 (PCDHB16)
120327 (PCDHB14)
081853 (PCDHGC5)
113580 (NR3C1)
169302
113667 (Y555)
145888 (GLRA1)
182344
185548
178392
185784 (Q8TAJ0)
168903 (BTNL3)
137273 (FOXF2)
184250 (Q86WA7 )
145945 (FAM50B)
124785 (NRN1)
137203 (TFAP2A)
176078 (Q8NAN4)
185694
180740 (Q9H6Z8)
095585 (BLNK )
Band
4p16.3
4p16.3
4p16.3
4p16.3
4p16.3
4p13
4q13.2
4q13.2
4q13.2
4q21.23
4q24
4q24
4q25
4q28.1
4q31.21
4q31.21
4q31.22
4q31.3
4q32.1
4q32.3
4q33
4q34.3
4q35.1
4q35.2
4q35.2
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.33
5p15.32
5p15.2
5p15.2
5p14.3
5p14.1
5p13.2
5p13.2
5q11.2
5q11.2
5q11.2
5q12.1
5q12.1
5q14.1
5q14.1
5q14.1
5q15
5q21.1
5q21.1
5q21.3
5q22.3
5q23.3
5q23.3
5q31.1
5q31.1
5q31.3
5q31.3
5q31.3
5q31.3
5q31.3
5q32
5q32
5q33.1
5q35.2
5q35.3
5q35.3
5q35.3
5q35.3
6p25.3
6p25.2
6p25.2
6p25.1
6p24.3
6p24.3
6p22.1
10q23.31
10q24.1
Pred.
E,S
P
E,S
M
S
P
S
M
S
M
E
M
S
P
E,S
P
E,S
P
S
M
S
P
E
P
S
P
S
P
S
M
S
P
S
M
S
M
E
P
S
P
S
M
S
P
E
M
E,S
M
E,S
P
S
M
S
M
S
M
S
M
S
M
S
M
S
M
S
M
S
M
S
P
S
M
E,S
M
E
P
E
P
E,S
P
S
P
E
P
S
P
S
P
S
P
S
P
S
M
S
P
S
M
S
M
S
M
E
M
E,S
P
S
M
E
M
S
M
S
M
E,S
M
S
P
E
P
S
M
S
P
E
P
S
M
E
P
S
P
E
M
E
P
S
M
S
M
S
M
E
M
S
P
S
P
S
M
E,S
M
S
M
S
M
S
M
E
P
E,S
P
S
P
161877 (C6orf10)
168426 (BTNL2)
168383 (HLA-DPB1)
161896 (IHPK3)
156582
137252 (HCRTR2)
146151 (HMGCLL1)
179713 (Q8N480)
135324 (C6orf117 )
135315 (C6orf84)
184486 (POU3F4)
183075
153989 (C6orf68)
146350 (C6orf170)
184362 (Q9BZ63)
175211 (Q9BXE6)
135521 (C6orf93)
118508 (RAB32)
112499 (SLC22A2)
146477 (SLC22A3)
060762 (BRP44L)
153471 (TCP10)
186340 (THBS2)
164493 (Q96N37 )
170767 (C6orf208)
177706 (FAM20C)
184773 (Q96GH9)
122691 (TWIST2)
105855 (ITGB8)
105996 (HOXA2)
105997 (HOXA3)
164519 (Q96MZ3)
106001 (HOXA4)
106004 (HOXA5)
106006 (HOXA6)
005073 (HOXA11)
106038 (EVX1)
106483 (SFRP4)
106571 (GLI3)
164543 (STK17A)
058404 (CAMK2B)
164742 (ADCY1)
185292
179869 (NM 152701)
042813 (ZPBP)
185037
185947 (Q8IVV5)
135211 (C7orf35)
187391 (MAGI2)
185191
182348 (NM 181646)
105810 (CDK6)
006377 (DLX6)
121716 (PILRB)
128594 (NM 022143)
106028 (SSBP1)
181551
184412
133624 (NM 024910)
164889 (SLC4A2)
164896 (FASTK )
164690 (SHH)
187177
146909 (C7orf3)
130675 (HLXB9)
178158 (Q8N7D3)
155093 (PTPRN2)
180204 (NM 181648)
104284 (DLGAP2)
036448 (MYOM2)
186550
186553
186555
186558
186560
186647
185161 (Q8N9I4)
158815 (FGF17 )
168487 (BMP1)
013573 (DDX11)
177627 (NM 152319)
123364 (HOXC13)
123388 (HOXC11)
180818 (HOXC10)
180806 (HOXC9)
186426 (HOXC4)
170338 (HOXC6)
172789 (HOXC5)
174604 (Q9BXE6)
135502 (SLC26A10)
135446 (CDK4)
6p21.32
6p21.32
6p21.32
6p21.31
6p21.2
6p12.1
6p12.1
6q14.1
6q14.2
6q14.2
6q16.1
6q21
6q22.1
6q22.31
6q22.31
6q23.2
6q24.2
6q24.3
6q25.3
6q25.3
6q27
6q27
6q27
6q27
6q27
7p22.3
7p22.3
7p21.1
7p21.1
7p15.2
7p15.2
7p15.2
7p15.2
7p15.2
7p15.2
7p15.2
7p15.2
7p14.1
7p14.1
7p13
7p13
7p13
7p13
7p12.3
7p12.2
7q11.21
7q11.21
7q11.23
7q21.11
7q21.12
7q21.13
7q21.2
7q21.3
7q22.1
7q32.1
7q34
7q34
7q34
7q36.1
7q36.1
7q36.1
7q36.3
7q36.3
7q36.3
7q36.3
7q36.3
7q36.3
8p23.3
8p23.3
8p23.3
8p23.1
8p23.1
8p23.1
8p23.1
8p23.1
8p23.1
8p23.1
8p21.3
8p21.3
12p11.21
12q13.11
12q13.13
12q13.13
12q13.13
12q13.13
12q13.13
12q13.13
12q13.13
12q13.2
12q13.3
12q14.1
S
E,S
E
S
S
S
S
S
E,S
S
S
S
S
E
S
S
S
S
E,S
S
E,S
S
S
S
E
S
E
S
E
E,S
E,S
S
E,S
E,S
S
E,S
E,S
S
E,S
E
S
S
S
S
S
E,S
E,S
E,S
E,S
S
S
S
S
S
S
S
S
S
S
E,S
E,S
S
E
E
S
S
S
E,S
E,S
S
E
E
E
E
E
E
E,S
S
S
S
E
S
S
S
E,S
E,S
S
E
S
E,S
E,S
M
M
P
M
M
P
P
P
P
P
M
P
P
P
P
P
M
P
P
P
P
P
P
P
M
P
M
M
M
M
M
M
M
M
M
M
P
P
M
P
P
M
M
P
P
M
P
P
M
P
P
M
P
M
P
M
P
P
P
M
M
P
M
P
M
M
M
P
P
M
M
M
P
P
M
M
P
M
P
M
P
M
M
M
M
M
M
M
P
M
M
172733 (PURG)
167912 (Q96QE0)
183226
185942 (FAM77D)
165084 (NM 052958)
184234 (NM 172239)
180694 (Q8N3G6)
156486 (KCNS2)
164796 (CSMD3)
104406 (NM 032205)
169427 (KCNK9)
184489 (PTP4A3)
181790 (BAI1)
180838 (Q8NAM3)
167656 (LY6D)
179142 (CYP11B2)
182851 (NM 178172)
158106 (RHPN1)
181528
179950 (NM 078480)
185189 (NM 178564)
186574 (Q8ND02)
178719 (GRINA)
167701 (GPT )
160959 (Y014)
177742 (NM 178535)
120215 (MLANA)
186758 (Q8N7I0)
174994 (Q96M55)
170152
154537 (Q8NCQ8)
178784 (Q96F02)
184879
182368 (Q8NCQ8)
170215 (Q8NCQ8)
170217
107282 (APBA1)
155621 (NM 182505)
186788 (NP 001001670)
177992 (NM 178828)
186359 (Q8NDS1)
130222 (GADD45G)
169027 (NM 030970)
131662 (PHF2)
119523 (NM 033087 )
177945 (NM 016158)
136944 (LMX1B)
123454 (DBH)
186459
160345 (NM 144654)
148411 (NM 144653)
160360 (Q9UFS8)
148400 (NOTCH1)
172889 (EGFL7 )
169692 (AGPAT2)
054148 (PHPT1)
184709
185863
176248 (NM 013366)
176058 (NM 173691)
182569 (NM 053045)
186909
151632 (AKR1C2)
178462 (NM 024803)
178372 (CLSP)
176730 (Q8N218)
107485 (GATA3)
182077 (NP 001030014.1)
099250 (NRP1)
175395 (ZNF25)
165511 (NM 145022)
165406 (MARCH8)
148611 (SYT15)
165606
107671 (NM 018245)
165443 (NM 032439)
148575 (NM 178505)
182771 (GRID1)
138135 (CH25H)
183643 (C15orf32)
184254 (ALDH1A3)
140479 (PACE4)
103326 (SOLH)
127585 (NM 153350)
127586 (CHTF18)
005513 (SOX8)
172268 (Q96S05)
172257 (Q96S03)
184471
073761 (CACNA1H)
140650 (PMM2)
8p12
8q12.1
8q12.3
8q12.3
8q13.2
8q21.2
8q21.3
8q22.2
8q23.3
8q24.22
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
8q24.3
9p24.1
9p21.1
9p12
9p11.2
9p11.2
9q12
9q13
9q13
9q13
9q13
9q21.11
9q21.12
9q21.32
9q22.1
9q22.1
9q22.2
9q22.31
9q22.31
9q22.33
9q33.3
9q33.3
9q34.2
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
9q34.3
10p15.3
10p15.1
10p15.1
10p15.1
10p15.1
10p14
10p12.1
10p11.22
10p11.21
10q11.21
10q11.21
10q11.22
10q11.23
10q11.23
10q21.1
10q21.2
10q23.2
10q23.31
15q26.1
15q26.3
15q26.3
16p13.3
16p13.3
16p13.3
16p13.3
16p13.3
16p13.3
16p13.3
16p13.3
16p13.2
E,S
E,S
E
E,S
E
S
S
S
S
E
E,S
S
S
E
E,S
S
E
S
S
S
S
S
E
E,S
S
E
S
E,S
S
S
S
S
S
S
S
S
E,S
E,S
E,S
S
S
S
S
S
S
E,S
E,S
S
S
E,S
S
S
S
E,S
S
E,S
S
S
S
S
S
E,S
S
S
S
E
E,S
E
E
E
S
E
S
S
S
S
S
E
S
E
S
S
S
S
S
E,S
E,S
S
S
S
S
P
M
P
P
M
M
P
P
M
P
M
P
M
M
P
M
P
M
M
P
M
M
P
M
P
M
M
M
P
M
M
P
M
M
M
M
P
P
M
P
P
P
P
P
P
P
M
M
P
P
M
M
M
P
M
M
M
M
M
M
M
P
P
M
P
M
P
M
P
M
M
P
M
M
M
M
M
M
P
M
M
M
M
M
M
P
P
P
M
M
P
148820 (LDB1)
166275 (NM 144591)
176584
119965 (C10orf88)
108001 (EBF3)
165752 (NM 173575)
171813 (Q96F43)
180066 (C10orf91)
148826 (NKX6-2)
171811 (C10orf93)
151646 (GPR123)
171798 (Q8TEE5)
165824 (NM 152643)
171794 (UTF1)
151650 (VENTX2)
178592 (Q8N377 )
148832 (PAOX )
186730 (DUX4)
184243
179882 (DUX2)
177947 (ODF3)
174885 (PYA5)
185885 (IFITM1)
182272 (B4GALNT4)
184363 (PKP3)
176828 (Q8N9U2)
177700 (POLR2L)
184956 (MUC6)
183116
184545 (DUSP8)
130598 (TNNI2)
184682
183680 (Q8N2L8)
181963 (Q8NGK3)
180785 (NM 152430)
176904 (Q8NH63)
180974 (Q8NGH9)
051009 (NM 032127 )
166337 (TAF10)
170748 (NM 014469)
170688 (OR5E1P)
129152 (MYOD1)
184193 (Q8N7V1)
129151 (BBOX1)
007372 (PAX6)
183242 (WIT1)
182565
185927
186660 (ZFP91)
172289 (Q8NGI7 )
134824 (FADS2)
174903 (RAB1B)
174851 (YIF1)
173621 (NM 024036)
172932
162105 (SHANK2)
175534 (Q8TB74)
137474 (MYO7A)
168959 (GRM5)
182359 (KBTBD3)
150750 (C11orf53)
184824 (C1QTNF5)
154146 (NRGN)
182657
120462 (Q9P195)
182667 (NTRI)
170257 (NM 030970)
080854 (Q9UPX0)
151503 (Y056)
149328 (NM 138342)
109956 (B3GAT1)
139194 (RBP5)
150045 (KLRF1)
121374 (KLRC3)
171681 (ATF7IP)
111404 (NM 024730)
172572 (PDE3A)
111700 (SLC21A8)
069431 (ABCC9)
130876 (SLC7A10)
124302 (CHST8)
105698 (USF2)
126266 (GPR40)
105663 (TRX2)
180458 (Q8N3U1)
105737 (GRIK5)
159904 (ZNF225)
167383 (ZNF229)
176499 (Q9Y4U5)
175856 (Q8NB48)
186818 (LILRB4)
10q24.32
10q24.32
10q26.13
10q26.13
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
10q26.3
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.5
11p15.4
11p15.4
11p15.4
11p15.4
11p15.4
11p15.4
11p15.4
11p15.4
11p15.1
11p14.3
11p14.2
11p13
11p13
11p11.12
11q11
11q12.1
11q12.1
11q12.2
11q13.2
11q13.2
11q13.2
11q13.2
11q13.3
11q13.4
11q13.5
11q14.2
11q22.3
11q23.1
11q23.3
11q24.2
11q24.3
11q24.3
11q25
11q25
11q25
11q25
11q25
11q25
12p13.31
12p13.31
12p13.2
12p13.1
12p12.3
12p12.2
12p12.2
12p12.1
19q13.11
19q13.11
19q13.12
19q13.12
19q13.12
19q13.13
19q13.2
19q13.31
19q13.31
19q13.33
19q13.41
19q13.42
E,S
S
S
E
S
S
S
E,S
E,S
E,S
S
S
S
S
E,S
E,S
E,S
S
S
S
S
S
E,S
E,S
E,S
E,S
S
S
S
S
S
E,S
S
S
S
S
S
S
S
S
E
S
E,S
E
S
S
S
S
S
S
S
E,S
S
S
S
S
S
S
S
E,S
E
S
S
E,S
S
E,S
S
S
S
S
S
E,S
S
S
S
S
S
S
E,S
S
E,S
S
S
E
E,S
S
E,S
E,S
E
E
E,S
M
P
M
M
M
P
P
M
M
M
M
M
M
P
M
M
M
P
P
P
M
M
M
M
M
M
M
M
M
P
P
M
P
P
M
P
P
M
P
P
P
M
M
P
M
M
P
P
P
P
M
M
M
P
P
M
M
P
P
P
M
M
P
M
M
P
P
M
M
M
M
P
P
P
M
P
M
P
M
M
M
M
M
M
P
M
P
M
M
M
M
079081 (SRGAP1)
173401 (NM 152779)
165891 (Q96AV8)
111046 (MYF6)
151572 (NM 178826)
089116 (LHX5)
175727 (NM 014938)
184967 (NM 024078)
112787 (Q9HCM7 )
139495 (NM 153023)
169840 (GSH1)
102760 (NM 014059)
152207 (CYSLTR2)
171945 (NM 030970)
178215 (Q8N7V5)
178205 (Q8N7V5)
178200 (Q8N7V5)
177527 (Q8N7F4)
185498
152192 (POU4F1)
171650 (PTMA)
184052
165300 (Y918)
139800 (ZIC5)
102466 (FGF14)
185950 (IRS2)
153481 (NM 018210)
126218 (F10)
186009 (ATP4B)
184497 (FAM70B)
185989 (RASA3)
176294 (OR4N2)
136367 (ZFHX2)
176165 (FOXG1C)
136352 (TITF1)
186215 (Q86SZ3)
136327 (NKX2-8)
151338 (MIPOL1)
151748 (SAV1)
073712 (PLEKHC1)
125378 (BMP4)
184302 (SIX6)
177126 (C14orf141)
183992
140093 (SERPINA10)
036530 (CYP46A1)
140107 (Q86U14)
185469 (RTL1)
066735 (KIF26A)
184601 (Q8N912)
130235 (NM 032714)
184916 (JAG2)
184552 (Q8NAF8)
182351 (CRIP1)
177199 (IGHA2)
177154 (IGHE)
177145 (IGHG1)
126309 (HV1A)
126290 (HV2A)
151802 (Q9P168)
103832 (O60374)
134146 (NM 080650)
179315
184263
169856 (ONECUT1)
069667 (RORA)
138622 (HCN4)
186690
140557 (SIAT8B)
12q14.2
12q21.1
12q21.2
12q21.31
12q23.1
12q24.13
12q24.31
12q24.33
12q24.33
13q12.12
13q12.2
13q14.11
13q14.2
13q14.3
13q21.1
13q21.1
13q21.1
13q21.31
13q21.32
13q31.1
13q31.1
13q31.1
13q31.2
13q32.3
13q33.1
13q34
13q34
13q34
13q34
13q34
13q34
14q11.2
14q11.2
14q12
14q13.3
14q13.3
14q13.3
14q13.3
14q22.1
14q22.1
14q22.2
14q23.1
14q24.3
14q31.1
14q32.13
14q32.2
14q32.2
14q32.31
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
14q32.33
15q13.1
15q13.2
15q14
15q14
15q21.2
15q21.3
15q22.2
15q24.1
15q24.3
15q26.1
S
E
E,S
S
S
S
S
S
E,S
S
S
S
S
S
E,S
S
S
E,S
E,S
S
S
E
S
S
E
S
S
S
S
E,S
S
E
S
E,S
S
S
S
E
E
E,S
S
S
S
E,S
E
S
E
E,S
E
S
S
S
S
S
S
S
S
S
E,S
E,S
E
S
S
S
S
S
S
S
S
M
M
M
P
P
M
P
M
M
P
M
M
P
P
M
M
P
P
P
M
P
P
P
M
M
M
M
M
M
M
M
P
M
P
M
P
P
M
M
P
M
P
P
M
P
P
M
M
M
M
M
M
M
M
M
P
M
P
P
P
P
P
P
P
M
M
M
P
P
182375
185836
102924 (CBLN1)
103449 (SALL1)
183022
103005 (C16orf57 )
102890 (ELMO3)
102977 (ACD)
103056 (SMPD3)
103241 (FOXF1)
179588 (ZFPM1)
051523 (CYBA)
183788 (Q8N206)
183518
183688 (NM 182705)
167874 (TMEM88)
109061 (MYH1)
108448 (TRIM16)
160516 (RPS28)
181977 (PYY2)
184142 (TIAF1)
108587 (GOSR1)
172716 (NM 152270)
171532 (NEUROD2)
173917 (HOXB2)
120093 (HOXB3)
182742 (HOXB4)
108511 (HOXB6)
120068 (HOXB8)
141378 (YCE7 )
121068 (TBX2)
187013 (C17orf82)
136492 (BRIP1)
125398 (SOX9)
161547 (SFRS2)
167281
141570 (CBX8)
141582 (CBX4)
175901 (Q8NBT7 )
181428 (Q8N8L1)
181409 (AATK )
187207
186765 (FSCN2)
184703 (SIRT7 )
184715 (NM 032711)
169750 (RAC3)
169727 (GPS1)
154655 (NM 173464)
067900 (ROCK1)
141448 (GATA6)
141441 (FAM59A)
101746 (NOL4)
101489 (BRUNOL4)
152217 (SETBP1)
183677 (ELA2)
141644 (MBD1)
041353 (RAB27B)
141668 (NM 182511)
141665 (NM 152676)
101544 (NM 014913)
178184 (PARD6G)
141934 (PPAP2C)
118050 (NM 017914)
180866 (Q8NB05)
105655 (NM 016368)
172684 (Q8NE65)
172666
187135
121297 (TSH3)
16p11.2
16p11.2
16q12.1
16q12.1
16q12.2
16q13
16q22.1
16q22.1
16q22.1
16q24.1
16q24.2
16q24.2
16q24.3
17p13.3
17p13.3
17p13.1
17p13.1
17p12
17p11.2
17q11.2
17q11.2
17q11.2
17q12
17q12
17q21.32
17q21.32
17q21.32
17q21.32
17q21.32
17q23.2
17q23.2
17q23.2
17q23.2
17q24.3
17q25.1
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
17q25.3
18p11.31
18q11.1
18q11.2
18q12.1
18q12.1
18q12.2
18q12.3
18q21.1
18q21.1
18q21.2
18q22.3
18q22.3
18q23
18q23
19p13.3
19p13.3
19p13.2
19p13.11
19p13.11
19p13.11
19q12
19q12
S
S
S
E,S
S
E,S
S
E,S
S
E,S
S
S
E,S
E,S
S
E,S
S
E
S
E,S
E
S
S
S
E,S
E,S
S
S
S
E,S
S
E
S
S
E
S
S
S
S
E,S
S
S
S
S
S
S
S
S
S
E
E,S
S
E,S
E
S
S
E
S
S
S
S
E,S
S
E,S
S
E,S
E,S
S
E,S
P
P
M
M
M
M
P
M
M
M
M
M
M
M
M
M
P
M
M
P
M
P
M
P
M
M
M
M
M
M
M
M
P
P
M
P
M
M
M
P
M
M
P
M
M
P
M
P
M
M
P
M
M
P
M
M
P
P
P
M
P
M
M
P
M
P
P
M
P
105132 (ZN550)
130724 (CHMP2A)
099326 (ZNF42)
175487 (Q9BPX8)
178591 (DEFB125)
088782 (DEFB127 )
125906 (Q9H4I0)
125861 (GFRA4)
101230 (C20orf82)
172264 (C20orf133)
125798 (FOXA2)
125810 (C1QR1)
125831 (CST11)
154930 (ACAS2L)
183029 (Q8NCY9)
026559 (KCNG1)
124222 (STX16)
179242 (CDH4)
101180 (HRH3)
130702 (LAMA5)
174407 (C20orf166)
101188 (NTSR1)
101189 (C20orf20)
060491 (OGFR)
092758 (COL9A3)
101204 (CHRNA4)
075043 (KCNQ2)
130589 (P285)
125520 (SLC2A4RG)
171700 (RGS19)
171695 (Q8TD35)
181872
175302 (Q9NSI9)
184856 (C21orf74)
186930 (KRTAP6-2)
185569 (OLIG2)
159263 (SIM2)
183067 (Q9NSI5)
141956 (PRDM15)
014442 (ADARB1)
182586 (C21orf89)
186866 (C21orf80)
187153
142156 (COL6A1)
160294 (MCM3AP)
160305 (DIP2)
160307 (S100B)
160310 (HRMT1L1)
183628 (DGCR6)
100075 (SLC25A1)
183099
100208 (IGLC1)
186746
178803 (Q8NAW6)
100104 (SRR1)
169184 (MN1)
184390 (Q6ICM0)
166897 (Q96PY3)
184687 (Q8ND38)
075275 (CELSR1)
182858 (NM 024105)
128159 (TUBGCP6)
185386 (MAPK12)
100239 (K685)
025770 (NM 014551)
182786
19q13.43
19q13.43
19q13.43
19q13.43
20p13
20p13
20p13
20p13
20p12.1
20p12.1
20p11.21
20p11.21
20p11.21
20p11.21
20q11.21
20q13.13
20q13.32
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
20q13.33
21q11.2
21q21.1
21q22.11
21q22.11
21q22.13
21q22.2
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
21q22.3
22q11.21
22q11.21
22q11.21
22q11.22
22q11.22
22q11.23
22q12.1
22q12.1
22q12.2
22q13.1
22q13.31
22q13.31
22q13.33
22q13.33
22q13.33
22q13.33
22q13.33
22q13.33
E,S
E,S
E,S
S
S
S
E
S
E,S
S
S
S
S
E
S
S
E
S
S
S
S
S
E,S
S
E,S
E
S
E
S
S
S
S
S
E
S
S
E,S
E
S
E
E
S
S
S
E
S
E
E
E,S
S
E,S
S
E
S
E
S
E,S
S
E,S
E
S
S
S
S
S
S
Genes predicted to be imprinted by both the linear and RBF kernel classifiers learned by
Equbits are denoted by E, and those predicted by both the linear and RBF kernel classifiers
learned by SMLR by S. Genes predicted to be imprinted by both programs are denoted by E,S
and represent the high-confidence set presented in Table 1 of the article. Genes predicted
to be expressed from the maternal or paternal allele are denoted by M or P, respectively. To
enhance legibility, the common prefix ENSG00000 has been dropped from the Ensembl ID.
M
M
M
P
M
P
P
P
P
M
M
M
M
P
P
P
P
M
M
M
M
M
M
M
M
M
M
M
M
M
P
P
P
P
P
M
P
P
M
M
P
P
M
M
M
M
P
P
P
M
M
P
M
P
M
P
P
P
P
M
M
M
M
P
M
P
Supplementary Table 2. Chromosomal bands with high frequencies of genes proved or predicted with
high confidence to be imprinted.
Band
11p15.5
Freq. (# known)
10/82 (5)
P
< 3 1016
1p36.32
5/24 (1)
< 3 1016
7p15.2
6/26 (0)
< 3 1016
10q26.3
6/44 (0)
9 1016
Novel candidates
PKP3, an oncogene involved in lung cancer 1 , located distal to the IGF2/H19 cluster.
PRDM16, whose orthologue was also predicted to be imprinted in mouse 2 , and is
associated with leukemia 3 .
Several loci are involved in development and are susceptible to epigenetic regulation.
NKX6-2, which was also predicted to be imprinted in the mouse 2 , is preferentially
expressed in the brain 4 . NKX6-2, along with five neighboring candidate genes,
was predicted to show maternal expression. This region on 10q26 is near the
marker D10S217, which has been found to be maternally linked to male sexual
orientation 5 . A germline differentially methylated region was found in this region 6 ,
lending further support to the prediction of imprinted genes within the immediate
vicinity of this region.
RTL1, imprinted in the mouse 7 and sheep 8 .
14q32.31
2/5 (1)
1 1011
15q12
2/6 (2)
7 1010
7q21.3
4/35 (4)
2 108
P -values derived from a 2 -test with 1 degree of freedom.
Supplementary Table 3. High-confidence imprinted gene candidates predicted in human and mouse.
Gene
Band
GFI1
1p22
Expression
Human
Mouse
P
M
PRDM16, MEL1
Q96PX6
MAGI2, ACVRIP1, AIP1
1p36
2p16
7q21
P
P
M
P
P
M
LY6D
KCNK9
8q24
8q24
P
M
M
M
NM 173572
NKX6-2
10q26
10q26
M
M
M
M
ENSG00000184682
11p15
FOXG1C
14q12
NM 024598
16q13
Description
Oncogenic growth factor 9 , also involved in development 10 .
Myeloid leukemia gene 3 .
Specifically expressed in human brain and interacts
specifically with atrophin-1 11 . A mutation in atrophin1 causes dentatorubral and pallidoluysian atrophy (DRPLA), a progressive neurodegenerative disorder 1214 .
MAGI2 is also involved in zebrafish development 15
Expressed in head and neck squamous carcinoma 16, 17
K+ channel protein involved in neuron apoptosis and
cell tumorigenesis 18 .
Shows tissue-specific regulation with highest expression in the brain 4 and is located near marker D10S217
that 5 found was maternally linked to male sexual orientation.
Contained within an intron of LSP1, both in human and
in mouse.
Shows haploinsufficiency in a patient with severe
mental retardation, brain malformations and microcephaly 19 . Mouse orthologue is essential for normal
development of the telencephalon 20 .
Genes predicted to be expressed from the maternal or paternal allele are denoted by M or
P, respectively. For brevity, we did not include genes previously known to be imprinted.
Equbits
0.05
100kb downstr.
5kb downstr.
10kb downstr.
2kb downstr.
Exons
1kb downstr.
Introns
1kb upstr.
100kb upstr.
+/ count ratio
+/ percentage ratio
Counts
Percentage
Rep. elements
Miscellaneous
e
0.15
Absolute weight
0.15
0.10
0.05
0.05
SIF
CP1
IgPE2
MLTF
NFuE3
GTIIC
SRF
NFkB
ICP4
Sp1
PEA1
E2F
CEBP
PEA2
MIR
ERVL
MaLR
ERVK
ERV
ERV1
L2
L1
LTR
HAL1
FRAM
FAM
FLAM
DNAElem.
Alu
0.00
CR1
0.00
0.10
NFuE1
Absolute weight
0.05
0.00
Transc. factors
0.00
CpG islands
0.00
0.10
2kb upstr.
0.05
0.10
5kb upstr.
0.10
0.15
Absolute weight
0.15
Absolute weight
Absolute weight
0.15
10kb upstr.
SMLR
0.4
0.4
0.4
100kb downstr.
10kb downstr.
5kb downstr.
2kb downstr.
1kb downstr.
Exons
E2F
ETFA
PEA1
EFC
NFuE1
ICP4
APF
SRF
NFuE3
MIR
MaLR
ERVL
ERV
ERV1
ERVK
LTR
L2
L1
HAL1
FRAM
FAM
0.0
FLAM
0.1
AR
0.2
0.0
DNAElem.
1kb upstr.
0.3
0.1
Alu
Introns
0.4
CR1
Sp1
0.4
Absolute weight
0.5
0.2
2kb upstr.
0.5
0.3
10kb upstr.
100kb upstr.
Percentage
Counts
Rep. elements
+/ percentage ratio
0.0
+/ count ratio
0.0
Transc. factors
0.1
0.0
CpG islands
0.1
5kb upstr.
0.2
0.1
d
Absolute weight
0.3
PEA2
0.2
CEBP
0.2
0.3
IgPE2
0.3
Absolute weight
0.5
Absolute weight
0.5
Miscellaneous
Absolute weight
a
0.5
Supplementary Figure 1. Distributions of the weights of features characteristic of imprinted genes, as

