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Datasets:
nicolynnvila
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splicing_epistasis_okgp_noncancer1000

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Modalities:
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Size:
100K - 1M
Tags:
genomics
splicing
epistasis
1000-genomes
non-cancer-control
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pandas
Polars
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epistasis_id
stringlengths
33
57
arm
stringclasses
2 values
gene
stringclasses
904 values
chrom
int64
1
22
mut1
stringlengths
16
28
mut2
stringlengths
16
28
distance
int64
1
100
n_mut1
int64
3
254
n_mut2
int64
3
254
n_both
int64
0
247
TMEM234:1:32222303:C:T|TMEM234:1:32222308:C:A
observed
TMEM234
1
TMEM234:1:32222303:C:T
TMEM234:1:32222308:C:A
5
4
4
4
GATC:12:120460241:G:A|GATC:12:120460242:C:A
observed
GATC
12
GATC:12:120460241:G:A
GATC:12:120460242:C:A
1
18
18
18
PRSS50:3:46714202:A:G|PRSS50:3:46714257:G:A
observed
PRSS50
3
PRSS50:3:46714202:A:G
PRSS50:3:46714257:G:A
55
231
17
15
ARHGAP25:2:68820916:A:T|ARHGAP25:2:68820977:A:G
observed
ARHGAP25
2
ARHGAP25:2:68820916:A:T
ARHGAP25:2:68820977:A:G
61
9
210
1
NFE2L3:7:26177426:A:G|NFE2L3:7:26177465:C:T
observed
NFE2L3
7
NFE2L3:7:26177426:A:G
NFE2L3:7:26177465:C:T
39
115
3
2
STK32C:10:132254995:G:A|STK32C:10:132255047:A:G
observed
STK32C
10
STK32C:10:132254995:G:A
STK32C:10:132255047:A:G
52
58
113
1
IBA57:1:228166026:G:C|IBA57:1:228166080:C:G
observed
IBA57
1
IBA57:1:228166026:G:C
IBA57:1:228166080:C:G
54
8
133
1
TMEM106B:7:12223434:C:A|TMEM106B:7:12223465:A:G
observed
TMEM106B
7
TMEM106B:7:12223434:C:A
TMEM106B:7:12223465:A:G
31
198
61
7
EIF2D:1:206604790:G:A|EIF2D:1:206604810:C:T
observed
EIF2D
1
EIF2D:1:206604790:G:A
EIF2D:1:206604810:C:T
20
39
12
1
IQCE:7:2611439:T:C|IQCE:7:2611502:C:T
observed
IQCE
7
IQCE:7:2611439:T:C
IQCE:7:2611502:C:T
63
7
3
1
SPIDR:8:47665436:G:A|SPIDR:8:47665457:T:C
observed
SPIDR
8
SPIDR:8:47665436:G:A
SPIDR:8:47665457:T:C
21
13
79
1
HEBP1:12:12985253:T:A|HEBP1:12:12985332:G:T
observed
HEBP1
12
HEBP1:12:12985253:T:A
HEBP1:12:12985332:G:T
79
14
96
1
GOLGA8R:15:30407770:C:T|GOLGA8R:15:30407774:C:G
observed
GOLGA8R
15
GOLGA8R:15:30407770:C:T
GOLGA8R:15:30407774:C:G
4
7
85
1
PHOSPHO2:2:169694509:T:A|PHOSPHO2:2:169694512:G:A
observed
PHOSPHO2
2
PHOSPHO2:2:169694509:T:A
PHOSPHO2:2:169694512:G:A
3
56
20
1
OR8H2:11:56105504:A:G|OR8H2:11:56105552:C:T
observed
OR8H2
11
OR8H2:11:56105504:A:G
OR8H2:11:56105552:C:T
48
192
13
1
DNAJC25:9:111639933:C:T|DNAJC25:9:111639942:C:G
observed
DNAJC25
9
DNAJC25:9:111639933:C:T
DNAJC25:9:111639942:C:G
9
10
34
1
MTA1:14:105453149:G:A|MTA1:14:105453222:C:T
observed
MTA1
14
MTA1:14:105453149:G:A
MTA1:14:105453222:C:T
73
8
250
8
DSTYK:1:205177250:A:G|DSTYK:1:205177256:G:A