determined by two feature selection methods, those of Equbits and SMLR. Absolute weights are shown
as box plots, the dotted line represents the overall mean of all selected features. (a) Distribution of
feature type. (b) Distribution of different ways of quantifying repetitive elements. Ratios of counts
carried the greatest weight (P < 6 1011). (c) Distribution of different repetitive element locations. The
1 kb downstream window was of least importance (P < 1 103 ). (d) Distribution of different families
of repetitive elements. Alus carried the lowest weight (P < 4 103 ), whereas endogenous retroviruses
were of greatest importance (P < 3 103). (e) Distribution of counts of the highest scoring transcription
factor binding sites.
Supplementary Table 4. Relevant features for prediction of imprinting by Equbits classifiers.

Feature
downstream 10:100 SINE Alu2
downstream 10:100 AluS2
upstream 60:0 LTR ERVL2
upstream 9:8 Sp11
upstream 100:10 AluJ2
upstream 5:4 NFuE11
downstream 0:5 MIR32
upstream 100:downstream 100 CCACGTGG within THE1B/B-int elements3
upstream 8:7 GTIIC1
upstream 3:2 Sp11
upstream 5:0 LTR ERV11
downstream 5:10 L1ME1
intron LTR ERV12
upstream 100:downstream 100 CCACGTGG within THE1B/B-int elements1
downstream 10:100 L1M42
intron CpGi2
upstream 10:9 Sp11
downstream 10:100 L1P2
downstream 10:100 SINE MIR1
upstream 50:0 L21
upstream 100:10 L1ME1
upstream 2:1 PEA21
upstream 5:4 AP11 downstream 0:100 MLT1C phase change2
downstream 5:10 L1PB1
upstream 100:10 DNA Tip1001 upstream 6:5 GTIIC3
upstream 4:3 PEA11
upstream 100:10 AluJ1
intron LTR ERV11
downstream 5:10 L1MC2
upstream 100:10 L1MA1
upstream 6:5 SIF3 upstream 2:0 BPVE23
upstream 9:8 CEBP1
downstream 40:100 LTR ERV11
exon 0.225:0.41 nucleosome potential 2
upstream 3:2 Sp13
downstream 5:10 Alu2
upstream 100:10 MIR31
upstream 3:2 BPVE21 upstream 1:0 Pit13
upstream 30:20 CpGi2,10
upstream 100:10 L1MC1
upstream 8:7 EFC1
upstream 8:7 GT2B1 upstream 9:8 Sp13
upstream 9:8 Sp13 upstream 8:7 GT2B3
downstream 5:10 LINE L22
upstream distance to closest recomb. hotspot
upstream 100:10 L1M42 upstream 1:0 MLTF3
upstream 8:7 SIF3 upstream 5:0 ETFA3
upstream 5:0 LINE CR12
intron L1M21
upstream 9:8 MLTF3
upstream 0.83:0.61 nucleosome potential 1
downstream 5:10 DNA MER2 type2
downstream 5:10 CpGi1 upstream 10:9 NFuE53
upstream 7:6 NFuE53
upstream 8:7 ICP41
upstream 4:3 PEA21
upstream 100:10 DNA Tip1001 upstream 3:2 Pit13
downstream 0:100 MLT1A0 phase change1
upstream 1:0 BPVE21 upstream 10:9 NFuE53
upstream 9:8 MLTF1
upstream 7:6 NFuE41
upstream 100:10 DNA Tip1002
upstream 9:8 CEBP3
upstream 2:0 Oct13
upstream 10:9 GT2B1 upstream 3:2 Pit13
downstream 5:10 AluY2
upstream 2:0 CpGi1 upstream 9:8 E4F13
upstream 8:7 GTIIC3
Weight
16.96
11.28
10.08
9.75
9.16
9.14
8.89
8.86
8.73
8.59
8.58
8.57
8.39
8.27
8.22
8.17
8.15
8.14
8.13
7.97
7.94
7.91
7.89
7.84
7.79
7.77
7.65
7.6
7.57
7.53
7.5
7.36
7.31
7.29
7.26
7.22
7.17
7.08
7.07
7.06
7.02
6.98
6.96
6.87
6.86
6.82
6.8
6.79
6.78
6.76
6.75
6.73
6.71
6.62
6.59
6.57
6.55
6.54
6.52
6.51
6.47
6.45
6.44
6.43
6.42
6.37
6.32
6.31
6.29
6.24
6.22
6.18
6.17
6.12
6.11
6.08
6.07
Mean (Standard deviation)

All Genes
Imprinted
4.11
(61.50)
1.68
(0.81)
16.89
(162.70)
161.12
(557.13)
11.31
(21.28)
34.03
(55.48)
0.34
(1.09)
0.15
(0.53)
61.09
(228.98)
193.30
(372.53)
0.04
(0.21)
0.13
(0.33)
0.33
(0.99)
0.45
(1.34)
0.13
(0.33)
0.30
(0.46)
0.34
(0.61)
0.53
(0.78)
0.36
(1.13)
0.93
(1.40)
0.36
(1.07)
0.58
(2.11)
0.01
(0.99)
0.28
(1.18)
173.80
(743.12)
617.58
(1711.93)
0.15
(0.43)
0.43
(0.78)
0.70
(1.11)
1.45
(1.77)
44.47
(86.92)
102.33
(186.25)
0.34
(1.11)
0.30
(0.61)
0.31
(1.06)
0.14
(0.58)
0.11
(2.25)
0.41
(2.31)
0.29
(2.90)
1.05
(4.42)
0.29
(4.79)
1.72
(3.94)
0.02
(0.15)
0.05
(0.22)
0.77
(2.32)
0.03
(0.16)
0.14
(0.41)
0.18
(0.50)
0.04
(0.29)
0.13
(0.56)
0.18
(0.72)
0.00
(0.00)
0.01
(0.41)
0.10
(0.44)
0.10
(0.32)
0.13
(0.40)
0.27
(2.37)
1.17
(2.83)
0.49
(2.02)
1.75
(4.90)
71.64
(271.78)
129.05
(386.82)
0.07
(2.70)
1.13
(3.64)
0.13
(0.33)
0.00
(0.00)
0.04
(0.20)
0.10
(0.38)
0.59
(2.87)
1.95
(6.14)
0.67
(0.92)
0.10
(1.06)
0.21
(0.41)
0.43
(0.50)
0.01
(0.06)
0.01
(0.09)
0.14
(1.84)
0.51
(1.74)
0.14
(0.44)
0.00
(0.00)
0.13
(0.28)
0.17
(0.35)
459.12
(1253.59)
183.25
(433.61)
0.24
(4.23)
1.23
(5.64)
0.00
(0.04)
0.03
(0.16)
0.11
(0.44)
0.00
(0.00)
0.08
(0.27)
0.00
(0.00)
106.50
(243.27)
116.37
(272.10)
315.02
(1369.12)
122.40
(94.52)
229.05
(605.18)
25.45
(91.09)
0.06
(0.24)
0.00
(0.00)
12.41
(69.05)
38.48
(121.07)
0.05
(0.37)
0.00
(0.00)
0.34
(0.85)
0.03
(0.16)
0.57
(0.50)
0.70
(0.46)
0.23
(0.69)
0.01
(0.08)
0.16
(0.50)
0.00
(0.00)
182.33
(154.05)
102.79
(169.84)
0.78
(2.85)
1.29
(3.87)
46.30
(230.76)
190.05
(602.01)
0.12
(0.44)
0.00
(0.00)
0.28
(0.45)
0.35
(0.48)
0.10
(0.37)
0.00
(0.00)
0.05
(0.24)
0.03
(0.16)
0.02
(0.13)
0.10
(0.30)
0.29
(0.89)
0.00
(0.00)
0.40
(0.86)
0.83
(1.03)
0.12
(0.40)
0.00
(0.00)
0.91
(1.13)
1.23
(1.10)
0.04
(0.21)
0.05
(0.22)
90.37
(251.03)
69.05
(309.29)
0.04
(0.19)
0.08
(0.27)
0.61
(0.49)
0.73
(0.45)
0.17
(0.49)
0.00
(0.00)
80.80
(155.01)
145.40
(217.27)
0.12
(2.35)
0.23
(2.46)
0.07
(0.26)
0.00
(0.00)
0.28
(0.45)
0.38
(0.49)
P
4.76 109
5.70 102
7.28 103
1.64 102
1.63 102
6.88 102
2.91 101
1.31 102
7.02 102
8.41 103
2.68 101
6.79 102
5.68 102
1.70 102
5.85 103
2.98 102
3.46 101
3.61 102
8.33 102
1.47 101
1.42 103
2.18 101
0
3.43 101
1.75 101
0
1.01 101
3.50 101
2.73 102
5.78 102
1.80 101
3.81 102
0
1.64 101
8.60 102
2.65 105
5.46 103
3.05 101
9.53 102
0
2.47 101
1.56 104
1.40 101
1.82 101
0
0
4.11 101
0
0
0
9.33 102
0
5.55 1016
4.03 102
0
0
2.87 103
2.06 101
7.20 102
0
1.73 101
0
1.58 101
4.92 102
0
7.45 103
0
4.28 102
3.85 101
3.35 101
1.99 101
5.29 102
0
3.55 102
1.84 101
0
1.05 101
downstream 10:100 FLAM2 upstream 10:9 ATF1

upstream 6:5 ATF3
upstream 9:8 Sp13 upstream 1:0 ICSBP3
upstream 7:6 NFkB3
upstream 100:10 HAL12 upstream 9:8 TFIID3
upstream 2:0 MIR2 upstream 8:7 GT2B3
downstream 10:100 DNA1 upstream 10:9 PU13
exon LINE L21
upstream 100:10 DNA Tip1001 upstream 8:7 ICSBP3
upstream 2:0 L1M21
upstream 100:10 L1P1
downstream 5:10 LTR ERVK1
downstream 0:1 CpGi1
upstream 100:10 HAL11 upstream 8:7 GT2B1
downstream 10:100 MIR32 upstream 4:3 GATA11
downstream 10:100 L1MB2
upstream 2:0 MIR1 upstream 8:7 GT2B3
upstream 100:10 DNA2
upstream 9:8 Sp13 upstream 10:0 CpGi1,11
upstream 2:1 SIF3
downstream 0:100 LTR phase change2,99
upstream 10:5 L1MC2
upstream 4:3 E2F1
upstream 2:0 SINE MIR2 upstream 8:7 GT2B3
upstream 1:0 CP13
downstream 0:5 DNA Tip1002
downstream 10:100 L1MC1 downstream 0:100 MLT1C phase change2
intron CpGi3
intron CpGi1
downstream 0:2 AluY1 upstream 10:9 MLTF3
upstream 9:8 PEA21
upstream 350:350 downstream recomb1
downstream 5:10 DNA MER1 type1 upstream 3:2 Pit13
upstream 10:5 LTR MaLR2 upstream 6:5 APF3
upstream 9:8 ATF3 upstream 5:4 NFuE53
upstream 100:10 L1PB2
downstream 5:10 L1MD1
downstream 0:2 MIR2
upstream 5:0 PEA23
upstream 9:8 Sp11 upstream 1:0 ICSBP3
downstream 5:10 LINE L22
upstream 100:10 L1MB2 upstream 5:4 ATF3
intron DNA1
intron MIR32 upstream 4:3 TFIID1
downstream 10:100 MIR32 upstream 4:3 GATA13
upstream 2:0 LINE L21 upstream 5:4 GATA13
upstream 9:8 NFkB1
upstream 10:9 NFuE53 upstream 1:0 BPVE23
I5 downstream 10:100 DNA Mariner1
upstream 2:0 LINE L22
downstream 5:10 CpGi1 upstream 10:9 NFuE51
downstream 10:100 FLAM2 upstream 10:9 ATF3
upstream 7:6 NFkB1
upstream 5:0 L1M21
downstream 10:100 DNA Mariner1 upstream 3:2 MLTF3
downstream 50:90 LTR ERVL1
upstream 90:20 MIR1
upstream 6:5 PEA13
upstream 2:1 Oct13
upstream 8:7 E4F11
downstream 10:100 DNA2
downstream 10:100 L1MC1 downstream 0:100 MLT1C phase change2
downstream 10:100 DNA1
upstream 4:3 E4F13
upstream 3:2 NFuE31
6.06
6.05
6.03
6.01
6
5.95
5.92
5.86
5.85
5.83
5.82
5.79
5.78
5.74
5.71
5.7
5.68
5.66
5.65
5.64
5.61
5.58
5.57
5.55
5.53
5.49
5.48
5.47
5.46
5.45
5.43
5.42
5.41
5.4
5.39
5.37
5.36
5.35
5.33
5.32
5.28
5.27
5.26
5.25
5.24
5.23
5.21
5.2
5.19
5.18
5.17
5.16
5.15
5.12
5.11
5.08
5.07
5.06
5.05
5.04
5.03
5.02
5.01
4.98
4.97
4.96
4.95
4.94
4.93
4.92
4.91
4.9
4.89
4.88
4.86
4.85
4.84
4.83
4.82
4.81
4.8
34.06
0.36
0.50
0.36
0.26
0.14
0.08
141.37
0.79
0.23
0.00
0.53
0.09
0.00
0.42
0.00
0.04
0.49
48.09
0.03
1.24
0.12
45.51
0.38
0.66
0.24
0.29
1.00
0.09
0.77
0.01
0.93
0.07
0.10
1.96
2.26
0.08
0.47
0.07
0.02
4.84
0.15
94.23
0.11
0.49
0.00
1.73
0.12
0.24
1.52
188.41
0.00
16.59
33.26
0.14
0.08
0.10
0.05
0.17
2.88
0.15
25.49
0.01
0.08
0.00
2.65
0.23
0.43
0.21
0.07
0.10
0.42
0.20
0.06
0.59
0.02
0.18
0.01
0.03
0.77
0.08
(129.03)
(0.85)
(2.39)
(0.48)
(1.42)
(0.35)
(0.27)
(392.44)
(2.90)
(0.66)
(0.23)
(1.14)
(0.27)
(0.10)
(0.96)
(0.26)
(0.19)
(1.88)
(147.61)
(0.27)
(1.54)
(0.45)
(150.10)
(1.24)
(1.70)
(0.43)
(0.28)
(2.50)
(0.32)
(2.82)
(0.11)
(3.19)
(0.25)
(1.02)
(5.89)
(2.27)
(0.27)
(1.10)
(0.30)
(0.14)
(2.75)
(0.53)
(233.79)
(0.31)
(1.48)
(0.47)
(3.99)
(0.32)
(0.93)
(3.00)
(642.54)
(0.50)
(66.36)
(88.69)
(0.48)
(0.29)
(0.30)
(2.87)
(0.57)
(7.56)
(0.63)
(84.33)
(0.36)
(0.29)
(0.16)
(3.61)
(0.64)
(1.55)
(2.27)
(0.36)
(0.29)
(0.49)
(0.49)
(0.17)
(1.67)
(0.80)
(0.38)
(1.05)
(0.68)
(1.14)
(0.29)
0.22
0.45
1.90
0.48
0.77
0.00
0.15
13.28
0.00
0.00
0.05
0.08
0.01
0.03
0.28
0.15
0.03
0.03
1.72
0.15
1.67
0.00
99.38
0.83
0.08
0.28
0.40
0.10
0.00
0.57
0.00
0.00
0.03
0.00
0.13
2.93
0.28
1.05
0.00
0.03
6.15
0.00
3.92
0.00
0.69
0.00
1.80
0.25
0.00
1.65
6.87
0.15
1.43
1.62
0.00
0.13
0.00
0.79
0.00
3.35
0.00
0.22
0.10
0.15
0.03
2.50
0.00
1.19
0.85
0.20
0.18
0.50
0.45
0.02
0.06
0.10
0.20
0.13
0.23
0.40
0.15
(0.62)
(1.30)
(6.02)
(0.51)
(2.42)
(0.00)
(0.36)
(47.90)
(0.00)
(0.00)
(0.22)
(0.27)
(0.04)
(0.16)
(0.55)
(0.95)
(0.16)
(0.16)
(9.34)
(0.95)
(2.02)
(0.00)
(312.29)
(1.89)
(0.27)
(0.45)
(0.27)
(0.38)
(0.00)
(2.26)
(0.00)
(0.00)
(0.16)
(0.00)
(0.40)
(2.55)
(0.45)
(1.52)
(0.00)
(0.16)
(2.18)
(0.00)
(23.86)
(0.00)
(1.89)
(0.45)
(4.79)
(0.44)
(0.00)
(3.31)
(40.74)
(0.58)
(6.31)
(9.32)
(0.00)
(0.40)
(0.00)
(3.97)
(0.00)
(10.80)
(0.00)
(0.62)
(0.50)
(0.36)
(0.16)
(3.07)
(0.00)
(2.30)
(2.69)
(0.46)
(0.38)
(0.51)
(1.45)
(0.05)
(0.20)
(0.50)
(0.41)
(1.02)
(0.58)
(0.50)
(0.43)
0
3.28
7.69
7.39
9.71
0
1.14
0
0
0
8.77
1.61
0
1.82
6.08
1.64
2.86
0
0
2.23
9.54
0
1.44
7.35
0
3.22
1.09
0
0
2.83
0
0
5.73
0
0
5.61
5.48
1.10
0
4.06
2.96
0
0
0
2.64
5.00
4.63
3.12
0
3.99
0
5.62
0
0
0
2.45
0
1.26
0
3.93
0
0
9.50
1.27
1.94
3.82
0
2.34
7.48
5.03
1.01
1.62
1.49
2.98
0
1.56
3.77
2.47
2.01
2.14
1.49
101
102
102
102
101
102
1013
101
102
101
101
101
102
101
102
101
102
101
102
102
103
102
101
104
101
101
101
102
101
102
101
101
101
102
101
101
101
102
102
102
101
101
101
106
101
101
101
102
105
101

exon DNA MER2 type2
upstream 1:0 NFkB3
I5 upstream 2:1 BPVE23
upstream 2:0 DNA MER1 type1 upstream 6:5 AP13
upstream 5:4 SIF3 upstream 4:3 PU13
downstream 5:10 L1PA2
upstream 9:8 SIF3 m3 m11
upstream 2:0 CpGi2
downstream 10:100 DNA MER1 type2 upstream 10:5 LTR MaLR2
upstream 100:10 HAL11 upstream 8:7 GT2B3
downstream 10:100 Other2
upstream 6:5 NF13
downstream 10:100 FLAM2 upstream 100:10 MIR32
upstream 2:1 MLTF1
upstream 100:10 L1M11
upstream 5:0 LTR MaLR2
upstream 10:5 LTR MaLR2 upstream 100:10 LINE L22
upstream 10:0 ETFA1 upstream 10:9 E4F13
upstream 3:2 APF1 downstream 0:100 MLT1C phase change2
upstream 10:5 LTR MaLR2 upstream 10:9 COUP3
upstream 3:2 Oct13 downstream 0:100 MLT1C phase change2
downstream 0:5 FRAM1
downstream 10:100 CpGi3 upstream 100:10 L1MB2
downstream 10:100 DNA Mariner1 upstream 10:0 ETFA3
downstream 35:68 L21
upstream 7:6 E2F1
upstream 5:4 NFuE51 upstream 9:8 ATF3
upstream 10:0 NFkB1
exon L12
upstream 10:9 E4F13 upstream 3:2 MLTF3
upstream 6:5 MLTF3
upstream 8:7 BPVE23 upstream 8:7 SIF3
upstream 8:7 MLTF1
downstream 10:100 HAL11
upstream 6:5 ATF1
upstream 2:0 LINE L21 upstream 5:4 GATA11
upstream 100:10 DNA Mariner1
upstream 2:0 DNA MER1 type1 upstream 10:9 AP13
intron DNA Tip1001
upstream 9:8 GATA13 downstream 0:100 MLT1C phase change2
upstream 6:5 APF3 upstream 5:4 E4F13
upstream 10:9 NFuE51 upstream 10:0 NFuE33
upstream 10:9 E4F11 upstream 9:8 PU13
upstream 10:5 SINE MIR2 upstream 7:6 BPVE23
intron DNA Tip1001
upstream 100:10 HAL12 upstream 9:8 TFIID1
upstream 10:9 E4F11 upstream 10:0 ETFA3
upstream 2:0 DNA MER1 type2
upstream 10:9 NFuE51 upstream 1:0 BPVE23
upstream 100:10 L1MB1
upstream 100:10 LTR ERV11 upstream 10:0 NFuE43
upstream 7:6 CP11
upstream 100:10 L1MD1
upstream 2:1 AP21
downstream 10:100 DNA Tc21
upstream 9:8 ATF1 upstream 5:4 NFuE51
upstream 6:5 GT2B1
downstream 10:100 DNA Mariner1 upstream 1:0 ATF1
upstream 100:10 DNA2
upstream 10:9 E4F13 upstream 3:2 GATA13
upstream 10:5 LTR MaLR2 upstream 3:2 AP13
upstream 4:3 NFuE53 upstream 4:3 Pit13
4.78
4.76
4.75
4.74
4.73
4.72
4.71
4.7
4.68
4.67
4.66
4.63
4.62
4.61
4.59
4.57
4.56
4.55
4.53
4.52
4.51
4.5
4.49
4.48
4.47
4.46
4.45
4.44
4.43
4.42
4.41
4.4
4.39
4.38
4.37
4.36
4.35
4.34
4.33
4.32
4.31
4.3
4.29
4.28
4.27
4.26
4.25
4.24
4.23
4.22
4.21
4.2
4.19
4.18
4.17
4.15
4.14
4.13
4.12
4.11
4.1
4.09
4.08
4.07
4.06
4.05
4.04
4.03
4.02
4.01
4
3.99
3.98
3.97
3.96
3.95
3.94
3.93
3.92
3.9
3.89
2.06
0.18
0.11
0.16
0.11
34.74
0.12
0.00
2.70
0.09
152.21
128.89
231.39
0.37
0.28
0.19
0.12
47.19
5099.30
0.96
0.04
87.69
315.39
3.62
0.01
0.34
0.14
0.05
1.01
1.26
0.05
0.00
286.48
0.17
0.52
0.01
0.13
0.85
0.03
0.10
0.57
0.11
0.09
0.90
0.03
1.02
0.49
0.20
0.41
0.11
0.41
0.12
112.34
0.19
2.52
0.06
0.15
0.17
0.12
0.35
23.93
0.00
0.00
264.58
0.11
19.25
0.12
3.70
2.12
0.05
0.04
0.42
0.01
0.11
0.19
0.44
0.35
0.06
0.08
91.79
0.10
(4.34)
(2.98)
(0.31)
(0.37)
(0.40)
(150.24)
(0.32)
(0.56)
(10.90)
(0.29)
(161.47)
(371.35)
(1001.15)
(1.26)
(0.92)
(0.60)
(0.33)
(117.94)
(18824.72)
(1.06)
(0.87)
(215.92)
(889.70)
(3.92)
(1.37)
(0.81)
(0.48)
(1.24)
(2.96)
(2.92)
(0.18)
(0.23)
(761.12)
(0.55)
(2.58)
(0.10)
(0.43)
(0.98)
(1.56)
(0.30)
(0.50)
(0.43)
(0.28)
(1.08)
(1.92)
(1.55)
(0.78)
(0.75)
(0.83)
(0.40)
(1.56)
(0.64)
(241.50)
(0.76)
(10.32)
(0.18)
(0.35)
(0.48)
(0.38)
(3.49)
(74.12)
(0.59)
(0.66)
(860.20)
(0.38)
(74.01)
(0.42)
(3.98)
(5.53)
(0.26)
(2.40)
(0.82)
(0.63)
(2.47)
(0.74)
(0.77)
(1.23)
(0.17)
(0.27)
(229.88)
(0.30)
2.02
2.21
0.08
0.00
0.00
60.40
0.00
0.18
2.43
0.00
222.15
6.60
179.41
0.03
0.10
0.06
0.18
54.10
54.26
1.10
0.23
64.15
25.95
4.08
0.03
0.23
0.00
0.30
0.05
0.12
0.00
0.05
22.01
0.00
0.98
0.05
0.00
1.08
0.17
0.00
0.63
0.00
0.00
1.20
0.44
0.58
0.63
0.00
0.23
0.00
0.11
0.18
164.27
0.10
0.41
0.00
0.00
0.00
0.00
1.46
0.02
0.00
0.18
17.11
0.00
2.20
0.00
4.38
0.18
0.08
0.06
0.90
0.03
0.58
0.00
0.70
0.00
0.10
0.00
0.15
0.00
(4.90)
(10.17)
(0.27)
(0.00)
(0.00)
(234.23)
(0.00)
(0.78)
(10.47)
(0.00)
(212.49)
(32.09)
(978.02)
(0.16)
(0.38)
(0.27)
(0.38)
(122.05)
(133.79)
(1.22)
(0.97)
(132.75)
(109.14)
(3.86)
(1.05)
(0.62)
(0.00)
(1.32)
(0.22)
(0.57)
(0.00)
(0.22)
(95.07)
(0.00)
(2.07)
(0.22)
(0.00)
(1.02)
(1.09)
(0.00)
(0.49)
(0.00)
(0.00)
(1.86)
(2.23)
(0.76)
(0.81)
(0.00)
(0.58)
(0.00)
(3.58)
(0.66)
(305.43)
(0.38)
(1.91)
(0.00)
(0.00)
(0.00)
(0.00)
(6.49)
(0.14)
(0.39)
(0.75)
(63.06)
(0.00)
(13.91)
(0.00)
(4.80)
(0.50)
(0.27)
(2.73)
(1.46)
(0.66)
(1.90)
(0.00)
(0.94)
(0.00)
(0.31)
(0.00)
(0.65)
(0.00)
4.80 101
1.09 101
2.33 101
0
0
2.49 101
0
8.61 102
4.37 101
0
2.33 102
0
3.71 101
0
3.00 103
1.37 103
2.00 101
3.63 101
0
2.34 101
4.79 102
1.38 101
0
2.31 101
4.63 101
1.21 101
0
1.23 101
0
7.77 1016
0
8.06 102
0
0
8.56 102
1.35 101
0
9.27 102
2.13 101
0
2.44 101
0
0
1.60 101
1.29 101
4.61 104
1.43 101
0
2.43 102
0
1.84 101
2.84 101
1.48 101
7.26 102
1.65 108
0
0
0
0
1.45 101
0
4.73 101
7.32 102
0
0
1.34 109
0
1.93 101
0
2.84 101
4.09 101
2.38 102
4.34 101
6.53 102
0
4.81 102
0
2.08 101
0
0
0
upstream 10:9 GT2B1 upstream 1:0 MLTF1

downstream 10:100 DNA Mariner1 upstream 1:0 TFIID3
exon LINE L21
upstream 1:0 NFuE31
upstream 10:9 GTIIC3 upstream 4:3 BPVE23
upstream 7:6 COUP3 upstream 2:1 E4TF13
upstream 5:4 GATA13 downstream 0:100 MLT1C phase change2
upstream 2:1 BPVE23 upstream 5:0 ETFA3
upstream 2:0 LINE L21 upstream 7:6 Pit13
upstream 2:1 TFIID3 downstream 0:100 MLT1C phase change2
upstream 7:6 Sp13
upstream 7:6 GTIIC3 upstream 5:0 CP13
upstream 2:1 SRF1
upstream 4:3 Pit13 downstream 0:100 MLT1C phase change2
upstream 2:0 E4TF11
upstream 9:8 NFuE51 upstream 6:5 Oct13
upstream 7:6 SIF3
upstream 5:4 E4F11 upstream 6:5 APF3
upstream 7:6 AP13 upstream 2:1 E4TF13
upstream 4:3 CEBP3
upstream 5:0 L1M2
upstream 10:5 MIR31
downstream 0:5 FAM1
downstream 5:10 L1MD2
upstream 3:2 Pit11 upstream 7:6 BPVE23
downstream 0:2 FLAM1
upstream 2:0 SINE MIR2 upstream 8:7 GT2B3
upstream 2:0 DNA MER1 type1 upstream 8:7 ICSBP3
upstream 6:5 ETFA3
downstream 0:1 L1M1
downstream 0:100 MLT1C phase change2
upstream 10:0 GTIIC3 upstream 10:0 Oct13
upstream 9:8 Sp13
upstream 10:5 AluJ2 upstream 10:0 CP13
upstream 100:10 L1P2
upstream 6:5 AP23 upstream 3:2 Pit13
upstream 100:10 L1MB1
downstream 10:100 FRAM2 upstream 8:7 SIF3
upstream 4:3 ETFA1
upstream 6:5 PU11
upstream 1:0 L1MA1
upstream 2:1 NFIII1 upstream 10:9 E4F13
ditan10kup
upstream 2:0 NFkB3
upstream 10:0 IgPE21
upstream 9:8 GATA13 upstream 2:0 NFkB3
upstream 4:3 PU11
upstream 10:5 LTR MaLR2 upstream 1:0 MLTF3
upstream 2:1 E4TF13 upstream 10:0 NFuE53
upstream 10:5 L1M31
upstream 10:9 E4F13 upstream 3:2 TFIID3
upstream 9:8 GATA11
upstream 10:9 SIF1
upstream 100:10 HAL12
upstream 2:0 LINE L21 upstream 6:5 Oct13
upstream 9:8 APF1
upstream 10:5 DNA AcHobo2
upstream 3:2 SIF3 upstream 5:0 NFkB3
upstream 10:0 IgPE23
3.88
3.87
3.86
3.85
3.84
3.83
3.82
3.81
3.8
3.79
3.78
3.77
3.76
3.75
3.73
3.72
3.71
3.7
3.69
3.68
3.67
3.66
3.65
3.63
3.62
3.61
3.6
3.59
3.58
3.57
3.56
3.55
3.54
3.53
3.52
3.51
3.5
3.49
3.48
3.47
3.46
3.45
3.44
3.43
3.42
3.41
3.4
3.39
3.38
3.37
3.36
3.35
3.34
3.33
3.32
3.31
3.3
3.29
3.28
3.27
3.26
3.25
3.24
3.23
3.22
3.21
3.2
3.19
3.18
3.17
3.16
3.15
3.14
3.13
3.12
3.11
3.1
3.09
3.08
3.07
3.06
0.58
0.21
0.06
0.04
0.05
0.10
0.06
32.24
0.19
0.11
0.13
0.24
0.20
0.00
0.06
0.13
0.02
0.18
0.21
0.14
2.32
0.32
0.22
0.17
0.06
0.11
2.76
0.04
0.01
0.14
0.01
26.33
0.25
0.00
13.67
0.10
0.06
0.00
0.22
0.12
0.92
0.20
0.78
5.05
44.66
230.89
0.35
0.09
0.14
6.24
18.57
0.06
0.89
53.61
0.01
0.10
0.36
23.10
0.18
0.20
0.08
0.18
0.37
0.88
68.32
0.07
0.01
0.11
0.10
0.68
0.27
221.71
1.06
0.13
2.42
0.01
0.06
0.08
71.24
60.96
0.18
(1.54)
(0.62)
(0.37)
(0.24)
(0.24)
(0.30)
(0.25)
(145.71)
(0.65)
(0.31)
(0.46)
(0.73)
(0.40)
(0.28)
(0.24)
(0.44)
(0.13)
(0.63)
(0.48)
(0.42)
(2.09)
(0.66)
(0.41)
(0.50)
(0.25)
(0.31)
(3.56)
(0.19)
(0.21)
(0.41)
(0.13)
(197.25)
(0.77)
(0.22)
(50.16)
(0.39)
(0.23)
(0.02)
(0.47)
(0.25)
(0.26)
(0.40)
(2.91)
(8.09)
(129.92)
(832.85)
(0.83)
(0.28)
(3.76)
(7.74)
(67.07)
(0.24)
(1.05)
(230.70)
(0.12)
(0.30)
(1.09)
(54.47)
(0.38)
(0.46)
(0.27)
(0.64)
(0.69)
(1.04)
(203.70)
(0.25)
(0.14)
(0.31)
(2.33)
(0.89)
(0.65)
(473.89)
(1.45)
(0.47)
(1.99)
(0.37)
(0.51)
(0.27)
(118.59)
(281.86)
(0.38)
0.08
0.00
0.00
0.05
0.03
0.00
0.00
13.18
0.00
0.00
0.00
0.00
0.35
0.03
0.00
0.03
0.00
0.00
0.13
0.00
2.48
0.25
0.30
0.00
0.00
0.00
3.03
0.10
0.06
0.08
0.00
24.09
0.00
0.03
0.00
0.00
0.10
0.03
0.25
0.06
1.00
0.10
0.03
5.06
2.10
61.10
0.28
0.00
0.51
6.30
0.07
0.10
1.10
98.35
0.00
0.00
0.00
15.50
0.13
0.25
0.00
0.00
0.50
1.13
0.08
0.00
0.08
0.00
0.31
0.78
0.28
119.00
1.89
0.00
1.65
0.08
0.22
0.00
35.53
84.80
0.23
(0.27)
(0.00)
(0.00)
(0.22)
(0.16)
(0.00)
(0.00)
(70.83)
(0.00)
(0.00)
(0.00)
(0.00)
(0.48)
(0.58)
(0.00)
(0.16)
(0.00)
(0.00)
(0.46)
(0.00)
(1.97)
(0.59)
(0.46)
(0.00)
(0.00)
(0.00)
(3.09)
(0.30)
(0.36)
(0.27)
(0.00)
(152.26)
(0.00)
(0.16)
(0.00)
(0.00)
(0.30)
(0.16)
(0.49)
(0.20)
(0.00)
(0.30)
(0.16)
(8.30)
(13.28)
(160.04)
(0.64)
(0.00)
(3.60)
(7.51)
(0.36)
(0.30)
(1.19)
(454.18)
(0.00)
(0.00)
(0.00)
(23.28)
(0.33)
(0.49)
(0.00)
(0.00)
(0.75)
(1.20)
(0.51)
(0.00)
(0.47)
(0.00)
(3.55)
(1.07)
(0.55)
(233.60)
(2.96)
(0.00)
(1.48)
(0.27)
(1.24)
(0.00)
(72.54)
(423.47)
(0.42)
5.88 1015
0
0
3.73 101
1.31 101
0
0
5.09 102
0
0
0
0
2.81 102
3.95 101
0
7.19 105
0
0
1.32 101
0
3.14 101
2.16 101
1.31 101
0
0
0
2.95 101
9.64 102
1.96 101
6.80 102
0
4.64 101
0
2.08 101
0
0
1.85 101
1.66 101
3.67 101
3.07 102
0
2.67 102
0
4.97 101
0
3.76 108
2.33 101
0
1.35 101
4.80 101
0
1.96 101
1.34 101
2.71 101
0
0
0
2.46 102
1.64 101
2.73 101
0
0
1.44 101
1.09 101
0
0
1.96 101
0
3.63 101
2.88 101
4.59 101
4.63 103
4.46 102
0
1.18 103
3.23 102
2.09 101
0
1.95 103
3.64 101
2.59 101
downstream 10:100 LINE CR11 upstream 3:2 Pit13