observed
DSTYK
1
DSTYK:1:205177250:A:G
DSTYK:1:205177256:G:A
6
5
46
5
GALNT8:12:4827157:T:C|GALNT8:12:4827245:C:T
observed
GALNT8
12
GALNT8:12:4827157:T:C
GALNT8:12:4827245:C:T
88
23
149
2
OPN4:10:86666163:G:A|OPN4:10:86666228:C:G
observed
OPN4
10
OPN4:10:86666163:G:A
OPN4:10:86666228:C:G
65
9
14
1
MTHFD1L:6:151075931:C:T|MTHFD1L:6:151075977:G:T
observed
MTHFD1L
6
MTHFD1L:6:151075931:C:T
MTHFD1L:6:151075977:G:T
46
6
118
1
ITGBL1:13:101679110:G:T|ITGBL1:13:101679186:G:A
observed
ITGBL1
13
ITGBL1:13:101679110:G:T
ITGBL1:13:101679186:G:A
76
42
81
1
KCNC3:19:50324544:G:A|KCNC3:19:50324549:C:T
observed
KCNC3
19
KCNC3:19:50324544:G:A
KCNC3:19:50324549:C:T
5
73
75
1
ZNF443:19:12437167:T:C|ZNF443:19:12437172:T:A
observed
ZNF443
19
ZNF443:19:12437167:T:C
ZNF443:19:12437172:T:A
5
7
224
1
C8orf88:8:90967643:G:A|C8orf88:8:90967706:C:G
observed
C8orf88
8
C8orf88:8:90967643:G:A
C8orf88:8:90967706:C:G
63
156
19
2
FXR2:17:7610025:T:C|FXR2:17:7610065:C:T
observed
FXR2
17
FXR2:17:7610025:T:C
FXR2:17:7610065:C:T
40
6
233
2
TCF24:8:66948068:T:C|TCF24:8:66948134:C:T
observed
TCF24
8
TCF24:8:66948068:T:C
TCF24:8:66948134:C:T
66
5
146
1
CSE1L:20:49049356:A:T|CSE1L:20:49049376:G:T
observed
CSE1L
20
CSE1L:20:49049356:A:T
CSE1L:20:49049376:G:T
20
226
19
2
ANKAR:2:189703398:G:T|ANKAR:2:189703492:G:C
observed
ANKAR
2
ANKAR:2:189703398:G:T
ANKAR:2:189703492:G:C
94
25
207
4
SPOPL:2:138520885:A:T|SPOPL:2:138520919:G:A
observed
SPOPL
2
SPOPL:2:138520885:A:T
SPOPL:2:138520919:G:A
34
32
22
1
NRP2:2:205747996:G:A|NRP2:2:205748076:C:T
observed
NRP2
2
NRP2:2:205747996:G:A
NRP2:2:205748076:C:T
80
8
76
1
HTR2B:2:231111848:A:G|HTR2B:2:231111901:A:G
observed
HTR2B
2
HTR2B:2:231111848:A:G
HTR2B:2:231111901:A:G
53
27
116
27
ATP1A2:1:160140882:G:C|ATP1A2:1:160140948:C:T
observed
ATP1A2
1
ATP1A2:1:160140882:G:C
ATP1A2:1:160140948:C:T
66
57
130
1
SMUG1:12:54127935:G:A|SMUG1:12:54128027:A:C
observed
SMUG1
12
SMUG1:12:54127935:G:A
SMUG1:12:54128027:A:C
92
4
4
4
SLC12A8:3:125138679:G:T|SLC12A8:3:125138730:G:A
observed
SLC12A8
3
SLC12A8:3:125138679:G:T
SLC12A8:3:125138730:G:A
51
29
29
29
FXR2:17:7598232:C:T|FXR2:17:7598266:C:T
observed
FXR2
17
FXR2:17:7598232:C:T
FXR2:17:7598266:C:T
34
5
157
5
CACNA1H:16:1198842:A:G|CACNA1H:16:1198867:T:G
observed
CACNA1H
16
CACNA1H:16:1198842:A:G
CACNA1H:16:1198867:T:G
25
34
5
5
MTMR12:5:32246441:A:G|MTMR12:5:32246456:C:T
observed
MTMR12
5
MTMR12:5:32246441:A:G
MTMR12:5:32246456:C:T
15
86
12
2
ROR2:9:91888390:G:A|ROR2:9:91888483:A:C
observed
ROR2
9
ROR2:9:91888390:G:A
ROR2:9:91888483:A:C
93
10
26
1
CYLC2:9:103001602:T:C|CYLC2:9:103001674:T:C
observed
CYLC2
9
CYLC2:9:103001602:T:C
CYLC2:9:103001674:T:C
72
12
51
1
GALNTL6:4:172546329:G:A|GALNTL6:4:172546419:C:T
observed
GALNTL6
4
GALNTL6:4:172546329:G:A
GALNTL6:4:172546419:C:T