upstream 2:0 NFkB1 upstream 5:4 TFIID3
upstream 1:0 SRF1
upstream 10:5 LINE L11 downstream 0:100 MLT1C phase change2
upstream 5:0 CpGi2
upstream 4:3 SIF1
downstream 5:10 DNA AcHobo1
downstream 0:2 LINE L21 upstream 8:7 ICSBP1
upstream 9:8 SIF1 upstream 1:0 ATF3
upstream 8:7 NFkB3
upstream 4:3 IgPE21
Motif9
7
upstream 2:0 ETFA3 downstream 0:100 MIR phase change2
upstream 9:8 NFuE51
upstream 6:5 AP21
upstream 5:4 TFIID1 upstream 2:0 NFkB3
downstream 10:100 FRAM2 upstream 5:0 GATA11
downstream 10:100 LINE CR12 upstream 100:10 MIR31
upstream 4:3 BPVE23 downstream 0:100 MLT1C phase change2
upstream 5:0 L1PA1
upstream 10:5 DNA MER1 type2 upstream 5:4 Pit13
downstream 10:100 AluJ1
downstream 10:100 LINE CR11 upstream 9:8 TFIID3
upstream 2:0 SINE MIR2 upstream 10:9 BPVE23
upstream 9:8 TFIID3 upstream 2:0 ICP43
upstream 2:1 BPVE21 upstream 6:5 Pit13
exon CpGi2
upstream 100:10 FAM2 upstream 6:5 Pit13
downstream 5:10 AluS2 upstream 1:0 MLTF3
upstream 2:0 PEA21
upstream 3:2 ICP43
upstream 100:10 SINE MIR1
upstream 10:5 FAM1
upstream 10:5 L1PB2
upstream 5:0 LTR ERV12 upstream 4:3 TFIID3
upstream 100:10 CpGi1 upstream 100:10 AluS2
upstream 2:0 Sp13
upstream 8:7 AP13 upstream 7:6 NF13
upstream 8:7 GT2B1 upstream 5:4 NFuE53
downstream 0:1 LINE CR12
downstream 0:5 AluS1 upstream 3:2 TFIID1
upstream 100:10 AluJ2 upstream 10:9 NFuE53
upstream 2:0 NFuE33
upstream 1:0 PU11
upstream 100:10 CpGi1 upstream 100:10 SINE Alu2
upstream 10:5 Alu1
downstream 10:100 CpGi3 upstream 2:0 PEA11
upstream 2:0 NFuE31
upstream 8:7 SRF1
upstream 7:6 APF3
upstream 1:0 MLTF1
downstream 10:100 DNA Mariner1 upstream 9:8 Pit11
downstream 0:5 LTR MaLR1 upstream 2:0 BPVE21
upstream 100:10 DNA Tc22
upstream 100:10 AluJ2 upstream 10:9 E4F11
upstream 7:6 NF11 upstream 7:6 AP13
upstream 5:4 E4F13 upstream 1:0 MLTF3
upstream 4:3 TFIID3 downstream 0:100 MLT1C phase change2
downstream 10:100 LINE CR12 upstream 100:10 DNA MER1 type1
upstream 10:5 LTR MaLR2 upstream 1:0 MLTF1
upstream 4:3 AP11 upstream 5:4 E4F13
upstream 9:8 ICSBP1
upstream 2:0 ETFA1 upstream 10:9 MLTF3
upstream 10:5 L1PA1
upstream 10:5 FRAM2
upstream 1:0 NFuE53
upstream 2:0 MIR2 upstream 10:9 BPVE23
3.05
3.04
3.03
3.02
3.01
3
2.99
2.98
2.97
2.96
2.95
2.94
2.93
2.92
2.91
2.9
2.89
2.88
2.87
2.86
2.85
2.84
2.83
2.82
2.81
2.8
2.79
2.78
2.77
2.76
2.75
2.74
2.73
2.72
2.71
2.7
2.69
2.68
2.67
2.66
2.65
2.64
2.63
2.62
2.61
2.6
2.59
2.58
2.57
2.56
2.55
2.54
2.53
2.52
2.51
2.5
2.49
2.48
2.47
2.46
2.45
2.44
2.43
2.42
2.41
2.4
2.39
2.38
2.37
2.36
2.35
2.34
2.33
2.32
2.31
2.3
2.29
2.28
2.27
2.26
0.58
0.12
0.01
0.61
91.87
0.27
0.07
0.00
0.00
0.32
0.15
0.07
0.02
0.00
0.06
0.34
0.03
0.38
0.20
235.74
0.77
0.04
0.35
0.14
0.01
2.85
0.17
0.28
0.08
0.84
1.03
0.08
0.21
161.59
0.02
3.47
0.07
0.05
0.10
0.00
0.15
58.25
37.02
0.86
0.62
0.10
0.13
0.19
1.83
1.11
0.11
0.26
1.00
0.01
60.28
0.02
0.08
0.12
0.01
0.83
1.23
0.38
0.33
0.37
0.04
0.72
0.11
601.34
0.12
0.25
1.70
129.34
0.33
1.50
0.10
0.12
8.63
0.00
0.20
0.88
(1.31)
(0.37)
(0.12)
(2.34)
(92.76)
(0.68)
(1.61)
(0.26)
(0.22)
(1.07)
(0.49)
(0.26)
(0.14)
(0.17)
(0.16)
(0.63)
(0.24)
(0.79)
(0.72)
(440.52)
(1.91)
(0.16)
(0.80)
(0.41)
(0.35)
(3.93)
(2.41)
(1.09)
(2.42)
(1.50)
(3.37)
(0.27)
(0.52)
(186.01)
(0.06)
(5.11)
(0.28)
(0.22)
(2.22)
(0.13)
(1.51)
(241.18)
(53.50)
(1.21)
(0.49)
(0.29)
(0.45)
(2.17)
(3.74)
(2.27)
(0.31)
(1.08)
(1.09)
(0.38)
(85.57)
(0.16)
(0.32)
(0.38)
(0.12)
(0.37)
(1.32)
(0.86)
(1.34)
(1.23)
(0.13)
(2.14)
(0.36)
(769.54)
(0.32)
(0.72)
(3.44)
(473.41)
(0.91)
(1.21)
(0.34)
(0.45)
(36.14)
(0.63)
(0.40)
(3.06)
0.10
0.00
0.00
0.00
126.55
0.13
0.11
0.05
0.03
0.00
0.00
0.05
0.03
0.05
0.00
0.25
0.03
0.65
0.00
35.12
0.06
0.00
0.53
0.20
0.05
3.68
0.00
0.00
0.05
0.10
0.00
0.00
0.00
272.77
0.00
0.34
0.08
0.03
0.33
0.03
0.00
1.42
12.01
0.65
0.73
0.00
0.00
0.47
0.28
0.12
0.10
0.00
0.73
0.08
22.82
0.00
0.00
0.10
0.03
0.88
0.63
0.63
0.00
0.00
0.11
0.04
0.00
185.70
0.00
0.00
0.31
0.08
0.00
1.35
0.00
0.13
7.60
0.07
0.15
0.00
(0.30)
(0.00)
(0.00)
(0.00)
(121.01)
(0.33)
(1.11)
(0.22)
(0.16)
(0.00)
(0.00)
(0.22)
(0.16)
(0.22)
(0.00)
(0.54)
(0.16)
(1.00)
(0.00)
(90.45)
(0.19)
(0.00)
(1.13)
(0.41)
(0.22)
(6.61)
(0.00)
(0.00)
(2.65)
(0.30)
(0.00)
(0.00)
(0.00)
(250.19)
(0.00)
(0.92)
(0.27)
(0.16)
(3.43)
(0.16)
(0.00)
(8.07)
(11.29)
(0.83)
(0.45)
(0.00)
(0.00)
(2.97)
(0.82)
(0.37)
(0.30)
(0.00)
(0.85)
(0.35)
(21.91)
(0.00)
(0.00)
(0.30)
(0.16)
(0.33)
(0.90)
(0.95)
(0.00)
(0.00)
(0.43)
(0.14)
(0.00)
(151.99)
(0.00)
(0.00)
(0.63)
(0.51)
(0.00)
(1.05)
(0.00)
(0.46)
(33.59)
(0.77)
(0.36)
(0.00)
1.47
0
0
0
4.07
5.44
1.52
8.95
1.73
0
0
2.54
4.22
7.52
0
1.49
3.57
5.07
0
0
0
0
1.71
1.88
1.12
2.19
0
0
3.78
0
0
0
0
4.22
0
0
4.77
1.59
3.36
1.61
0
0
0
6.03
7.79
0
0
2.78
4.77
0
4.15
0
2.39
7.23
1.48
0
0
3.18
3.27
2.22
6.82
5.63
0
0
1.47
0
0
0
0
0
0
0
0
1.89
0
4.87
4.25
2.86
1.96
0
1012
102
103
101
102
101
101
101
102
101
101
102
101
101
101
101
101
103
101
101
101
101
102
102
101
1015
101
102
102
1013
101
101
101
105
102
101
101
101
101
101
101
upstream 100:10 MIR32 upstream 1:0 MLTF1

downstream 10:100 FAM1 upstream 4:3 TFIID1
upstream 10:5 LTR MaLR2 upstream 2:0 BPVE23
downstream 10:100 LINE CR12 upstream 100:10 SINE MIR2
downstream 10:100 LINE CR12 upstream 9:8 APF3
downstream 10:100 LINE CR12 downstream 5:10 SINE MIR1
intron L1P1
upstream 8:7 GT2B3 upstream 2:0 NFkB3
upstream 5:0 L1MA2
exon LTR ERV11
upstream 5:0 AluY2 upstream 9:8 Pit13
downstream 10:100 FRAM2 upstream 5:0 TFIID1
intron LINE L11
downstream 0:5 AluJ1 upstream 4:3 GTIIC3
downstream 10:100 LTR MaLR1
downstream 0:2 MIR1 upstream 1:0 ATF3
upstream 100:10 Other1 upstream 100:0 MIR phase change2
intron MIR2 upstream 6:5 APF3
upstream 100:10 Other1 upstream 5:4 ICSBP3
downstream 0:2 DNA2
upstream 2:1 BPVE21 upstream 4:3 ATF3
upstream 7:6 NF11 upstream 2:0 ATF3
upstream 4:3 Pit11
upstream 2:0 NFuE41 upstream 5:0 GATA13
upstream 5:0 E2F1
downstream 0:2 SINE MIR1 upstream 1:0 ATF3
upstream 8:7 SIF3
upstream 5:4 PEA11 upstream 3:2 APF3
downstream 10:100 AluY2 downstream 0:2 LINE L21
downstream 10:100 Alu1
upstream 5:0 AluY2 upstream 6:5 PU13
upstream 100:10 FRAM1
downstream 0:2 SINE MIR2 upstream 1:0 ATF3
upstream 3:2 TFIID1
upstream 10:9 ICP43
upstream 5:0 L1PA1
upstream 9:8 TFIID3 upstream 8:7 Sp13
intron L1PB1
upstream 10:5 SINE MIR2 upstream 5:0 AluS1
upstream 5:0 AluS2 upstream 2:0 AP23
exon L1ME2
upstream 10:5 FAM2
upstream 1:0 AP11 upstream 10:9 NFuE53
upstream 10:5 SINE MIR2
upstream 4:3 AP23
upstream 100:10 AluJ2 upstream 70:60 CpGi1,11
upstream 100:10 AluY1
downstream 10:100 LINE CR11 upstream 10:5 AluS2
upstream 2:0 BPVE21 upstream 5:0 NFuE51
upstream 2:0 ETFA3 downstream 0:100 MIR phase change1
upstream 3:2 BPVE21
downstream 0:5 DNA Mariner1
upstream 100:10 DNA T2 type2
downstream 0:1 L1ME1
upstream 100:10 DNA Tip1002
upstream 5:0 Pit11 downstream 0:100 MLT1C phase change2
upstream 10:5 AluJ2 upstream 2:0 BPVE23
exon SINE Alu1
upstream 2:0 L1M21
intron DNA MER2 type2
upstream 5:0 NFuE13
upstream 5:0 L1ME1 upstream 10:0 NF11
upstream 5:0 AluY1 upstream 100:0 MIR phase change2
upstream 5:4 APF3
upstream 10:5 LTR MaLR1 upstream 2:0 BPVE23
intron MIR2 upstream 5:0 AP23
upstream 2:1 COUP3 upstream 2:0 NFuE43
intron MIR2 upstream 7:6 NFIII3
downstream 0:5 AluJ2 upstream 5:4 SIF3
upstream 2:0 AluS2 upstream 1:0 Pit13
2.25
2.24
2.23
2.22
2.21
2.2
2.19
2.18
2.17
2.16
2.15
2.14
2.13
2.12
2.11
2.1
2.09
2.08
2.07
2.06
2.05
2.04
2.03
2.02
2.01
2
1.99
1.98
1.97
1.96
1.95
1.94
1.93
1.92
1.91
1.9
1.89
1.88
1.87
1.86
1.85
1.84
1.83
1.82
1.81
1.8
1.79
1.78
1.77
1.76
1.75
1.74
1.73
1.72
1.71
1.7
1.69
1.68
1.67
1.66
1.65
1.64
1.63
1.62
1.61
1.6
1.59
1.58
1.57
1.56
1.55
1.54
1.53
1.52
1.51
1.5
1.49
1.48
1.47
1.46
87.83
1.12
0.30
62.93
0.60
0.45
0.20
0.20
0.26
0.13
0.06
30.55
40.07
0.01
0.75
411.51
1.28
0.17
8.71
0.14
0.04
0.07
36.15
0.14
0.06
0.18
0.09
0.60
0.70
0.00
0.07
0.09
0.17
0.21
0.09
0.39
0.02
1.03
1.09
1.08
1.14
0.05
0.09
1.41
0.10
0.26
2.08
5.68
0.23
0.02
0.40
63.22
0.26
7.82
0.29
249.42
1.57
0.01
1.16
0.48
0.00
12.81
0.03
0.12
0.43
1.27
0.00
0.01
40.83
0.20
0.34
0.38
0.14
0.84
0.31
33.71
0.07
34.33
0.88
2.32
(235.51)
(0.84)
(1.03)
(194.19)
(1.19)
(2.01)
(1.82)
(0.34)
(0.72)
(0.61)
(0.24)
(188.23)
(209.05)
(0.16)
(2.43)
(770.95)
(3.60)
(0.59)
(7.00)
(0.45)
(0.24)
(0.23)
(112.42)
(0.48)
(1.08)
(0.49)
(0.33)
(2.74)
(1.20)
(0.71)
(0.28)
(0.31)
(0.51)
(0.41)
(0.31)
(1.33)
(0.58)
(2.86)
(1.29)
(3.30)
(1.29)
(0.21)
(0.37)
(1.55)
(0.30)
(1.11)
(4.66)
(9.31)
(3.77)
(0.20)
(0.94)
(108.32)
(0.44)
(11.89)
(2.38)
(708.04)
(2.87)
(0.13)
(3.68)
(0.71)
(0.18)
(88.09)
(0.21)
(0.30)
(1.24)
(2.41)
(0.43)
(0.11)
(121.55)
(0.40)
(0.32)
(1.64)
(0.29)
(0.37)
(0.84)
(108.04)
(0.25)
(109.61)
(3.00)
(7.10)
11.73
1.23
0.00
0.00
0.07
0.00
0.83
0.04
0.03
0.03
0.00
0.00
7.73
0.00
0.00
93.55
1.64
0.00
7.75
0.00
0.03
0.00
0.72
0.00
0.00
0.00
0.00
0.36
0.50
0.13
0.00
0.10
0.00
0.13
0.00
0.01
0.00
0.00
0.88
0.00
0.85
0.08
0.10
1.43
0.00
0.45
0.23
1.28
3.17
0.03
0.03
53.71
0.38
2.40
0.09
23.28
0.28
0.05
0.00
0.58
0.00
0.00
0.08
0.10
0.04
0.02
0.05
0.03
36.63
0.25
0.22
0.00
0.01
0.80
0.00
0.77
0.00
0.78
0.00
0.00
(37.57)
(0.97)
(0.00)
(0.00)
(0.17)
(0.00)
(5.23)
(0.10)
(0.07)
(0.16)
(0.00)
(0.00)
(48.86)
(0.00)
(0.00)
(208.60)
(3.66)
(0.00)
(5.15)
(0.00)
(0.16)
(0.00)
(1.16)
(0.00)
(0.00)
(0.00)
(0.00)
(2.27)
(0.88)
(1.22)
(0.00)
(0.30)
(0.00)
(0.33)
(0.00)
(0.05)
(0.55)
(0.00)
(1.28)
(0.00)
(1.12)
(0.27)
(0.44)
(1.64)
(0.00)
(2.25)
(0.63)
(2.82)
(20.06)
(0.22)
(0.16)
(117.12)
(0.49)
(3.04)
(1.98)
(81.55)
(0.55)
(0.32)
(0.00)
(0.84)
(0.23)
(0.00)
(0.35)
(0.35)
(0.17)
(0.13)
(0.22)
(0.16)
(89.65)
(0.44)
(0.23)
(0.00)
(0.07)
(0.41)
(0.00)
(1.32)
(0.00)
(1.20)
(0.00)
(0.00)
3.33 1016
2.45 101
0
0
0
0
2.31 101
2.76 1013
0
1.61 104
0
0
1.02 104
0
0
4.38 1012
2.68 101
0
1.26 101
0
3.17 101
0
0
0
0
0
0
2.56 101
7.67 102
2.66 101
0
4.17 101
0
5.63 102
0
0
4.10 101
0
1.56 101
0
5.99 102
2.70 101
4.59 101
4.69 101
0
2.98 101
0
2.27 1012
1.83 101
3.89 101
0
3.08 101
8.00 102
3.97 1014
2.70 101
0
0
2.13 101
0
2.54 101
4.81 101
0
2.27 101
3.51 101
0
0
7.73 102
2.52 101
3.86 101
2.55 101
1.57 103
0
7.22 1015
2.95 101
0
0
0
0
0
0
upstream 6:5 NFuE31

downstream 0:5 SINE Alu1 upstream 5:4 SIF3
upstream 5:0 AluY1 upstream 2:0 PU13
upstream 10:5 L1MD1
intron MIR2 upstream 9.04:8.99 nucleosome potential sd
upstream 100:10 AluS2 upstream 10:9 NFuE53
upstream 100:10 AluS1 upstream 100:10 MIR32
downstream 0:1 AluS2 upstream 4:3 PU13
upstream 5:0 CpGi1 upstream 2:0 AluJ1
upstream 2:0 AluJ2 upstream 10:9 PU13
exon MIR32
downstream 0:5 AluJ2 upstream 10:0 NFuE43
downstream 10:100 DNA Mariner1 upstream 100:10 LTR ERV11
downstream 0:5 AluJ2 upstream 7:6 GTIIC1
upstream 9:8 COUP1
upstream 10:5 L1MD2
upstream 2:1 NFkB1
upstream 100:10 MIR1 upstream 100:10 SINE Alu2
upstream 10:5 AluS2 upstream 2:1 BPVE23
upstream 5:0 CEBP3
downstream 10:100 LINE CR12 upstream 10:0 AP11
upstream 100:10 AluS1 upstream 3:2 COUP3
upstream 10:9 NFuE51
exon LTR ERV12
downstream 0:2 AluS1 upstream 1:0 BPVE21
upstream 2:0 L1MC1
downstream 0:1 SINE MIR1 upstream 3:2 AP11
upstream 10:5 SINE MIR2 upstream 2:0 AluS2
downstream 0:1 SINE Alu2 upstream 7:6 GTIIC1
upstream 1:0 SINE Alu1 upstream 7:6 Oct13
upstream 5:0 SINE Alu2 upstream 8:7 GT2B1
upstream 100:10 SINE MIR1 upstream 100:0 Alu phase change1
upstream 2:0 AluS2 upstream 5:0 ETFA3
downstream 10:100 AluY1 upstream 100:10 AluS1
downstream 10:100 LINE CR12 upstream 3:2 TFIID1
upstream 5:0 AluS2 m3upIndicator
upstream 6:5 GATA11
upstream 7:6 Sp11
upstream 5:0 SINE Alu2 upstream 5:0 BPVE21
upstream 3:2 Pit11 upstream 10:9 NFuE53
upstream 4:3 AR1
downstream 10:100 LINE CR12 upstream 5:0 SINE Alu2
upstream 5:0 SINE Alu1 upstream 5:0 AP11
upstream 2:0 AluS2 m11intronIndicator
downstream 10:100 AluJ2
downstream 5:10 L1MA2
upstream 8:7 BPVE21 upstream 2:0 E4TF13
upstream 1:0 NFIII3
upstream 10:5 GC2 upstream 100:10 AluS1
upstream 100:10 AluS2 upstream 3:2 AP13
upstream 9:8 CP11
upstream 10:5 L1MA1
downstream 10:100 SINE Alu2 upstream 10:0 AP11
upstream 10:5 FLAM1
downstream 10:100 AluJ2 downstream 5:10 SINE Alu2
upstream 5:0 SINE Alu2 upstream 2:0 Sp13
upstream 100:0 MIR phase change2
upstream 2:0 SINE Alu2 upstream 2:1 AP21
downstream 0:1 MIR1 upstream 1:0 AP13
upstream 5:0 AluS1 upstream 8:7 SIF3
upstream 10:5 SINE MIR1 upstream 2:0 SINE Alu2
upstream 5:0 NFuE31
upstream 5:0 SINE Alu2 upstream 9:8 COUP3
intron MIR2 upstream 90:80 CpGi1,11
downstream 0:5 AluJ1 upstream 50:40 CpGi1,11
1.45
1.44
1.43
1.42
1.41
1.4
1.39
1.38
1.37
1.36
1.35
1.34
1.33
1.32
1.31
1.3
1.29
1.28
1.27
1.26
1.25
1.24
1.23
1.22
1.21
1.2
1.19
1.18
1.17
1.16
1.15
1.14
1.13
1.12
1.11
1.1
1.09
1.08
1.07
1.06
1.05
1.04
1.03
1.02
1.01
1
0.99
0.98
0.97
0.96
0.95
0.94
0.93
0.92
0.91
0.9
0.89
0.88
0.87
0.86
0.85
0.84
0.83
0.82
0.81
0.8
0.79
0.78
0.77
0.76
0.75
0.74
0.73
0.72
0.71
0.7
0.69
0.68
0.67
0.66
0.08
0.78
0.28
0.00
0.08
17.79
3.02
2450.40
3.83
0.12
1.57
0.20
36.43
21.32
2.71
1.01
1.97
0.28
0.11
0.09
220.09
2.29
0.16
4.29
30.04
0.34
0.44
0.83
0.03
0.27
0.07
0.29
9.05
3.58
0.16
7.19
0.94
0.18
447.93
0.39
2.19
291.62
0.27
6.98
0.68
50.39
0.35
43.86
0.17
12.17
17.48
3.49
33.65
76.80
3.43
0.85
0.09
0.70
1585.80
8.16
7.68
0.05
0.00
0.08
290.85
0.17
1.64
38.62
11.27
0.67
0.41
4.12
0.09
0.53
11.65
0.36
14.50
81.39
1.58
48.94
(0.29)
(2.14)
(0.61)
(0.64)
(0.48)
(52.21)
(6.15)
(5083.01)
(11.21)
(0.48)
(4.94)
(1.75)
(116.04)
(16.93)
(8.90)
(3.61)
(1.44)
(1.95)
(0.39)
(0.30)
(225.99)
(4.66)
(0.37)
(6.65)
(26.21)
(0.64)
(5.96)
(1.71)
(0.68)
(0.84)
(0.34)
(1.00)
(25.90)
(13.55)
(0.47)
(17.39)
(4.69)
(0.15)
(440.90)
(0.90)
(7.07)
(389.69)
(0.68)
(10.28)
(0.88)
(302.85)
(1.14)
(59.14)
(0.63)
(4.69)
(33.29)
(7.39)
(40.19)
(162.84)
(2.48)
(4.96)
(0.36)
(0.46)
(1238.67)
(7.16)
(13.27)
(0.25)
(0.49)
(2.12)
(240.38)
(0.44)
(1.98)
(53.95)
(15.08)
(1.46)
(0.16)
(13.16)
(0.33)
(1.46)
(29.39)
(0.64)
(15.32)
(319.80)
(3.89)
(128.50)
0.13
0.05
0.03
0.00
0.00
1.61
0.41
449.61
0.00
0.00
0.00
0.00
0.00
22.00
0.00
0.00
1.90
0.00
0.00
0.05
78.31
0.15
0.20
0.96
12.90
0.20
0.00
0.05
0.00
0.00
0.08
0.00
0.00
0.00
0.00
1.40
0.45
0.17
157.03
0.04
0.00
97.25
0.01
1.40
0.58
96.83
0.50
12.93
0.00
10.98
0.30
0.29
10.73
4.68
2.20
0.58
0.00
0.65
795.33
2.97
5.61
0.00
0.05
0.46
144.13
0.10
0.50
12.50
3.61
0.05
0.37
0.00
0.00
0.03
0.66
0.43
4.48
1.38
0.20
31.56
(0.33)
(0.22)
(0.16)
(0.51)
(0.00)
(8.15)
(1.13)
(1068.36)
(0.00)
(0.00)
(0.00)
(0.00)
(0.00)
(14.76)
(0.00)
(0.00)
(1.68)
(0.00)
(0.00)
(0.22)
(77.03)
(0.93)
(0.41)
(1.61)
(11.02)
(0.56)
(0.00)
(0.32)
(0.00)
(0.00)
(0.35)
(0.00)
(0.00)
(0.00)
(0.00)
(3.55)
(1.79)
(0.12)
(154.06)
(0.13)
(0.00)
(119.91)
(0.05)
(3.52)
(0.78)
(305.95)
(0.96)
(19.79)
(0.00)
(4.59)
(1.91)
(0.78)
(15.01)
(29.57)
(1.31)
(2.57)
(0.00)
(0.48)
(490.41)
(3.15)
(10.69)
(0.00)
(0.45)
(2.72)
(86.25)
(0.30)
(0.75)
(15.75)
(5.46)
(0.22)
(0.26)
(0.00)
(0.00)
(0.16)
(2.91)
(0.59)
(5.56)
(3.50)
(0.65)
(80.74)
1.87 101
0
8.00 1013
4.88 101
0
7.77 1016
0
7.55 1015
0
0
0
0
0
3.87 101
0
0
3.94 101
0
0
1.54 101
1.77 1014
0
2.63 101
3.33 1016
2.74 1012
6.81 102
0
0
2.10 1012
0
4.45 101
0
0
0
0
5.11 1013
4.94 102
3.12 101
8.10 1015
0
0
7.77 1013
0
1.48 1012
2.13 101
1.75 101
1.66 101
2.28 1012
0
5.66 102
0
0
4.43 1012
0
3.56 107
2.61 101
0
2.43 101
9.69 1013
5.57 1013
1.17 101
0
2.34 101
1.10 101
1.96 1013
8.06 102
4.92 1012
3.94 1013
4.35 1011
0
1.74 101
0
0
0
0
2.40 101
3.46 1014
0
1.11 1016
9.38 102

downstream 5:10 AluS1 upstream 100:10 SINE Alu1
upstream 9:8 AP13
upstream 1:0 AluS2 upstream 2:1 NFIII1
downstream 5:10 AluS1 downstream 0:1 AluS2
downstream 10:100 AluS2 upstream 5:0 AluY2
upstream 10:5 AluJ2 upstream 10:5 MIR2
downstream 0:1 MIR1 upstream 2:0 AP11
downstream 10:100 MIR32 upstream 2:0 SINE Alu2
upstream 100:10 AluS1 upstream 6:5 ICSBP3
upstream 5:0 SINE Alu2 upstream 100:0 L2 phase change1
downstream 10:100 FRAM1 upstream 2:0 AluJ2
upstream 1:0 IgPE21
downstream 5:10 AluS2 downstream 0:1 AluS2
downstream 0:5 FLAM2 upstream 2:0 ICSBP1
upstream 8:7 CP13
intron SINE MIR2 upstream 90:80 CpGi1,11
downstream 0:1 SINE Alu1
upstream 5:0 CpGi2 upstream 1:0 SINE Alu2
downstream 5:10 AluS2 upstream 2:1 AR1
downstream 5:10 AluS2 upstream 2:0 AluJ2
upstream 2:0 SINE Alu2 upstream 10:9 GT2B1
downstream 10:100 FLAM1 downstream 5:10 AluS2
upstream 5:0 AluY2 upstream 2:0 BPVE21
upstream 2:0 FAM1
downstream 5:10 SINE Alu2 upstream 10:5 SINE Alu1
upstream 100:10 AluJ2 upstream 7:6 AP11
upstream 10:5 L1MB2
downstream 10:100 FLAM2 downstream 5:10 AluS2
downstream 10:100 FAM1
upstream 100:10 AluS2 upstream 2:0 AluJ1
upstream 2:0 ATF1 upstream 2:0 E4TF13
upstream 1:0 AluS1 upstream 2:0 Sp13
upstream 5:0 SINE Alu1 upstream 4:3 TFIID3
upstream 2:0 AluS2 upstream 8:7 SIF3
downstream 5:10 AluS2 upstream 10:5 SINE Alu1
downstream 10:100 AluJ2 upstream 5:0 AluS2
downstream 10:100 AluY1 upstream 5:0 SINE Alu1
downstream 0:2 SINE Alu1 upstream 2:1 BPVE21
downstream 5:10 AluS1 upstream 1:0 AluS2
upstream 100:10 L1MB1 upstream 5:0 AluY1
downstream 5:10 AluS2 upstream 1:0 AluS1
intron DNA Tc22
downstream 0:2 Other2
upstream 2:0 SINE Alu2 upstream 5:0 Sp13
0.65
0.64
0.63
0.62
0.61
0.6
0.59
0.58
0.57
0.56
0.55
0.54
0.53
0.52
0.51
0.5
0.49
0.48
0.47
0.46
0.45
0.44
0.43
0.42
0.41
0.4
0.39
0.38
0.37
0.36
0.35
0.34
0.33
0.32
0.31
0.3
0.29
0.28
0.27
0.26
0.25
0.24
0.23
0.22
0.21
0.2
0.19
0.18
0.17
0.16
0.15
0.14
0.13
0.12
0.11
0.1
0.09
0.08
0.07
0.06
0.05
0.04
0.03
0.02
0.01
0.01
31.40
151.46
0.84
353.25
102.61
180.97
24.05
118.71
0.41
939.36
27.43
36.71
82.44
73.35
0.02
55.81
43.41
0.04
46.39
77.89
4.77
0.04
7072.20
57.25
6.19
20.65
5.98
19.73
2.02
0.00
41.12
7.16
1.16
0.68
2.38
87.38
0.26
152.03
3.39
0.30
0.14
72.30
0.05
2.12
2.32
25.68
0.61
0.21
0.15
0.11
45.82
0.48
28.15
0.56
0.04
7.26
15.56
1.46
24.38
1.66
42.54
292.21
14.45
0.62
10.60
35.57
(59.03)
(229.53)
(0.37)
(372.57)
(315.31)
(537.94)
(57.00)
(369.97)
(1.49)
(2652.77)
(26.55)
(59.08)
(101.53)
(256.02)
(0.15)
(160.17)
(149.18)
(0.20)
(113.64)
(320.76)
(11.64)
(0.82)
(19530.74)
(66.33)
(10.16)
(63.27)
(17.47)
(33.22)
(5.93)
(0.06)
(65.94)
(8.55)
(2.44)
(2.83)
(4.01)
(100.91)
(0.56)
(285.85)
(9.25)
(0.91)
(0.41)
(84.53)
(0.29)
(2.97)
(7.64)
(43.78)
(1.49)
(0.69)
(0.41)
(1.32)
(68.17)
(5.11)
(43.61)
(1.50)
(0.26)
(13.49)
(49.12)
(4.19)
(66.70)
(5.16)
(106.75)
(693.57)
(81.71)
(6.75)
(15.55)
(48.80)
2.78
24.95
0.80
115.04
0.00
0.00
2.15
8.33
0.00
66.28
11.55
7.97
25.81
0.00
0.00
0.00
0.14
0.03
0.00
1.47
0.31
0.00
465.95
18.73
0.75
0.00
0.26
3.74
0.14
0.00
10.41
2.49
0.18
0.60
0.47
30.50
0.13
21.61
0.19
0.03
0.00
30.48
0.03
0.60
0.00
3.78
0.05
0.18
0.08
0.00
8.98
0.22
5.80
0.03
0.05
1.45
0.00
0.15
1.18
0.00
3.85
450.10
6.91
0.00
2.05
11.25
(8.41)
(33.88)
(0.41)
(152.24)
(0.00)
(0.00)
(7.83)
(51.58)
(0.00)
(285.18)
(10.88)
(12.59)
(35.89)
(0.00)
(0.00)
(0.00)
(0.89)
(0.16)
(0.00)
(3.81)
(1.35)
(0.55)
(2091.10)
(26.75)
(2.32)
(0.00)
(1.62)
(7.76)
(0.91)
(0.00)
(15.68)
(3.04)
(0.50)
(1.84)
(0.97)
(29.91)
(0.33)
(74.28)
(0.73)
(0.16)
(0.00)
(26.66)
(0.16)
(1.08)
(0.00)
(6.36)
(0.22)
(0.50)
(0.27)
(0.00)
(17.67)
(1.36)
(9.77)
(0.16)
(0.22)
(3.33)
(0.00)
(0.58)
(7.46)
(0.00)
(16.09)
(1064.61)
(30.34)
(0.00)
(5.41)
(14.45)
0
0
2.92 101
2.27 1012
0
0
0
0
0
0
1.55 1011
0
1.75 1012
0
0
0
0
2.51 101
0
0
0
3.43 101
0
2.23 1011
0
0
0
3.33 1016
2.22 1016
0
2.00 1015
3.46 1012
1.55 1015
3.90 101
1.55 1015
6.00 1015
8.12 103
6.67 1014
0
5.10 1014
0
1.99 1012
1.75 101
4.59 1011
0
0
0
3.42 101
3.67 102
0
2.22 1016
1.16 101
0
0
3.94 101
7.67 1014
0
0
0
0
0
1.80 101
6.53 102
0
1.71 1012
2.53 1013
Unit is kilobases and it refers to the beginning of the first or the end of the last exon, respectively. Corresponding table for SMLR available upon request.
For example, downstream 10:100 refers to the 90 kb window from 10 kb to 100 kb downstream of the last exon.
1
Number of this feature within the sequence window.
1 denotes the ratio of repeated elements in + versus orientation with respect to the gene. It is the negative inverse if there are more elements in orientation than in +.
2
Percentage.
2 Ratio of the percentage of the sequence window covered by repeated elements in orientation.
3
Indicator for presence of this feature within the sequence window.
4
Indicator for presence of upstream CTCF consensus-binding site.
5
Indicator for presence of TGTTTGCAG consensus site.
6
The phase change happened at one of the following LTR elements: MLT1A0, MLT1B, MSTA, MSTB1, MLT1D, MLT2B4, or MLT1G1.
7
Indicator for presence of CpG island overlapping the last exon.
8 Indicator for presence of CpG island overlapping the first exon.
9
Orientation of motif relative to gene.
10
Methylation prone.
11
Methylation resistant.
indicates pairwise interaction between two variables.
Supplementary Table 5. Relevant features for prediction of parental preference by Equbits classifier.
Feature
downstream 10:100 AluJ1 upstream 1:0 ATF3
downstream 10:100 CpGi3 upstream 3:2 Oct13
downstream 10:100 CpGi1 upstream 10:0 GATA13
upstream 7:6 APF3 upstream 5:4 BPVE23
upstream 4:3 E4F13
upstream 10:9 MLTF3 upstream 7:6 AP13
upstream 4:3 E4F11
upstream 10:5 AluY1
upstream 10:5 AluY2
upstream 6:5 GTIIC1
upstream 7:6 CP11
upstream 100:10 L12
upstream 2:0 AluS1
exon 0.225:0.41 nucleosome potential2
downstream 10:100 LINE L12 upstream 5:4 APF1
upstream 9:8 NFuE41
upstream 6:5 GTIIC3
Weight
19.57
18.86
17.94
17.75
16.86
16.49
16.42
15.92
15.45
14.9
14.88
14.69
14.57
14
13.99
13.86
13.79
13.7
13.32
13.27
13.02
12.99
12.83
12.73
12.66
12.63
12.58
12.3
12.29
12.21
Mean (Standard deviation)

Maternally expressed
Paternally expressed
0.71
(1.15)
1.06
(1.46)
0.47
(0.51)
0
(0)
4.68
(3.37)
0.85
(0.99)
0.47
(0.51)
0
(0)
0.37
(0.50)
0.05
(0.22)
0.21
(0.54)
2.08
(2.97)
0.68
(0.48)
0.10
(0.31)
0.42
(0.61)
0.05
(0.22)
337.17
(781.15)
1.84
(1.10)
0.47
(0.61)
0.10
(0.31)
0.18
(0.35)
0.03
(0.11)
1.43
(1.86)
0.31
(0.95)
4.68
(3.37)
1.30
(1.45)
1.31
(1.80)
0.38
(2.51)
0.22
(2.05)
1.65
(2.90)
2.28
(3.47)
70.32
(153.20)
0.21
(0.42)
0.60
(0.68)
67.91
(99.59)
12.00
(29.01)
0.16
(0.37)
0
(0)
0.07
(0.21)
0.73
(1.28)
0.11
(0.32)
0.25
(0.55)
0.42
(1.24)
0.26
(0.81)
0
(0)
0.03
(0.08)
0
(0)
0.15
(0.37)
17.90
(22.58)
61.57
(37.34)
0
(0)
0.10
(0.31)
0.49
(1.74)
1.07
(2.53)
0.32
(0.66)
1.52
(1.76)
0.21
(0.42)
0.50
(0.51)
0.03
(0.05)
0.11
(0.17)
P
8.49
3.97
5.19
3.97
8.41
5.93
4.42
9.90
3.88
1.21
3.47
1.31
2.36
1.02
1.29
3.08
1.90
1.42
4.14
1.73
9.23
2.62
6.64
4.14
5.10
8.13
1.54
4.67
3.05
3.29
105
104
105
104
103
103
105
103
102
102
102
102
104
102
102
102
102
102
102
102
103
102
102
102
105
102
102
103
102
102
Unit is kilobases and it refers to the beginning of the first or the end of the last exon, respectively.
For example, downstream 10:100 refers to the 90 kb window from 10 kb to 100 kb downstream of the last exon.
1
Number of this feature within the sequence window.
1 denotes the ratio of repeated elements in + versus orientation with respect to the gene. It is the negative inverse if there are more elements in orientation than in +.
2
Percentage of the sequence window covered by this feature.
2 Ratio of the percentage of the sequence window covered by repeated elements in orientation.
3
Indicator for presence of this feature within the sequence window.
10
Methylation prone.
indicates pairwise interaction between two variables.
Supplementary Table 6. Genes proved or predicted with high confidence to be imprinted map to loci
linked to various human conditions.
Condition
Alcoholism
Band
Locus
Coordinate
Allele
Linkage/Reference
2p14
TSC0053926
OTX1
66.5
63.2
p
M
Linkage to alcoholism (LOD=1.52) 21 .

Involved in brain development 22 .
12q24
D12S1045
Q9HCM7
128.8
131.6
m
M
Linkage to alcoholism (LOD=3.17; MOD=3.68) 21, 23 .
21q22
D21S1440
SIM2
38.1
37.0
m
P
Linkage to alcoholism (MOD=3.86) 23 .

Involved in brain development 24 .
10q23
D10S583
Q9H6Z8
94.4
92.4
D10S1710
LDB1
102.8
103.8
D12S1623
RBP5
6.8
7.2
D12S1042
ABCC9
27.5
21.9
D12S398-D12S1632
HOXC9
HOXC4
51.5-54.7
52.7
52.7
M
M
3q21
D3S3606
FTHFD
128.7
128.3
m
M
Linkage to allergic sensitization (Zall =4.31) 29 .

Mice deficient in this gene show decreased hepatic folate
levels 30 .
14q24
D14S74
77.7
Suggestive linkage to atopy and indications for imprinting

(MOD=2.88) 31 .
ENSG00000183992
80.7
D1S1677-D1S1589
HSPA6
156-172.5
159.8
7q32
D7S530-D7S640
CPA4
MEST
128.9-132.3
129.7
129.9
m
M
P
9q34
D9S158-D9S905
PHPT1
EGFL7
136.3-137.2
137.0
136.8
M
P
D10S189
6.8
GATA3
8.1
D17S1800
D17S1871,D17S1824
26.7
21.9,23.7
PYY2
23.6
Alzheimers
10q24
12p13
12p11
12q13
Linkage to Alzheimers disease (LOD=3.3) 25, 26 .
Linkage to Alzheimers disease (LOD=0.9) 25 .
Asthma/Atopy
Autism
1q25
10p14
17q11
17q11
Linkage to autism 32 .
Linkage to autism (MLS=2.31) 33 .

Known human imprinted gene 34 .
Linkage to autism (MLS=1.67) 33 .
Linkage to autism (MLS=1.15) and schizophrenia

(LOD=3.60) 33, 36 .
Regulates the development of serotoninergic neurons 37 .
In 30% of autistic people the most frequent dysfunction
is the increase of serotonine 38 . Haploinsufficiency for
GATA3 was observed in a patient with autism and severe
mental retardation 39 .
Linkage to autism-spectrum disorders (MLS=2.83) 40 .
Suggestive linkage to ASD and indications for imprinting 32 .
Bipolar
1q41
D1S549
PTPN14
217.7
212.6
m
M
Linkage to bipolar disorder (MLS=1.43) 41 .
2q36
D2S396-D2S206
TIGD1
230.4-233.4
233.1
m
P
Linkage to bipolar disorder (HLOD=2.20) 42 .
8q24
D8S256
KCNK9
134.5
140.7
Linkage to bipolar disorder (NPL=3.13) 41 .

K+ channel protein involved in neuron apoptosis and cell
tumorigenesis 18 .
14q32
D14S65-D14S78
DLK1
MEG3
RTL1
96.7-99.5
100.3
100.4
100.4
p
P
M
M
Linkage to bipolar disorder (HLOD=2.47) 42 .

Known human imprinted gene 43, 44 .
Imprinted in mouse 7 and sheep 8 .
10q26
D10S217
C10orf91
NKX6-2
C10orf93
VENTX2
Q8N377
PAOX
129.4
134.1
134.4
134.6
134.9
135.0
135.1
m
M
M
M
M
M
M
Linkage to male sexual orientation (MLOD=1.81) 5 .
D2S2987
GATA23A02-GATA178G09M
242.5
235.7-237.7
Q9Y419
MYEOV2
239.4
240.7
M
P
3q24
AAT071
ZIC1
151.5
148.6
m
M
Linkage to BMI (LOD=1.97) 47 .
19q13
Mfd232
LILRB4
55.6
59.9
m
M
Linkage to BMI (LOD=1.81) 47 .
14q12
D14S608
FOXG1C
27.9
28.3
D1S2709
OBSCN
HIST3H2BB
228.3
224.7
225
P
M
D8S532
PURG
40.9
31
D9S922
NP 001001670
80
81.8
PRODH2-DGCR6
DGCR6
17.3
17.3
Homosexuality
Predominantly expressed in the brain 4 .
Obesity/Diabetes
2q37
2q37
Linkage to type 2 diabetes (LOD=3.19) 46 .

Linkage to body mass index (BMI) and percentage of fat
mass (LOD=2.23/3.34) 47 .
Paternal UPD
Paternal UPD results in fetal malformations 48 .
Shows haploinsufficiency in a patient with severe mental retardation, brain malformations and microcephaly 19 .
Mouse orthologue is essential for normal development of
the telencephalon 20 .
Schizophrenia
1q42
8p11
9q21
22q11
Linkage to schizophrenia (LOD=2.71) 49 .
Linkage to schizophrenia 52 .
Expressed in the developing and adult mouse brain 53 .
The table lists loci that have previously been linked to various human conditions, and high-confidence imprinted gene candidates that map into or near these loci. If a locus has been observed to have a parentof-origin effect, this is denoted by a lowercase m or p, for maternal or paternal effects, respectively. Genes
predicted to be expressed from the maternal or paternal allele are denoted by M or P, respectively. Alleles
that have been proved to be exclusively expressed are printed in bold face.
Supplementary Methods
Human Genome Data
DNA sequence and annotation data were obtained from Ensembl, Version 20 (http://www.ensembl.org).
We used a positive training set of 40 imprinted genes compiled from the Imprinted Gene Catalog
(http://cancer.otago.ac.nz/IGC/Web/home.html) and recent literature, and a negative training set of 52
genes, for which experimental evidence suggests biallelic expression. Additionally, we used random sets
of 500 control genes presumed to be non-imprinted for a number of tasks. These random control genes
were sampled from autosomal chromosomal bands known or not suspected to contain imprinted genes,
and were intended to represent the overall characteristics of biallelically expressed genes. Random control genes were used to compute top pairwise interaction terms, to carry out feature selection with the
Equbits classifier, and finally to supplement the final training set that was used to learn our classifiers. To
minimize bias, we resampled the set of 500 random control genes for each of these three tasks.
Feature Measurements
We acquired DNA sequence feature measurements in an analogous fashion to our previous study in
mouse2 , including an additional set of data derived from recombination hotspots, nucleosome formation
potential, and repeat phase changes, as explained below.
We introduced another statistic regarding the repetitive elements flanking a gene, which we will
term phase change. We define a phase change as an instance of a repeated element changing its orientation compared to a neighboring element of the same family. We counted the number of such phase
changes among retrotransposon classes such as Alus, MIRs, and LTRs within the 100 kb up- and downstream. In doing this, we noticed that within the downstream region of imprinted genes, compared to
a random sample, a phase change occurred more frequently in one of the following LTRs: MLT1A0,
MLT1B, MSTA, MSTB1, MLT1D, MLT2B4, or MLT1G1. Conversely, phase changes in an MLT1C
LTR were underrepresented in the flanking regions of imprinted genes.
We also wanted to study whether data on recombination could be used to discern imprinted genes.
We downloaded coordinates of recombination hotspots54 from the International HapMap Project website
(http://www.hapmap.org). Next, we mapped the recombination hotspots to our data set and for each gene
computed the number of hotspots within 350 kb up- and downstream, as well as the minimum distance to
the closest recombination hotspot up- and downstream. Interestingly, the retrovirus-like retrotransposon
THE1B was found to be among certain sequence features that are overrepresented in hotspots54 . In
particular, these authors found the 8-nucleotide motif CCACGTGG to be significantly more frequent in
hotspot THE1Bs compared to THE1Bs elsewhere in the genome. The same oligonucleotide motif is also
involved in serum-induced transcription at the G1/S-phase boundary in the hamster55 , and is known as
the G-box binding motif for plant basic leucine zipper (bZIP) proteins56 . We proceeded by counting the
occurrence of this oligomer within all THE1B elements in the 100 kb flanking each gene.
The last additional class of feature measurements involved nucleosome formation potential profiles. Such in silico estimates of nucleosome packaging density in the promoter region has previously
been used to distinguish tissue-specific genes from housekeeping genes and widely expressed genes57 .
Using the web interface at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon, we acquired nucleosome
formation potential estimates and summarized them as follows. We computed the sum within the 0.820.61 kb upstream, the standard deviation 5.86-5.81 kb upstream, the mean 0-1 and 0.31-0.49 kb within
the concatenated exons, and the standard deviation 6.7-6.75 and 7.02-7.07 kb downstream. These particular windows were picked following visual inspection of plotted potentials.
Statistical Methods
To be more robust in our imprinted gene predictions, we used two strategies for feature selection and
classifier learning: Equbits ForesightTM (which employs support vector machines and is documented at
http://www.equbits.com) and SMLR (which adopts a Bayesian approach to sparse multinomial logistic
regression and is documented in the literature58 and at http://www.cs.duke.edu/amink/software/smlr).
In each case, we learned two separate classifiers, one with a linear kernel and one with an RBF kernel.
The operating point on the ROC for each classifier was chosen so as to minimize the number of false
positives while retaining all true positives (Supplementary Fig. 2). To be more conservative in our
final predictions, we required joint agreement among all four classifiers before predicting a gene to be
imprinted. We refer to these as our high-confidence predictions. We chose to report the prediction
set sorted by chromosome because the confidence estimates provided by the different classifiers could
not be unified in a direct manner. The procedure of cross-validation, training, testing, and prediction is
conceptually depicted in Supplementary Fig. 3.
When using Equbits to predict imprinted genes, a 40-fold cross-validation (CV) procedure was
used; to prevent over-fitting or over-estimation of prediction accuracy, feature selection using a linear
kernel was performed afresh for each fold of the CV (without inclusion of the genes being held out
during that fold). Once features were selected in each fold, classifiers for imprint status with linear and
RBF kernels were learned for that fold. The number of retained features ranged from 613 to 638 during
CV, whereas 626 features were retained in the final classifier.
When using SMLR to predict imprinted genes, a similar scheme was adopted. At each step of a
40-fold CV, feature selection was performed afresh (without inclusion of the genes being held out during
that fold) by applying a sparsity-promoting prior directly on the weights of the features (no kernel).
Once features were selected in this manner in each fold, classifiers for imprint status with linear and
RBF kernels were learned. During CV, the number of retained features averaged 875, while 820 features
were retained in the final classifier.
SMLR is written in portable Java, with a GUI, and is available with complete source code under
a non-commercial use license from http://www.cs.duke.edu/amink. In addition, all data, and all scripts
used to produce the SMLR results, are also available.
To ensure that no straightforward relationships within the training data were obscured by sophisticated learning methods, we also performed cross-validation using three simple classifiers (as implemented in Weka 3.459 ). A Nave Bayes classifier showed a sensitivity of 40% (16 out of 40 imprinted
genes correctly recognized) and a specificity of 97% (535 out of 552 non-imprinted genes correctly classified). A Decision Stump simply classified all genes as non-imprinted. A Random Forest classifier
showed a sensitivity of 20% (8 out of 40 correct) and a specificity of 95% (522 out of 552 correct).
These experiments suggest that simple alternative classification approaches are not likely to result in
comparable classification accuracy.
To simplify the prediction of parental expression preference, we used Equbits only with a linear
kernel and the top 30 features. This procedure is exactly analogous to that used to predict parental
preference in the mouse2 .
We used 2 -tests to compare proportions and two-sided Students t-tests to compare means. To be
conservative, Bonferronis method was used when correcting for multiple testing (=0.05).
Supplementary Figure 2. A receiver operator characteristic (ROC) curve illustrating the relationship
between sensitivity and specificity for the SMLR classifier under the two different kernel functions, linear
and RBF.
Supplementary Figure 3. Flow-chart illustrating schematically the processes of cross-validation, training, testing, and prediction under two different kernels and employing both the Equbits and SMLR classifier learning strategies.
Experimental validation
DLGAP2 (Disks large-associated protein 2), also known as DAP-2, is annotated to have four splice variants (UCSC Genome Website, May 2004 assembly60 ). The four splice variants chr8.27.24, chr8.27.25,
chr8.27.26, and chr8.27.27, are referred to as DLGAP2-24, -25, -26, and -27, respectively. Variants DLGAP2-24 and DLGAP2-27 lack exon 7 compared to isoforms DLGAP2-25 and DLGAP2-26. Conversely,
isoforms DLGAP2-24 and DLGAP2-25 share a common 3 -UTR, which is different from the 3 -UTR
jointly shared by DLGAP2-26 and DLGAP2-27. Thus, we were able to distinguish the four transcripts
as follows. Isoforms DLGAP2-24 and DLGAP2-25 were reverse transcribed using primer DLGAP2RT1, while DLGAP2-RT2 was used to reverse transcribe DLGAP2-26 and DLGAP2-27. cDNA from
DLGAP2-24 and DLGAP2-27 was specifically amplified using reverse primer DLGAP2-M1R, while
DLGAP2-M2R was used to amplify DLGAP2-25 and DLGAP2-26. DLGAP2-M1F was used as a common forward primer to amplify cDNA. When amplifying cDNA, the primers bridged two long introns,
ruling out any potential influence of undigested genomic DNA. Genomic DNA was amplified and sequenced using DLGAP2-1F and DLGAP2-1R.
KCNK9 (potassium channel, subfamily K, member 9), also known as TASK-3, is annotated to have
one isoform. We used primers KCNK9-1F and -1R for the amplification of genomic DNA. cDNA was
amplified using KCNK9-M1F and -M1R, which bridge an 84 kb intron.
In order to rule out any stochastic effects, we repeated the PCR and the sequencing reactions
at least three times in all cases where exclusive monoallelic expression was observed. All sequencing
reactions were performed in both directions.
Supplementary Table 7. Independent negative test genes.