90
3
229
1
ABCB5:7:20733713:G:A|ABCB5:7:20733810:T:G
observed
ABCB5
7
ABCB5:7:20733713:G:A
ABCB5:7:20733810:T:G
97
74
104
4
MYO7B:2:127622375:G:A|MYO7B:2:127622376:C:G
observed
MYO7B
2
MYO7B:2:127622375:G:A
MYO7B:2:127622376:C:G
1
64
68
1
ATXN10:22:45782319:G:A|ATXN10:22:45782331:G:A
observed
ATXN10
22
ATXN10:22:45782319:G:A
ATXN10:22:45782331:G:A
12
46
69
1
ABCA8:17:68914158:A:G|ABCA8:17:68914240:A:G
observed
ABCA8
17
ABCA8:17:68914158:A:G
ABCA8:17:68914240:A:G
82
9
9
9
TTR:18:31564574:G:C|TTR:18:31564635:G:C
observed
TTR
18
TTR:18:31564574:G:C
TTR:18:31564635:G:C
61
9
50
1
KBTBD6:13:41129521:C:T|KBTBD6:13:41129563:T:C
observed
KBTBD6
13
KBTBD6:13:41129521:C:T
KBTBD6:13:41129563:T:C
42
3
13
1
PPP1R13L:19:45399420:C:G|PPP1R13L:19:45399421:G:A
observed
PPP1R13L
19
PPP1R13L:19:45399420:C:G
PPP1R13L:19:45399421:G:A
1
14
11
11
CRX:19:47837197:C:T|CRX:19:47837206:G:A
observed
CRX
19
CRX:19:47837197:C:T
CRX:19:47837206:G:A
9
14
11
1
PRELID3A:18:12426470:T:C|PRELID3A:18:12426471:G:C
observed
PRELID3A
18
PRELID3A:18:12426470:T:C
PRELID3A:18:12426471:G:C
1
30
12
12
CACNG3:16:24327624:A:G|CACNG3:16:24327722:G:A
observed
CACNG3
16
CACNG3:16:24327624:A:G
CACNG3:16:24327722:G:A
98
6
235
1
RPS17:15:82537277:C:G|RPS17:15:82537361:A:C
observed
RPS17
15
RPS17:15:82537277:C:G
RPS17:15:82537361:A:C
84
11
12
1
NMT2:10:15131440:C:T|NMT2:10:15131506:G:C
observed
NMT2
10
NMT2:10:15131440:C:T
NMT2:10:15131506:G:C
66
14
15
13
ABCA8:17:68910396:A:C|ABCA8:17:68910397:G:C
observed
ABCA8
17
ABCA8:17:68910396:A:C
ABCA8:17:68910397:G:C
1
7
7
7
EFCAB8:20:32927405:C:T|EFCAB8:20:32927489:T:C
observed
EFCAB8
20
EFCAB8:20:32927405:C:T
EFCAB8:20:32927489:T:C
84
18
114
2
TRNT1:3:3128946:C:T|TRNT1:3:3128994:C:G
observed
TRNT1
3
TRNT1:3:3128946:C:T
TRNT1:3:3128994:C:G
48
21
14
14
RAD54L2:3:51580183:C:T|RAD54L2:3:51580212:C:G
observed
RAD54L2
3
RAD54L2:3:51580183:C:T
RAD54L2:3:51580212:C:G
29
118
8
1
SLC43A3:11:57408093:T:G|SLC43A3:11:57408149:C:T
observed
SLC43A3
11
SLC43A3:11:57408093:T:G
SLC43A3:11:57408149:C:T
56
151
6
1
C1orf109:1:37687013:G:A|C1orf109:1:37687043:G:A
observed
C1orf109
1
C1orf109:1:37687013:G:A
C1orf109:1:37687043:G:A
30
17
182
16
CHKA:11:68063629:T:C|CHKA:11:68063706:A:G
observed
CHKA
11
CHKA:11:68063629:T:C
CHKA:11:68063706:A:G
77
11
5
1
ANPEP:15:89808114:G:A|ANPEP:15:89808133:A:C
observed
ANPEP
15
ANPEP:15:89808114:G:A
ANPEP:15:89808133:A:C
19
3
70
1
LDHC:11:18443135:G:T|LDHC:11:18443160:A:G
observed
LDHC
11
LDHC:11:18443135:G:T
LDHC:11:18443160:A:G
25
50
4
1
FCN2:9:134883020:G:C|FCN2:9:134883114:G:A
observed
FCN2
9
FCN2:9:134883020:G:C
FCN2:9:134883114:G:A
94
159
24
24
IHO1:3:49227480:C:T|IHO1:3:49227544:G:C
observed
IHO1
3
IHO1:3:49227480:C:T
IHO1:3:49227544:G:C
64
11
11
1
RPRD1A:18:36049355:A:G|RPRD1A:18:36049439:C:A
observed
RPRD1A