Gene
Band
Expression
Reference
Stochastic monoallelic expression

IL2
IL4
IL5
IL13
OR2A1
TLR4
SFTPD
KLRC1
KLRA1
NUBP2
IGFALS
JSAP1
OR7A17
4q27
5q23
5q23
5q23
7q35
9q33
10q22
12p13
12p13
16p13
16p13
16p13
19p13
X
X
X
X
X
X
X
X
X
X
X
X
X
Monoallelically expressed 61 .
Heterogeneous allele-specific expression in extrapulmonary tissues 66 .
Monoallelically expressed 68, 69 .
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Synchronously replicated 71 .
No evidence of imprinting 73 .
Biallelically expressed 74 .
Biallelically expressed in mouse 79 .
Biallelically expressed in mouse 78, 80 .
Imprinted in mouse but not in human 92 .
Biallelically expressed in human hydatidiform mole, mature teratoma,
and normal placenta 90 .
Presumed biallelic expression

CD2
APOB
GPD2
IGFBP5
RPL23
Gt(ROSA)26asSor
MSX1
GHR
OSMR
PRLR
IL7R
NPR3
SEMA5A
CDH10
GABRA6
SLC22A1
SOD2
TCP1
MAS1
PLG
COL1A2
ACTB
ACHE
UBE2H
MKRN1
SDC2
FZD6
NOV
MYC
DOCK8
TYRL
PAX6
GAS2
STIM1
TPH1
CARS
RNH
TH
ASCL2
CTSD
1p13
2p24
2q24
2q35
2q36
3p25
4p16
5p12
5p13
5p13
5p13
5p13
5p15
5p14
5q34
6q25
6q25
6q25
6q25
6q26
7q21
7p22
7q22
7q32
7q34
8q22
8q22
8q24
8q24
9p24
11p11
11p13
11p14
11p15
11p15
11p15
11p15
11p15
11p15
11p15
RRM1
DUSP8
NAP1L4
11p15
11p15
11p15
X
X
X
PYGM
CD3D
GAPD
CD4
DCN
RB1
YY1
WARS
PPP2R5C
DNCHC1
HERC2
NDNL2
DUOX1
SLC28A2
DUOX2
SLC30A4
GATM
TP53
RPL19
ERBB2
APLP1
MAG
SCN1B
GRIK5
APOE
KCNA7
SYT3
GRIN2D
HRC
KCNC3
RRAS
E2F1
BC10, BLCAP
PLCG1
PPGB
TNFRSF5
KCNB1
CYP24A1
EDN3
PCK1
NTSR1
BMP7
CDH4
RUNX1
PFKL
11q13
11q23
12p13
12p13
12q21
13q14
14q32
14q32
14q32
14q32
15q11
15q13
15q21
15q21
15q21
15q21
15q21
17p13
17q12
17q12
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
20q11
20q11
20q12
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
21q22
21q22
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Biallelic expression in multiple murine fetal and adult tissues
imprinted in the human 92 .
Biallelically expressed 105, 106 .
9597 ,
not
Expression can be one of the following: P (Imprinted and paternally expressed),

M (Imprinted and maternally expressed), or X (Not imprinted). All 101 genes were
correctly predicted not to be imprinted by the combined classifier. The experimental
results cited here may relate to either mouse or human.
Supplementary Table 8. Training genes of known imprint status.

Gene
Band
Expression
Reference
1p31
1p36
6q24
6q24
7p12
7q21
7q21
7q21
7q21
7q32
7q32
11p13
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
14q32
14q32
15q11
15q11
15q11
15q11
15q11
15q12
15q12
18q21
19q13
20q11
20q13
20q13
20q13
P
M
P
P
I
M
M
P
P
M
P
P
P
M
M
M
M
M
M
M
M
M
P
P
M
M
P
P
P
P
P
P
M
M
M
P
P
M
P
P
110, 111
1p13
1p32
2p15
6p21
6p25
6q25
7p11
7p12
7p12
7p13
7p13
7q32
7q32
7q32
X
X
X
X
X
X
X
X
X
X
X
X
X
X
P. Luedi (unpublished)
Imprinted
ARHI
TP73
HYMAI
PLAGL1
GRB10
DLX5
PPP1R9A
SGCE
PEG10
CPA4
MEST
WT1
IGF2
OSBPL5
SLC22A1L
CDKN1C
ZNF215
KCNQ1DN
PHLDA2
SLC22A1LS
KCNQ1
H19
IGF2AS
INS
SMPD1
MEG3
DLK1
SNURF
MKRN3
NDN
MAGEL2
IPW
UBE3A
ATP10A
TCEB3C
ZIM2
NNAT
NESP55
L3MBTL
GNAS1
112114
115
116
117, 118
119
120
121
122
34
35
123
124126
127
128, 129
130132
133
134
135
136, 137
138
126, 139, 140
141
142
143
45
43, 44
144
145148
149, 150
151, 152
153
154, 155
156, 157
158
159, 160
105
161
162
163
Non-imprinted
NGFB
CDKN2C
COMMD1
CDKN1A
SERPINB6
IGF2R
EGFR
COBL
DDC
IGFBP3
IGFBP1
CPA1
HSPC216
NRF1
164
165
164
P. P. Luedi (unpublished)
166168
169
170
170
171, 172
171, 172
173
83
83
TSGA14
KIAA0265
Flj14803
CPA2
UBE2H
CNTNAP2
EN2
C9ORF39
NOR1/NR4A3
SAMD6
C10orf9
SFMBT2
C10ORF28
PHEMX
DRD4
MUCDHL
MRPL23
CD81
TNNT3
HRAS
TSSC4
C11ORF2
NEU3
CDKN1B
NOVA1
CYFIP1
NIPA2
TUBGCP5
NIPA1
C15ORF2
OCA2
GABRB3
GABRG3
CABLES
IMPACT
JAG1
TH1L
CTSZ
7q32
7q32
7q32
7q32
7q32
7q36
7q36
9p22
9q22
9q22
10p11
10p14
10q24
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11q13
11q13
12p13
14q12
15q11
15q11
15q11
15q11
15q11
15q12
15q12
15q12
18q11
18q11
20p12
20q13
20q13
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
174
83
83
173
83
K. S. Kucera (unpublished)
92, 175
176
94
175, 177
92, 178, 179
180
94
175
181
164
K. S. Kucera, P. P. Luedi (unpublished)

102
102
102
102
182
102
102
102
183
184
184
Expression can be one of the following: P (Imprinted and paternally

expressed), M (Imprinted and maternally expressed), or X (Not imprinted). The GRB10 locus encodes oppositely imprinted transcripts
and was excluded from the maternal/paternal model (denoted by I).
The experimental results cited here may relate to either mouse or
human.
Supplementary Table 9. Randomly chosen control genes.

Ensembl ID
065183 (WDR3)
092621 (PHGDH)
134245 (WNT2B)
134253 (TRIM45)
007341 (ST7L)
116793 (PHTF1)
122481 (RWDD3)
173146 (Q96CI4)
117600 (NM 014839)
162688 (AGL)
142951
069702 (TGFBR3)
122417 (Q9ULJ1)
097096 (Q8NDB8)
171488 (NM 032270)
117174 (NM 017953)
153898 (MCOLN2)
162624 (Q9BYB7 )
178965 (Q8ND41)
079739 (PGM1)
117114 (LPHN2)
116641 (DOC7 )
162433 (AK3)
185483 (ROR1)
162402 (USP24)
134744 (Q12764)
162398 (NM 152607 )
121310 (NM 018281)
058804 (NM 018087 )
162384 (NM 017887 )
181150
186857 (Q9HBS7 )
142973 (CYP4B1)
186160 (NM 178134)
054116 (TRAPPC3)
132773 (TOE1)
126091 (SIAT6)
131238 (PPT1)
179178 (NM 144626)
117400 (MPL)
127129 (EDN2)
171812 (COL8A2)
117407 (ARTN)
185421
186444 (TMSL1)
186973
084628 (TCBA1)
175089 (Q9BXE6)
168528 (NM 178865)
134668 (NM 144569)
121774 (KHDRBS1)
183615 (YSEC)
125945 (ZNF436)
133226 (SRRM1)
173413 (Q9BXE6)
179589 (Q8NA34)
008130 (PPNK )
177799 (O4F3)
175262 (NM 173507 )
175087 (NM 152835)
160072 (NM 031921)
117701 (NM 022078)
127054 (NM 017871)
177000 (MTHFR)
008125 (MMP23A)
158748 (HTR6)
162426 (DNB5)
117682 (DHDDS)
162438 (CTRC)
169504 (CLIC4)
171735 (CAMTA1)
053371 (AKR7A2)
158803
186410
160670 (S100A6)
177954 (RPS27 )
143545 (RAB13)
163155 (Q96S90)
178527 (Q8N9C2)
143615 (O14634)
160741 (NM 181715)
143415 (NM 020239)
143621 (ILF2)
131781 (FMO5)
143369 (ECM1)
132043
Band
1p12
1p12
1p13
1p13
1p13
1p13
1p21
1p21
1p21
1p21
1p21
1p22
1p22
1p22
1p22
1p22
1p22
1p31
1p31
1p31
1p31
1p31
1p31
1p31
1p32
1p32
1p32
1p32
1p32
1p32
1p32
1p32
1p33
1p33
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p34
1p35
1p35
1p35
1p35
1p35
1p35
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1p36
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q21
i
f
t
t
t
f
t
t
t
f, i
f
i
t
i
t
f
f
t
f
i
t
t
f
t
t
i
i
i
i
i
i
f
i
i
f
f
i
t
t
i
t
f, t
i
f
f
f
f
f
f
i
t
f, t
f
i
t
t
f
t
t
t
f
t
f
t
t
i
f
f
i
f
f
t
f
i
f
i
i
t
t
i
t
t
t
t
t
i
Ensembl ID
053900 (NM 013367 )
159788 (RGS12)
177631 (NM 182524)
130997 (NM 181808)
178988 (NM 152301)
179010 (NM 033296)
159692 (CTBP1)
087269 (C4orf9)
170891 (C17 )
184855
109184 (NM 015115)
179378 (NM 006692)
124882 (EREG)
087128 (DES1)
124875 (CXCL6)
135222 (CSN2)
081051 (AFP)
079557 (AFM)
186942 (Q9BQR7 )
173130 (Q9P1E1)
138670 (NM 152545)
138759 (FRAS1)
138769 (CDKL2)
118785 (SPP1)
174421 (Q9P1E1)
163644 (NM 152542)
138641 (HERC3)
052592 (DMP1)
164035 (NM 016242)
179078
109534 (NOLA1)
174720 (NM 016648)
145384 (FABP2)
170917 (NUDT6)
138686 (BBS7 )
164057
109424 (UCP1)
153130 (SCOC)
137460 (Q9C0D6)
151623 (NR3C2)
137463 (NM 032623)
180484 (NM 024914)
109452 (INPP4B)
164142
151005 (NM 032136)
171557 (FGG)
164117 (FBXO8)
185075 (Q9H399)
173320 (Q9P2F5)
180712 (NM 173796)
164303 (NM 153343)
109771 (NM 018409)
168556 (ING1L)
151726 (FACL6)
075705 (DUX2)
182552 (NM 152682)
186158
172239 (NM 182789)
178846 (NM 175921)
113361 (CDH6)
113460 (BRIX )
182564
182977 (Q9P1I1)
153416 (ZDHHC11)
142319 (SLC6A3)
133398 (Q9BTT4)
164363 (NM 182632)
173545 (NM 033414)
125063 (NM 017808)
176788 (BASP1)
184204
164512 (NM 024669)
153914 (SFRS12)
113598 (NM 019072)
164253 (NM 018268)
132835 (NM 013303)
113161 (HMGCR)
181104 (F2R)
164300 (NM 178276)
164299 (NM 032567 )
174715
176819
183772 (CMYA5)
133302 (NM 032290)
185261 (NM 173665)
169736 (Q9NS32)
Band
4p15
4p16
4p16
4p16
4p16
4p16
4p16
4p16
4p16
4p16
4q11
4q13
4q13
4q13
4q13
4q13
4q13
4q13
4q13
4q21
4q21
4q21
4q21
4q22
4q22
4q22
4q22
4q22
4q24
4q24
4q25
4q25
4q26
4q27
4q27
4q28
4q31
4q31
4q31
4q31
4q31
4q31
4q31
4q31
4q32
4q32
4q34
4q34
4q35
4q35
4q35
4q35
4q35
4q35
4q35
4q35
4q35
5p12
5p13
5p13
5p13
5p13
5p13
5p15
5p15
5p15
5p15
5p15
5p15
5p15
5p15
5q11
5q12
5q12
5q13
5q13
5q13
5q13
5q14
5q14
5q14
5q14
5q14
5q15
5q15
5q21
t
t
t
f
t
i
f, t
t
f
t
i
i
f
i
t
f
i
i
i
t
t
i
t
t
t
i
t
i
f
i
t
f
t
i
i
t
i
f
f
t
t
f
i
f
f
f
i
t
t
i
i
t
f
f, t
t
t
i
t
f
f
i
t
t
t
i
i
i
i
f
i
f
f
f
i
i
t
f
f
f
i
f
t
f
f
i
f
Ensembl ID
184879
165059 (PRKACG)
135045 (NM 017998)
106782 (CHAC)
135049 (AGTPBP1)
186632
186747 (Q8N493)
136936 (XPA)
106809 (OGN)
021374 (IARS)
158122
185544
106692 (FCMD)
186943 (Q8NGS7 )
187003 (ACTL7A)
136868 (SLC31A1)
173238 (Q9P1E1)
173242
136856 (SLC2A8)
119446 (NM 033117 )
136950 (NM 030978)
136861 (CDK5RAP2)
160446 (ZDHHC12)
165699 (TSC1)
119363 (SPTAN1)
160271 (RALGDS)
107290 (NM 015046)
125484 (GTF3C4)
136877 (FPGS)
169583 (CLIC3)
148408 (CACNA1B)
160323 (ADAMTS13)
159247
177185
186350 (RXRA)
187195 (NM 030898)
136737 (ZNF25)
173776 (Q96HT2)
177353 (O75029)
177291 (NM 153368)
183621 (NM 182755)
151025 (Q9ULT3)
095739 (NMA)
150051 (NM 173576)
182649
152465 (NMT2)
134465 (Q8TE30)
180525 (Q8N8Z3)
134453 (NM 032905)
165568 (NM 031436)
134460 (IL2RA)
172619 (Y514)
177457 (NM 173524)
165388 (NM 153034)
170324 (NM 152428)
152728 (NM 147156)
148582
122952 (ZWINT )
108064 (TCF6L1)
170312 (CDC2)
079332 (SARA1)
107719 (Q9ULE6)
122861 (PLAU)
178365 (NUDT13)
166220 (NM 152710)
122359 (ANXA11)
182180 (DNAJC9)
182523
180850 (NM 178512)
152778 (IFT5)
165678 (GHITM)
138180 (C10orf3)
148835 (TAF5)
095637 (SORBS1)
156398 (SFXN2)
107816 (Q8N1I9)
171160 (NM 178832)
075826 (NM 015490)
065613 (NM 014720)
148820 (LDB1)
138136 (LBX1)
120053 (GOT1)
107831 (FGF8)
171311 (CSL4)
165851
151553 (Q9HCH2)
Band
9q13
9q21
9q21
9q21
9q21
9q21
9q21
9q22
9q22
9q22
9q22
9q22
9q31
9q31
9q31
9q32
9q32
9q32
9q33
9q33
9q33
9q33
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
9q34
10p11
10p11
10p11
10p11
10p11
10p12
10p12
10p12
10p12
10p13
10p15
10p15
10p15
10p15
10p15
10q11
10q11
10q11
10q11
10q11
10q11
10q21
10q21
10q21
10q22
10q22
10q22
10q22
10q22
10q22
10q22
10q22
10q23
10q23
10q23
10q23
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q24
10q25
i
f
f
f
t
f
f
f
f
t
i
t
f
t
f
i
t
f
t
t
i
i
f
t
f
f
t
t
t
f
t
t
t
f
f
f
f
f
f
f
f
f
i
i
f
i
f
i
f
i
t
i
t
t
i
f
f
t
i
i
t
f
t
f
i
f
t
t
i
i
t
i
i
i
f
f
f
t
f
i
t
t
t
i
f
f
Ensembl ID
183000
183208
184508 (Q8N4P3)
185442 (Q8NBH7 )
185594 (NM 173499)
185907 (NM 018621)
186092
180096 (SEPT1)
175995 (NM 175901)
179755 (NM 153227 )
179965 (NM 016643)
149925 (ALDOA)
169861
181601
183604 (Q9H2H6)
184110 (EIF3S8)
175758 (Y220)
169344 (UMOD)
047578 (Q8N803)
179038 (NM 145237 )
103275 (UBE2I)
103197 (TSC2)
095917 (TPSD1)
162009 (SSTR5)
162065 (Q9ULP9)
171559 (Q96EU1)
069651 (NPIP)
161998 (NM 145294)
153060 (NM 144674)
161995 (NM 053284)
168101 (NM 032349)
059122 (NM 032296)
033011 (NM 019109)
100726 (NM 016111)
072864 (NDE1)
102858 (MGRN1)
103313 (MEFV )
103222 (ABCC1)
103229 (ABAT )
166737
184629 (Q8NCX2)
069329 (VPS35)
129635 (Q9P1B8)
103460 (TNRC9)
103494 (Q9Y2K8)
166152 (NM 144602)
129636 (NM 030790)
171208 (NETO2)
169715 (MT1E)
102978 (POLR2C)
070729 (CNGB1)
187185 (Q86VG7 )
103043 (TAX1BP2)
140824 (TAT )
157405 (Q96JG3)
159708 (NM 018296)
090857 (NM 017990)
038358 (NM 014329)
168625 (HYDIN)
090863 (GLG1)
135723 (FHOD1)
103089 (FAXDC1)
103018 (CYM5)
141076 (CIRH1A)
062038 (CDH3)
067955 (CBFB)
166454 (Y431)
166455 (NM 152337 )
153815 (NM 030629)
140905 (GCSH)
168589 (DNCL2B)
166522
131149 (Y182)
140950 (Q9HCG3)
131153 (NM 016095)
124391 (IL17C)
178773 (CPNE7 )
182376 (NM 182605)
183967
133030 (NM 015134)
072210 (ALDH3A2)
154050
184185 (KCNJ12)
141028 (Q96T59)
108445 (O95611)
175091
Band
15q26
15q26
15q26
15q26
15q26
15q26
15q26
16p11
16p11
16p11
16p11
16p11
16p11
16p11
16p11
16p11
16p12
16p12
16p12
16p12
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16p13
16q11
16q11
16q12
16q12
16q12
16q12
16q12
16q12
16q13
16q13
16q13
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q22
16q23
16q23
16q23
16q23
16q23
16q23
16q24
16q24
16q24
16q24
16q24
16q24
16q24
17p11
17p11
17p11
17p11
17p12
17p12
17p12
i
t
f
f
f, i
f
t
t
t
f
t
f
t
f
i
t
t
i
i
f
i, t
i
f
i
t
i
f
t
f
i
i
i
i
t
f, t
f
t
t
i
i
f
t
t
t
t
f
i
f, t
f
f, i
i
f
f
i
f
i
f
i
f
i
i
f
i
i
i
t
i
t
i, t
t
f
f
t
f
i
f
f
f
f
t
f
t
f
i
i
f
163122
183558 (HIST1H2AH)
183598 (NM 021059)
187170 (SPRL4A)
187173 (NM 178428)
187223 (SPRL1A)
187428 (NM 178353)
160753 (RUSC1)
163239 (NM 182499)
160752 (FDPS)
160716 (CHRNB2)
143595 (AQP10)
132704 (SPAP1)
162729 (IGSF8)
158481 (CD1C)
158485 (CD1B)
186950 (Q96M18)
120370 (NM 152281)
000457 (NM 020423)
178454 (NM 018578)
143167 (GPA33)
094975 (C1orf9)
162666 (Y040)
116147 (TNR)
117586 (TNFSF4)
172762 (Q9P1E1)
135870 (Q8IVE6)
162779 (NM 182766)
162787 (NM 181572)
135862 (LAMC1)
183831
143355 (LHX9)
122185 (RPS27 )
174307 (PHLDA3)
174514 (NM 181644)
162757 (NM 152485)
158715 (NM 033102)
117153 (NM 021633)
077152 (NM 014176)
117691 (NM 013349)
117650 (NEK2)
118193 (KIF14)
162891 (IL20)
162809 (Q9NQI1)
162814 (NM 138796)
154309 (NM 032890)
186063 (NM 022831)
135763 (Y133)
116918 (TSNAX )
116957 (TBCE)
116991 (Q8NA38)
162913 (Q8N372)
162885 (NM 152490)
081692 (NM 023007 )
168148 (HIST3H3)
152904 (GGPS1)
143669 (CHS1)
173576
185495 (Q9H5Q3)
116984 (MTR)
117009 (KMO)
143700
182097 (Q96CB2)
185346 (Q96B84)
179510 (Q9H5F0)
162727 (Q96R29)
177564 (Q8TC70)
177535 (Q8NGW7 )
171163 (NM 017865)
162711 (CIAS1)
185420 (SMYD3)
187117 (Q8NG85)
178486 (Q8N1I5)
068654 (POLR1A)
173758 (KV2F )
153586 (IGKV4-1)
172116 (CD8B1)
183281 (PLGL)
184943 (NM 052871)
186854 (Q86V40)
115353 (TACR1)
163219 (Y053)
173027 (WBP1)
143977 (SNRPG)
075292 (NM 014497 )
135638 (EMX1)
144048 (DUSP11)
114956 (DGUOK )
115980 (ANXA4)
138072 (Q9NTE1)
011523 (NM 015147 )
143995 (MEIS1)
014641 (MDH1)
1q21
1q21
1q21
1q21
1q21
1q21
1q21
1q22
1q22
1q22
1q22
1q22
1q23
1q23
1q23
1q23
1q23
1q24
1q24
1q24
1q24
1q24
1q25
1q25
1q25
1q25
1q25
1q25
1q25
1q25
1q25
1q31
1q32
1q32
1q32
1q32
1q32
1q32
1q32
1q32
1q32
1q32
1q32
1q41
1q41
1q41
1q41
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q42
1q43
1q43
1q43
1q43
1q43
1q44
1q44
1q44
1q44
1q44
1q44
1q44
1q44
2p11
2p11
2p11
2p11
2p11
2p11
2p11
2p11
2p12
2p13
2p13
2p13
2p13
2p13
2p13
2p13
2p13
2p14
2p14
2p14
2p15
i
t
i
t
i
f
i
i
i
i
f
i
f
i
f
f
f, i, t
t
f
t
t
t
i
i
f
t
f
f, t
f
i
i
f
t
t
i
t
t
i
f
t
i
t
f
t
f
i
i
t
t
f
f
t
i
i
t
f
t
f
f
i
i
f, i
t
t
t
f
t
f
f, i
t
f
i
i
i
f
t
i
t
i
i
i
i
i
f
f, t
i
f
i
i
t
i
t
f
184213 (NM 173488)

134982 (APC)
125341 (SLC22A5)
180831 (Q8N933)
164406 (LEA2)
138829 (FBN2)
182549
073905 (VDAC1)
152700 (SARA2)
053108 (Q8TBU0)
078795 (PKD2L2)
113212 (PCDHB7 )
113070 (DTR)
173250 (Q8TDV0)
185777
155846 (NM 133263)
086570 (FAT2)
055163 (CYFIP2)
181884
183111
113327 (GABRG2)
145864 (GABRB2)
113328 (CCNG1)
118322 (ATP10B)
178187 (ZNF454)
170089 (THOC3)
131183 (SLC34A1)
181538 (Q8N0T8)
145912 (NOLA2)
170074 (NM 173663)
168246 (NM 152277 )
146067 (NM 019057 )
040275 (NM 017785)
064747 (NM 015043)
169045 (HNRPH1)
131459 (GFPT2)
160867 (FGFR4)
113732 (ATP6V0E)
183718 (TRIM52)
184550 (Q9H7L9)
184714
185005 (NM 022471)
112210 (RAB23)
112200 (ZNF451)
065308 (TRAM2)
112077 (RHAG)
174201 (Q9P1E1)
168116 (Q9HCI6)
124743 (Q9H511)
096087 (GSTA2)
146233 (CYP39A1)
112715 (VEGF )
137394 (TRIM10)
175802 (Q9UGE0)
168471 (Q9H3W0)
178214 (Q96QB7 )
168379 (Q8WM95)
172764 (Q8TDV1)
180911 (Q8N925)
176415 (Q8N1I6)
172738 (NM 145316)
096080 (MRPS18A)
111971 (LY6G5C)
096158 (LTB)
112095 (HLA-DOA)
137333 (DHX16)
112195 (C6orf76)
007816 (C6orf11)
168426 (BTNL2)
064999 (ANKS1)
124655 (AIF1)
137406
161912
173580
184729 (NM 018540)
137403 (HLA-F )
178458 (HIST1H3A)
146047 (HIST1H2BA)
161777 (HCG9)
112293 (GPLD1)
137414 (FAM8A1)
112242 (E2F3)
168405 (CMAH)
124508 (BTN2A2)
183679 (HIST1H4J)
185193 (Q9BXE2)
185694
112149 (CD83)
181590 (Q8NC12)
124827 (GCM2)
184431
185689
112280 (COL9A1)
5q21
5q22
5q23
5q23
5q23
5q23
5q23
5q31
5q31
5q31
5q31
5q31
5q31
5q32
5q32
5q33
5q33
5q33
5q33
5q33
5q34
5q34
5q34
5q34
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
5q35
6p11
6p12
6p12
6p12
6p12
6p12
6p12
6p12
6p12
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p21
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p22
6p23
6p24
6p24
6p24
6p25
6q13
f
i
f
t
f
t
f, i, t
t
t
t
f
f
i
f
f
t
i
t
i
i
i
t
t
i
t
i
t
f
t
t
f
t
i
t
i
f
t
i
t
f
i
t
f
t
i
t
t
f
i
f
i
i
f
f
t
t
f
t
i
f
t
i
i
f
t
t
t
i
f
i
f
i
f, t
t
t
t
t
f
i
t
i
i, t
i
t
f
f
i
f
t
i
i
f
t
151884
151893 (NM 153810)
154490 (NM 145235)
107902 (NM 022126)
119979 (NM 018472)
174755 (ACADSB)
176584
186730 (DUX4)
176567 (Q8NH49)
165905 (NM 152312)
110492 (MDK )
180210 (F2)
175104 (TRAF6)
110422 (HIPK3)
186688 (NM 181807 )
121621 (NM 031217 )
187398 (Q86TE4)
134339 (SAA2)
133818 (RRAS2)
151117 (NM 153347 )
166800 (NM 144972)
166788 (NM 138421)
179826 (NM 054031)
151116 (NM 018314)
129158 (NM 012139)
129152 (MYOD1)
181939 (Q8NGM1)
184741 (Q8NH20)
186117 (Q8NGL2)
149150 (SLC43A1)
172685 (Q96PG2)
176495 (Q8NGI8)
109991 (P2RX3)
162222 (NM 173810)
149532 (NM 024811)
162194 (NM 024099)
166930 (MS4A5)
149516 (MS4A3)
134825 (C11orf10)
173101 (SIPA1)
173959 (RBM14)
175514 (Q8TDT2)
179263 (Q8NH65)
166439 (Q8NCN4)
021300 (PLEKHB1)
171631 (P2RY6)
175591 (P2RY2)
178795 (NM 182833)
173914 (NM 031492)
172732 (NM 025128)
132749 (MTL5)
168056 (LTBP3)
172638 (EFEMP2)
175602 (DIPA)
175315 (CST6)
175334 (BANF1)
176245
184154 (NM 145309)
186642 (PDE2A)
187040
118369 (USP35)
137509 (PRCP)
172946 (Q9P1E1)
150312
137693 (YAP1)
110723 (SL2B)
166253 (Q96LP0)
137692 (NM 032299)
118113 (MMP8)
166648 (DNCH2)
176610
187069
036672 (USP2)
173524 (Q9BXE6)
160613 (PCSK7 )
154114 (NM 152715)
095110 (NM 152315)
137747 (NM 032046)
110367 (DDX6)
167283 (ATP5L)
110244 (APOA4)
182581 (Q9BXE6)
023171 (Q9ULL9)
170953 (Q8NGG6)
176952 (Q8N6I7 )
165526 (NM 032795)
149552 (NM 024556)
110013 (NM 018978)
120457 (KCNJ5)
151704 (KCNJ1)
109832 (DDX25)
183483 (Q8IZY5)
185688 (Q8NH79)
10q25
10q26
10q26
10q26
10q26
10q26
10q26
10q26
11p11
11p11
11p11
11p11
11p12
11p13
11p13
11p14
11p14
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11p15
11q11
11q11
11q11
11q12
11q12
11q12
11q12
11q12
11q12
11q12
11q12
11q12
11q12
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q13
11q14
11q14
11q21
11q21
11q22
11q22
11q22
11q22
11q22
11q22
11q22
11q22
11q23
11q23
11q23
11q23
11q23
11q23
11q23
11q23
11q23
11q23
11q24
11q24
11q24
11q24
11q24
11q24
11q24
11q24
11q24
11q24
11q24
i
f
t
t
f
i
f
f
f
t
t
i
i
t
i
t
t
f
i
t
f
i
f
i
t
f
t
i, t
f
i
i
f
t
t
i
t
i
f
i
f
f
i
t
f
t
i
i
t
f
f
t
f
i
f
i
t
t
t
f
t
i
t
t
t
f
f
i
i
t
f
i
i
i
t
t
i
t
t
i
f
i
f
t
f, t
t
t
f
t
t
i
t
f
i
154914 (USP43)
132388 (UBE2G1)
161955 (TNFSF13)
181856 (SLC2A4)
141504 (SAT2)
161929 (Q96MD0)
007168 (PAFAH1B1)
129235 (NM 032731)
132376 (NM 016532)
141503 (M4K6)
161958 (FGF11)
178999 (AURKB)
182335 (Q8TE90)
184166 (OR1D2)
185530 (NM 030970)
185561
187071 (GPS2)
076604 (TRAF4)
141316 (SPACA3)
160551 (Q9P2I6)
173012 (Q8TCQ8)
141298 (NM 033389)
087095 (NM 016231)
108651 (HC66)
108278 (TRIP3)
172660 (TAF15)
174111 (SOC6)
132142 (ACACA)
108270 (AATF )
178655
108379 (WNT3)
131462 (TUBG1)
073861 (TBX21)
167941 (SOST )
131096 (PYY )
108819 (PPP1R9B)
141696 (NO55)
167914 (NM 178171)
167105 (NM 153229)
167159 (NM 152466)
108825 (NM 025267 )
108800 (NM 014897 )
159224 (GIP)
178743
180386
182076 (NBR2)
183978 (NM 014019)
184502 (GAS)
185845 (Q8N0T2)
186916
178012 (PECAM1)
153951 (O4D2)
136490 (NM 030576)
108375 (NM 017763)
087995 (METTL2)
187013 (Q86X59)
141331 (HELZ )
108878 (CACNG1)
182481 (KPNA2)
132481 (TRIM47 )
178932 (Q8N811)
178789 (NM 174892)
173818 (NM 173627 )
167302 (NM 144679)
125457 (NM 020679)
141580 (NM 019613)
109065 (NM 015654)
125445 (MRPS7 )
166685 (COG1)
141527 (CARD14)
167281
184703 (SIRT7 )
185262 (NM 182565)
185298
175319 (Q14179)
176014 (NM 032525)
132199 (NM 017512)
168461
183206
141447 (OSBPL1A)
158201 (ABHD3)
134779 (NM 015476)
141434 (MEP1B)
134765 (DSC1)
186412
186496 (ZNF396)
081916 (SERPINB8)
179981 (SDCCAG33)
186411
168892 (ZNF253)
132010 (ZNF20)
150732 (YE73)
125735 (TNFSF14)
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17p13
17q11
17q11
17q11
17q11
17q11
17q11
17q11
17q12
17q12
17q12
17q12
17q12
17q12
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q21
17q23
17q23
17q23
17q23
17q23
17q23
17q24
17q24
17q24
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
17q25
18p11
18p11
18p11
18p11
18p11
18q11
18q11
18q12
18q12
18q12
18q12
18q12
18q21
18q22
18q23
19p13
19p13
19p13
19p13
f
t
t
t
i
t
t
i
i
f
i
i
t
t
f
f
f
i
f
f
i
f
t
i
f
t
f
i
i
i
i
f
t
t
i
i
f
i
i
f
f
f
f
t
i
t
i
f
i
i
i
t
i
t
t
i
t
i
t
i
f
t
f
t
t
i
i
t
i
t
f
f
i
t
t
t
t
t
f
f, t
i
i
i
t
f, t
f
i
t
i
f, t
i
f
i
152518 (ZFP36L2)
152527 (Q8IVE3)
138095 (LRPPRC)
172877 (Q9BXE6)
055332 (PRKR)
138068
084733 (RAB10)
163795 (NM 144631)
119777 (NM 017727 )
138028 (CGREF1)
186453 (Q96NH8)
068697 (LAPTM4A)
171863 (RPS7 )
130508 (Q92626)
174685 (NM 153011)
175652
182717
084090 (STARD7 )
163126 (NM 144994)
163699 (NM 025024)
158435 (NM 017546)
115446 (NM 014044)
071073 (MGAT4A)
168677 (HMGN1)
144191 (CNGA3)
115669 (SULT1C1)
170417 (NM 144632)
176120 (NM 032658)
015568 (RANBP2L1)
179757 (Q9P1E1)
175772 (NM 152518)
153214 (NM 032824)
136688 (IL1F9)
136696 (IL1F8)
184764 (RPL22)
074054 (CLASP1)
176119 (Q96N27 )
173302 (Q8TDV2)
136698 (NM 032545)
178206 (NM 032248)
076003 (MCM6)
182316
115919 (KYNU)
169432 (SCN9A)
144285 (SCN1A)
174470 (Q96M44)
169507 (NM 173512)
172292
155657 (TTN)
172845 (SP3)
163364 (Q96D13)
175892 (Q8NAT4)
128655 (PDE11A)
163492 (NM 173648)
163093 (NM 152384)
144306 (NM 024583)
115806 (GORASP2)
079150 (FKBP7 )
018510 (AGPS)
115942 (ORC2L)
155754 (NM 152525)
155729 (NM 152387 )
178420 (NM 030804)
115520 (NM 025147 )
155760 (FZD7 )
155755 (ALS2CR4)
186680
168582 (CRYGA)
135912 (Y173)
127831 (VIL1)
135913 (USP37 )
163526 (TUBA4)
115592 (PRKAG3)
115655 (NM 024085)
163497 (NM 017521)
066216 (TNRC15)
176946 (THA4)
173100 (Q9P0V4)
144488 (Q8IVU2)
066248 (NGEF )
115488 (NEU2)
135916 (ITM2C)
135930 (EIF4EL3)
163286 (ALPPL2)
182177
182202
184945 (Q8IXF9)
186235
064835 (POU1F1)
179021 (NM 173824)
179799 (Q8NHB5)
170837 (GPR27 )
157467 (O15083)
2p21
2p21
2p21
2p22
2p22
2p22
2p23
2p23
2p23
2p23
2p23
2p24
2p25
2p25
2p25
2p25
2p25
2q11
2q11
2q11
2q11
2q11
2q11
2q11
2q11
2q12
2q12
2q12
2q13
2q13
2q13
2q13
2q13
2q13
2q13
2q14
2q21
2q21
2q21
2q21
2q21
2q21
2q22
2q24
2q24
2q24
2q24
2q24
2q31
2q31
2q31
2q31
2q31
2q31
2q31
2q31
2q31
2q31
2q31
2q33
2q33
2q33
2q33
2q33
2q33
2q33
2q33
2q34
2q35
2q35
2q35
2q35
2q35
2q35
2q35
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
2q37
3p11
3p11
3p12
3p13
3p14
i
f
t
t
t
i
t
f
t
f
i
f
f
i
i
f
f
t
f
i
i
i
t
t
f
t
f, t
i
i
i
i
t
f
i
i
t
i
f
i
f
i
i
t
i
i
i
f
f
i
i
f
i
f
t
f
i
f
f
t
t
i
i
f
i
f
t
i
i
f
t
f
i
t
i
t
i
i, t
i
i
i
i
i
i
i
f
f
t
t
t
f
f
t
f
175596 (Q9P1E1)
085382 (HACE1)
132429 (POPDC3)
177214 (NM 173559)
123510 (BXDC1)
146374 (THSD2)
111817 (SART2)
152894 (PTPRK )
111912 (NCOA7 )
146376 (ARHGAP18)
146411 (SLC2A12)
154269 (ENPP3)
146386 (Q9P0A1)
135577 (NMBR)
111962 (UST )
130338 (TULP4)
122335 (SERAC1)
180821 (RBM16)
120253 (NUP43)
049618 (NM 175863)
120276
174218
185068 (Q9BST5)
185345 (PARK2)
153471 (TCP10)
120436 (GPR31)
146731 (CCT6A)
154997
180594 (Q96C79)
106628 (POLD2)
015676 (NM 015332)
106624 (AEBP1)
010270 (STARD3NL)
164542 (Q8NCT3)
181211 (Q8NA17 )
173862 (NM 017937 )
122641 (INHBA)
106105 (GARS)
187258 (Q86SP4)
176514 (Q9UDC8)
174487 (Q9BXE6)
105928 (DFNA5)
153790 (C7orf31)
105889
186179
186797
106443 (PHF14)
146530 (NM 182545)
173467 (NM 176813)
106541 (AGR2)
146587 (NM 021163)
164818 (NM 017802)
106263 (EIF3S9)
169549
174959
175987
179800
187127 (POL1)
009950 (WBSCR14)
135174 (Q9Y4L9)
133380 (NM 153363)
177585
184569
146745 (NM 032763)
105781 (GRM3)
157240 (FZD1)
127962
166526 (ZNF3)
169899 (Q96MA9)
167011 (Q8N8M0)
078319 (PMS2L1)
146834 (NM 019606)
021461 (CYP3A43)
173685
184414 (IRS3L)
185055
128519 (TAS2R16)
135272 (Q9P1T7 )
106034 (NM 024913)
106041 (FAM3C)
180324 (CAPZA2)
146809 (ASB15)
128578 (Q9ULQ0)
064419 (NM 012470)
105875 (Q96AE5)
122786 (CALD1)
127364 (TAS2R4)
171082 (Q8N3Z8)
184412
122063 (XRCC2)
106615 (RHEB)
181652 (NM 173681)
133574 (NM 018326)
6q14
6q16
6q21
6q21
6q21
6q22
6q22
6q22
6q22
6q22
6q23
6q23
6q24
6q24
6q25
6q25
6q25
6q25
6q25
6q25
6q25
6q25
6q25
6q26
6q27
6q27
7p11
7p11
7p13
7p13
7p13
7p13
7p14
7p14
7p14
7p14
7p14
7p14
7p14
7p15
7p15
7p15
7p15
7p15
7p15
7p15
7p21
7p21
7p21
7p21
7p22
7p22
7p22
7p22
7p22
7p22
7p22
7p22
7q11
7q11
7q11
7q11
7q11
7q21
7q21
7q21
7q21
7q22
7q22
7q22
7q22
7q22
7q22
7q22
7q22
7q22
7q31
7q31
7q31
7q31
7q31
7q31
7q32
7q32
7q33
7q33
7q34
7q34
7q34
7q36
7q36
7q36
7q36
t
f
i
t
t
t
i
i
f
f
f
i
t
f
t
f
f
t
i
f
t
f
i
t
i
t
t
t
f
t
i
f
t
i
t
i
t
f
f
f
f, t
f
f
t
i
t
t
t
i
f
i
t
f
f
i
i
f
t
i
t
f
i
i
t
t
i
i
t
f
t
t
f
t
t
f
t
f, i
f
t
i
f
t
t
i
t
f
t
f
f
t
f
f
i
187072
175724 (NM 152711)
177340 (NM 024799)
123106 (NM 018318)
110888 (C1QDC1)
151490 (PTPRO)
067182 (TNFRSF1A)
121314 (TAS2R8)
121379 (TAS2R14)
013588 (RAI3)
126838 (PZP)
173342 (PRB1)
173391 (OLR1)
172322 (NM 138337 )
111671 (NM 032641)
171792 (NM 031465)
126740 (NM 007273)
121373 (KLRC4)
111218 (HRMT1L3)
111664 (GNB3)
118972 (FGF23)
111652 (COPS7A)
180574
151229 (SLC2A13)
151233 (Q8IXV1)
186518 (Q96SJ6)
166888 (STAT6)
172602 (RHO6)
076067 (RBMS2)
167566 (Q9HCH0)
179962 (Q8NGE6)
139645 (Q8NB46)
139540 (NM 173596)
139579 (NM 024068)
139625 (MAP3K12)
170477 (KRT4)
135472 (FAIM2)
139631 (CSAD)
177981 (ASB8)
167580 (AQP2)
135409 (AMHR2)
185389 (NM 018507 )
185971
186897 (Q86Z23)
177221 (Q8WYW9)
155974 (GRIP1)
111537 (IFNG)
166225 (FRS2)
111596 (CNOT2)
185393 (Q9BTS6)
185563
165899 (NM 173591)
139330 (KERA)
139292 (GPR49)
083782 (DSPG3)
180318 (CART1)
182127
187111
028203 (VEZA)
139343 (SNRPF )
136051 (Q9NV91)
166629 (Q96L24)
151136 (NM 152322)
111670 (NM 024312)
139420 (NM 007076)
174600 (CMKLR1)
139352 (ASCL1)
120868 (APAF1)
183395 (PMCH)
185046 (NM 020140)
139370 (SLC15A4)
061936 (SFRS8)
089232 (SCA2)
139697 (SBNO1)
178043 (Q9HA69)
180645 (Q9BUH0)
177213 (Q96LP1)
139767 (Q96JH4)
089159 (PXN)
177192 (PUS1)
089250 (NOS1)
130921 (NM 152269)
111412 (NM 024738)
135090 (NM 016281)
135148 (NM 006700)
122965 (K682)
158104 (HPD)
135108 (FBXO21)
111249 (CUTL2)
111707
184967 (NM 024078)
132950 (ZNF237 )
023957 (TUBA2)
11q24
11q25
12p11
12p11
12p11
12p12
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12p13
12q12
12q12
12q12
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q13
12q14
12q14
12q15
12q15
12q15
12q15
12q15
12q21
12q21
12q21
12q21
12q21
12q21
12q21
12q22
12q23
12q23
12q23
12q23
12q23
12q23
12q23
12q23
12q23
12q23
12q23
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
12q24
13q12
13q12
i
t
f
t
f
f
f
i
i
f
t
f
f
f
i
f
f
i
t
f
i
t
t
t
f
t
i
i
t
i
t
i
i
f
i
f
t
i
i
i
f
f
i
f
t
t
f
f
t
t
f
f
i
f
i
f
t
f
f, i
i
f
f
i
i
f
i
f
f
i
t
t
t
t
f, i
f
t
i
i
t
f
i
t
t
t
i
t
i
i
f
f, t
f
t
i
181143 (Q9H8T7 )
132001 (Q9H0M5)
141933 (Q96GE2)
129933 (Q8N7K4)
099817 (POLR2E)
130313 (PGLS)
104883 (PEX11G)
176995 (OR7C1)
099308 (O60307 )
175217 (NM 138774)
167807 (NM 080665)
130307 (NM 031941)
129951 (NM 024888)
132000 (NM 024825)
079313 (NM 020695)
125912 (NM 020170)
130813 (NM 018381)
167487 (NM 018316)
171466 (NM 017656)
105229 (NM 015897 )
127666 (NM 014261)
064489 (MEF2B)
099617 (EFNA2)
123146 (CD97 )
161082 (BRUNOL5)
115268
183617 (MRPL54)
185113 (NM 032281)
185293
187365 (NM 175910)
159905 (ZNF234)
018607 (ZNF221)
159882 (ZNF155)
063244 (U2AF )
063176 (SPHK2)
160296 (SIGLECL1)
168995 (SIGLEC7 )
161681 (SHANK1)
180281 (Q8N843)
179873 (PYA6)
104960 (PTOV1)
011485 (PPP5C)
105568 (PPP2R1A)
087074 (PPP1R15A)
105223 (PLD3)
104967 (NOVA2)
179932 (NM 178511)
176472 (NM 174945)
161652 (NM 152358)
104892 (NM 145275)
142544 (NM 145232)
105479 (NM 144577 )
160410 (NM 138392)
126249 (NM 032346)
104865 (NM 018111)
076650 (NM 018025)
160505 (NAL4)
174562 (KLKF )
167749 (KLK4)
105063 (KB15)
167644 (IMUP)
160007 (GRLF1)
126262 (GPR43)
105220 (GPI)
123859 (FPRL2)
104884 (ERCC2)
142025 (DMRTC2)
105205 (CLC)
170956 (CEACAM3)
142273 (CBLC)
008364 (AP2A1)
142513 (ACPT )
176898
179930
182582 (Q96GE3)
186888
187092 (Q8N0S4)
187116 (NM 181879)
187356
177587 (Q96MG3)
179447 (Q8N7Z9)
132661 (NXT1)
101004 (NM 025176)
173404 (INSM1)
101435 (CST9L)
125815 (CST8)
077984 (CST7 )
125872 (C20orf75)
101247 (C20orf7 )
172296 (C20orf38)
089177 (C20orf23)
089123 (C20orf13)
132623 (ANKRD5)
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19p13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
19q13
20p11
20p11
20p11
20p11
20p11
20p11
20p11
20p11
20p12
20p12
20p12
20p12
20p12
20p12
t
f, i
t
i
i
f
f
f
t
i
i
f
i
f
t
t
f
i
f
i
f
i
t
f
f
f
i
f
t
t
t
i
t
i
t
t
i
t
i
f
f
f
t
f
t
f
f
i
f, t
i
i
t
i
f
i
t
t
i
t
f
t
i
t
i
t
f
f
i
i
t
t
t
f
t
f
f
i
i
f
t
t
i, t
i
t
i
i
i
f
i
f
f
f
i
177664 (DNAH12)
168374 (ARF4)
163638 (ADAMTS9)
163825 (TMEM7 )
162244 (RPL29)
168237 (NM 145262)
163817 (NM 020208)
145029 (NICN1)
160808 (MYL3)
180929 (GPR62)
088538 (DOCK3)
121797 (CCRL2)
121807 (CCR2)
164062 (APEH)
184345 (Q8IXL9)
186748 (NM 018651)
163673 (Q9C098)
168026 (NM 145755)
114853 (NM 145166)
172936 (MYD88)
157036 (ENDOGL1)
185313 (SCN10A)
187091 (PLCD1)
170266 (GLB1)
163513 (TGFBR2)
131374 (TBC1D5)
185690 (Q9NYD7 )
186032
171148 (TADA3L)
157103 (SLC6A1)
171135 (NM 032492)
154743 (NM 025265)
088726 (NM 018306)
163703 (CRELD1)
131375 (CAPN7 )
178700 (NM 176815)
178694 (NM 022072)
178660
181065 (Q9P161)
163428 (Q96CX6)
144848 (NM 022488)
121570 (NM 018189)
091972 (MOX2)
082701 (GSK3B)
121594 (CD80)
144811
182491
058262 (S612)
114544 (NM 017836)
065534 (MYLK )
173702 (MUC13)
184621 (Q9HDC0)
163785 (RYK )
170883 (Q9BXE5)
163770 (Q86XG3)
163864 (NMNAT3)
175110 (MRPS22)
114124 (GPRK7 )
152977 (ZIC1)
181467 (RAP2B)
174928 (NM 173657 )
144974 (NM 024621)
118855 (NM 022736)
163659 (NM 015508)
114771 (AADAC)
169760 (NLGN1)
136521 (NDUFB5)
171109 (MFN1)
176494
177694
073849 (SIAT1)
145012 (LPP)
090539 (CHRD)
161204 (ABCF3)
058705 (IL1RAP)
119231 (SEN5)
178413 (Q8N266)
173950 (NM 152531)
163975 (MFI2)
075711 (DLG1)
170455 (CNGA1)
145246 (ATP10D)
170462
183380
163281 (NM 138335)
174123 (TLR10)
154279 (Q8WZ27 )
121895 (NM 024943)
174343 (CHRNA9)
175524 (Q9UN81)
163142 (Q8TE30)
3p14
3p14
3p14
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p21
3p22
3p22
3p22
3p22
3p22
3p22
3p22
3p23
3p24
3p24
3p24
3p24
3p25
3p25
3p25
3p25
3p25
3p25
3p25
3q11
3q11
3q11
3q13
3q13
3q13
3q13
3q13
3q13
3q13
3q13
3q13
3q21
3q21
3q21
3q21
3q21
3q22
3q22
3q22
3q23
3q23
3q23
3q24
3q25
3q25
3q25
3q25
3q25
3q25
3q26
3q26
3q26
3q26
3q26
3q27
3q27
3q27
3q27
3q28
3q29
3q29
3q29
3q29
3q29
4p12
4p12
4p12
4p12
4p13
4p14
4p14
4p14
4p14
4p15
4p15
i
f
f
t
t
t
i
t
i
i
i
f
f
i
i
f
t
i
f
t
t
i
i
t
t
i
f
i
i
f, i
t
t
f
i
f
f
t
i
f
i
f
t
f
f
i
f
f
i
i
i
t
i
t
t
f
i
f
i
i
t
t
f, i
f
i
f
t
i
f, t
t
f
t
t
f
t
t
f
i
i, t
f
i
i
f
t
f
f
f
f
f
t
i
f
126870 (NM 018051)

106560 (NM 015660)
127360 (IAN4L1)
106648 (GALNT15)
105993 (DNAJB6)
164885 (CDK5)
170279 (C7orf33)
168172 (NM 032410)
104371 (DKK4)
185900 (NM 032237 )
181329 (O95724)
133872 (NM 016127 )
184844
147454 (NM 016612)
147443 (DOK2)
069206 (ADAM7 )
182406
184661 (CDCA2)
181897 (NM 018422)
156011 (NM 015310)
154316 (TDH)
177405 (Q8NAJ9)
154359 (NM 152271)
147364 (FBXO25)
177023 (DEFB104)
171060
184608 (C8orf12)
186600 (Q9UDD8)
082556 (OPRK1)
047249 (ATP6V1H)
157556 (Q8NHT1)
165093 (BTF3L2)
121039 (RDH10)
176731 (Q8N0T1)
176206 (NM 030970)
155099 (NM 018710)
176623 (NM 016033)
156170 (NM 152416)
104324 (NM 016134)
164949 (GEM)
155097 (ATP6V1C1)
147666
147667
183299
147654 (EBAG9)
104415 (WISP1)
147804 (SLC39A4)
161016 (RPL8)
170616 (Q9BRH9)
180838 (Q8NAM3)
132297 (OC90)
167702 (NM 145754)
153310 (NM 016623)
147724 (NM 015912)
147684 (NDUFB9)
104419 (NDRG1)
172172 (MRPL13)
179527 (C8orf17 )
177205
185582
035445 (UNC13)
165006 (UBAP1)
107371 (RR40)
165012 (Q96GJ8)
175768 (Q8N4H5)
180810 (NM 014113)
137104 (GALT )
122735 (DNAI1)
122705 (CLTA)
164972 (C9orf24)
165269 (AQP7 )
159712
182355 (NM 015667 )
120247 (IFNA13)
147885 (IFNA13)
147889 (CDKN2A)
186758 (Q8N7I0)
186802 (IFNA16)
147893
155156
147852 (VLDLR)
080503 (SMARCA2)
120158 (RCL1)
170777 (NM 033516)
107020 (NM 018465)
120210 (INSL6)
064218 (DMRT3)
183276
183354 (Q8IVE5)
178798 (Q8NGA9)
170215 (Q8NCQ8)
7q36
7q36
7q36
7q36
7q36
7q36
7q36
8p11
8p11
8p11
8p12
8p12
8p12
8p21
8p21
8p21
8p21
8p21
8p22
8p22
8p23
8p23
8p23
8p23
8p23
8p23
8p23
8p23
8q11
8q11
8q13
8q13
8q21
8q21
8q21
8q21
8q21
8q22
8q22
8q22
8q22
8q22
8q22
8q22
8q23
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
8q24
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p13
9p21
9p21
9p21
9p21
9p21
9p22
9p22
9p24
9p24
9p24
9p24
9p24
9p24
9p24
9p24
9p24
9q12
9q13
t
t
i
t
i
i
t
i
f
i
i
i
f
f
i
t
f
i
t
i
f
f
f
i
f
t
f
f
f
t
f
i, t
i
f
i
f
i
i
t
f
f
t
t
f
i
t
i
t
i
i
f
f
t
f
i
f
f
t
f
f
t
f
i
t
f
i, t
i
f
t
f
f
f
i
i
f
i
f
f, i
i
f
f
t
t
i
t
t
f
i
f
f
f
139514 (SLC7A1)
150459 (SAP18)
180776 (Q8N2S7 )
121390 (PSPC1)
122038 (POLR1D)
150456 (NM 174928)
102699 (ADPRTL1)
073910 (NM 023037 )
133101 (CCNA1)
179630 (U124)
180331 (Q8IX95)
083635 (NUFIP1)
171945 (NM 030970)
102837 (NM 006418)
150506 (PCDH20)
118946 (PCDH17 )
005810 (NM 015057 )
165621 (GPR80)
134900 (TPP2)
139780
139832 (RAB20)
134905 (NM 024537 )
139835 (GRTP1)
057593 (F7 )
130177 (CDC16)
102606 (ARHGEF7 )
129563 (TVA2)
166056 (TCA)
169488 (Q8NH41)
176281 (Q8NGD3)
136315 (Q12762)
100813 (ACINUS)
182545
185271
092108 (C14orf163)
176127 (C14orf128)
129518 (C14orf11)
185941
092208 (SIP1)
165506 (C14orf104)
182090 (C14orf25)
131959 (Q9H373)
131969 (C14orf29)
126778 (SIX1)
126821 (SGPP1)
100612 (NM 016029)
179008 (C14orf39)
184902
140044 (NM 130469)
133997 (MED6)
139985 (ADAM21)
072110 (ACTN1)
187073 (Q86TS2)
165417 (GTF2A1)
042088 (TDP1)
140090 (SLC24A4)
178069 (Q8WYT3)
166428 (NM 138790)
165943 (MOAP1)
130076 (IGHA1)
165521
183940
153684 (Q8NDK0)
169926 (KLF13)
179938
175779 (Q8NAA6)
178351 (Q8N345)
159495 (TGM7 )
103932 (NM 015540)
128928 (IVD)
166947 (EPB42)
092529 (CAPN3)
179646 (Q9UI57 )
166262 (NM 152647 )
140274
166466
170236
140416 (TPM2)
074621 (SLC24A1)
090470 (PDCD7 )
140368 (PSTPIP1)
140367 (NM 173469)
173546 (CSPG4)
169553 (Q8N824)
173867 (MRPL46)
140607
184206
140545 (SPAG10)
140534 (NM 152259)
131873 (CHSY1)
173607
13q12
13q12
13q12
13q12
13q12
13q12
13q12
13q13
13q13
13q14
13q14
13q14
13q14
13q14
13q21
13q21
13q22
13q32
13q33
13q33
13q34
13q34
13q34
13q34
13q34
13q34
14q11
14q11
14q11
14q11
14q11
14q11
14q11
14q11
14q12
14q12
14q13
14q13
14q21
14q21
14q21
14q22
14q22
14q23
14q23
14q23
14q23
14q23
14q24
14q24
14q24
14q24
14q24
14q31
14q32
14q32
14q32
14q32
14q32
14q32
14q32
14q32
15q13
15q13
15q13
15q14
15q14
15q15
15q15
15q15
15q15
15q15
15q21
15q21
15q21
15q21
15q21
15q22
15q22
15q22
15q24
15q24
15q24
15q25
15q25
15q25
15q25
15q26
15q26
15q26
15q26
t
t
i
f, t
t
f
t
i
t
i
t
i
f
i
i
i
f
i
t
f
i
t
i
t
f
i
t
i
i
i
t
f
i
f
t
t
f
i
f
i
i
f
f
f
t
f
t
f
t
t
f
t
i
f
i
f, t
t
t
t
f
f
i
i
t
i
t
f
f
i
t
i
t
f
i
f
i
i
t
t
i
f
i
t
i
t
i
t
f
i
t
f
149497 (Q9BYW8)
171864 (PRND)
125787 (GNRH2)
125903 (DEFB129)
125843 (C20orf29)
149451 (ADAM33)
183994 (Q9Y2V8)
101400 (SNTA1)
125991 (SDBCAG84)
088303 (Q9NQF5)
101464 (CDC91L1)
149611 (C20orf93)
167104 (BPIL3)
182171
183566 (NM 173859)
171940 (ZNF217 )
064205 (WISP2)
180305 (WFDC10A)
101150 (TPD52L2)
101448 (SPINLW1)
124216 (SNAI1)
174334 (Q9H3Z8)
177410 (Q8N5E3)
168734 (PKIG)
132786 (O43713)
149657 (NM 144703)
124217 (MOCS3)
101052 (C20orf9)
132823 (C20orf111)
130706 (ADRM1)
184402 (SS18L1)
155282
185272 (RBM11)
156253 (C21orf6)
182598
160305 (DIP2)
159055 (C21orf45)
182871 (COL18A1)
184724 (KRTAP6-1)
184809 (C21orf88)
184836 (C21orf86)
184900 (SMT3H1)
185225 (C21orf32)
185397 (C21orf51)
185706 (Q8TCY0)
187026 (KRTAP21-2)
128218 (VPREB3)
138842 (Q9BWW2)
133525 (Q99919)
099958 (Q96Q80)
178026 (Q8N0S9)
100034 (PPM1F )
100023 (PPIL2)
161149 (NM 145042)
177663 (IL17R)
100056 (DGCR14)
159664
172963
172981
183229
183307 (CECR6)
183506 (Q8WUK7 )
183785 (PEX26)
184273
099995 (SF3A1)
099985 (OSM)
100350 (NM 024955)
100365 (NCF4)
100385 (IL2RB)
100118 (HMG1L10)
128284 (APOL3)
175329
182763 (Q96EQ7 )
183579 (Q9ULT6)
184117 (NIPSNAP1)
184122 (Q96NJ4)
184654 (Q8N9L7 )
100426 (ZBED4)
100106 (TARA)
100241 (SBF1)
100413 (RPC8)
073150 (PANX2)
100266 (PACSIN2)
176177 (NM 152512)
100101 (NM 024313)
128285 (GPR24)
184472 (YV02)
185022 (MAFF )
20p13
20p13
20p13
20p13
20p13
20p13
20p13
20q11
20q11
20q11
20q11
20q11
20q11
20q11
20q11
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
20q13
21q11
21q11
21q21
21q21
21q22
21q22
21q22
21q22
21q22
21q22
21q22
21q22
21q22
21q22
21q22
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q11
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q12
22q13
22q13
22q13
22q13
22q13
22q13
22q13
22q13
22q13
22q13
22q13
Genes used for the calculation of the pairwise interactions, feature selection, and model training
are denoted by i, f, and t, respectively. To enhance legibility, the common prefix ENSG00000 has
been dropped from the Ensembl ID.
i
i
t
t
f, t
t
f
t
i
i
f
t
t
i
t
t
i
t
i
f
f
t
f
t
f
t
f
i
f
i
i
f
i
f
f
f
i
i
t
i
f
t
t
t
i
t
i
f
t
f
i, t
i
t
f
f
t
i
t
i
f
i
f, i
t
i
i, t
f
i
t
f
f
t
i
t
f
f
i
t
f, t
f
t
f
t
i
i, t
i
i
f
i
Supplementary Table 10. Primers used for expression analysis of DLGAP2 and KCNK9.
Name
DLGAP2-1F
DLGAP2-1R
DLGAP2-RT1
DLGAP2-RT2
DLGAP2-M1F
DLGAP2-M1R
DLGAP2-M2R
Sequence 5 -. . . -3
TAGGCTAGACGTCCAGGAACA
TATTGGCAGGACTGAGTGGAG
ACATGAGAAGCTGGGCACTC
CGTCACCTCCATCGACTTCT
CAGCTACCTTCGAGCCATTC
GGCCGTTTCCACCTGAATC
TGATGCTCTGGGAATTCAG
Position
1603779-1603799
1604304-1604284
2585-2604
2651-2670
1605-1624
2048-2066
2059-2077
KCNK9-1F
CAAGGCCTTCTGCATGTTCT
53849487-53849468
KCNK9-1R
GTGAATGACCATGCTGTTGC
53848983-53849002
KCNK9-M1F
TCCTTCTACTTTGCGATCACG
53933168-53933148
KCNK9-M1R
CATGGTCAAGAACCTGAGGAC
53849058-53849078
Positions for DLGAP2 primers refer to GI37552484, chr8.27.24 (), and chr8.27.26 ().
Positions for KCNK9 primers are given for GI51467074.
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Supplementary Results

Supplementary Table 1. High- and lower-confidence imprinted gene candidates.

Supplementary Figure 1. Distributions of the weights of features characteristic of imprinted genes, as

Supplementary Table 4. Relevant features for prediction of imprinting by Equbits classifiers.

Mean (Standard deviation)

downstream 10:100 FLAM2 upstream 10:9 ATF1

downstream 0:2 SINE MIR2

upstream 10:9 GT2B1 upstream 1:0 MLTF1

downstream 10:100 LINE CR11 upstream 3:2 Pit13

upstream 100:10 MIR32 upstream 1:0 MLTF1

upstream 6:5 NFuE31

upstream 100:10 SINE Alu1 upstream 2:1 BPVE21

Mean (Standard deviation)

Linkage to alcoholism (LOD=1.52) 21 .

Linkage to alcoholism (LOD=3.17; MOD=3.68) 21, 23 .

Linkage to alcoholism (MOD=3.86) 23 .

Linkage to allergic sensitization (Zall =4.31) 29 .

Suggestive linkage to atopy and indications for imprinting

Linkage to Alzheimers disease (LOD=3.3) 25, 26 .

Linkage to Alzheimers disease (LOD=0.9) 25 .

Linkage to Alzheimers disease (LOD=3.15) 27 .

Linkage to Alzheimers disease (LOD=1.43) 27 .

Linkage to Alzheimers disease (LOD=1.40) 28 .

Linkage to autism (MLS=2.31) 33 .

Linkage to autism (MLS=1.15) and schizophrenia

Linkage to bipolar disorder (MLS=1.43) 41 .

Linkage to bipolar disorder (HLOD=2.20) 42 .

Linkage to bipolar disorder (NPL=3.13) 41 .

Linkage to bipolar disorder (HLOD=2.47) 42 .

Linkage to male sexual orientation (MLOD=1.81) 5 .

Linkage to BMI (LOD=1.97) 47 .

Linkage to BMI (LOD=1.81) 47 .

Predominantly expressed in the brain 4 .

Linkage to type 2 diabetes (LOD=3.19) 46 .

Linkage to schizophrenia (LOD=2.71) 49 .

Linkage to schizophrenia (LOD=3.06) 50 .

Linkage to schizophrenia (LOD=1.95) 51 .

were retained in the final classifier.

Supplementary Table 7. Independent negative test genes.

Stochastic monoallelic expression

Presumed biallelic expression

Expression can be one of the following: P (Imprinted and paternally expressed),

Supplementary Table 8. Training genes of known imprint status.

K. S. Kucera, P. P. Luedi (unpublished)

Expression can be one of the following: P (Imprinted and paternally

Supplementary Table 9. Randomly chosen control genes.

184213 (NM 173488)

126870 (NM 018051)

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