18
RPRD1A:18:36049355:A:G
RPRD1A:18:36049439:C:A
84
103
17
4
HLA-DPB1:6:33086581:G:C|HLA-DPB1:6:33086644:T:G
observed
HLA-DPB1
6
HLA-DPB1:6:33086581:G:C
HLA-DPB1:6:33086644:T:G
63
23
29
1
SLC43A3:11:57408225:G:C|SLC43A3:11:57408316:T:C
observed
SLC43A3
11
SLC43A3:11:57408225:G:C
SLC43A3:11:57408316:T:C
91
19
151
1
NUP88:17:5367913:C:A|NUP88:17:5368004:G:A
observed
NUP88
17
NUP88:17:5367913:C:A
NUP88:17:5368004:G:A
91
25
38
1
MAP1LC3B:16:87399867:A:G|MAP1LC3B:16:87399888:C:G
observed
MAP1LC3B
16
MAP1LC3B:16:87399867:A:G
MAP1LC3B:16:87399888:C:G
21
26
9
1
ZNF823:19:11729001:C:T|ZNF823:19:11729100:G:A
observed
ZNF823
19
ZNF823:19:11729001:C:T
ZNF823:19:11729100:G:A
99
5
113
1
RGMB:5:98774461:C:A|RGMB:5:98774530:G:A
observed
RGMB
5
RGMB:5:98774461:C:A
RGMB:5:98774530:G:A
69
3
3
3
CLDN1:3:190319623:C:G|CLDN1:3:190319647:G:A
observed
CLDN1
3
CLDN1:3:190319623:C:G
CLDN1:3:190319647:G:A
24
61
24
1
NBR1:17:43206243:G:A|NBR1:17:43206335:C:T
observed
NBR1
17
NBR1:17:43206243:G:A
NBR1:17:43206335:C:T
92
19
53
1
TSEN15:1:184074413:G:A|TSEN15:1:184074455:T:C
observed
TSEN15
1
TSEN15:1:184074413:G:A
TSEN15:1:184074455:T:C
42
18
18
18
CORO2A:9:98154358:A:T|CORO2A:9:98154362:C:T
observed
CORO2A
9
CORO2A:9:98154358:A:T
CORO2A:9:98154362:C:T
4
30
30
30
SLC25A18:22:17582245:G:A|SLC25A18:22:17582246:G:T
observed
SLC25A18
22
SLC25A18:22:17582245:G:A
SLC25A18:22:17582246:G:T
1
4
3
3
PPP4R3A:14:91464323:C:A|PPP4R3A:14:91464355:T:C
observed
PPP4R3A
14
PPP4R3A:14:91464323:C:A
PPP4R3A:14:91464355:T:C
32
43
85
1
CYBA:16:88649138:T:C|CYBA:16:88649144:A:G
observed
CYBA
16
CYBA:16:88649138:T:C
CYBA:16:88649144:A:G
6
202
22
1
SAR1A:10:70150180:A:G|SAR1A:10:70150276:C:G
observed
SAR1A
10
SAR1A:10:70150180:A:G
SAR1A:10:70150276:C:G
96
14
135
1
THRB:3:24378778:C:G|THRB:3:24378841:T:C
observed
THRB
3
THRB:3:24378778:C:G
THRB:3:24378841:T:C
63
8
116
4
S100A16:1:153608939:C:T|S100A16:1:153609019:G:A
observed
S100A16
1
S100A16:1:153608939:C:T
S100A16:1:153609019:G:A
80
136
8
1
CHCHD3:7:133029272:T:C|CHCHD3:7:133029286:T:C
observed
CHCHD3
7
CHCHD3:7:133029272:T:C
CHCHD3:7:133029286:T:C
14
224
58
57
PDE3A:12:20559513:G:A|PDE3A:12:20559563:C:T
observed
PDE3A
12
PDE3A:12:20559513:G:A
PDE3A:12:20559563:C:T
50
72
3
1
SEMA5A:5:9386594:C:T|SEMA5A:5:9386629:C:T
observed
SEMA5A
5
SEMA5A:5:9386594:C:T
SEMA5A:5:9386629:C:T
35
57
6
1
UQCRC1:3:48607198:C:T|UQCRC1:3:48607263:A:G
observed
UQCRC1
3
UQCRC1:3:48607198:C:T
UQCRC1:3:48607263:A:G
65
17
58
1
SYNGR3:16:1993983:A:G|SYNGR3:16:1994058:A:G
observed
SYNGR3
16
SYNGR3:16:1993983:A:G
SYNGR3:16:1994058:A:G
75
16
12
12
PLCD3:17:45126193:G:A|PLCD3:17:45126248:G:A
observed
PLCD3
17
PLCD3:17:45126193:G:A
PLCD3:17:45126248:G:A
55
6
5
1
SPTA1:1:158651888:T:G|SPTA1:1:158651959:T:C
observed
SPTA1
1
SPTA1:1:158651888:T:G
SPTA1:1:158651959:T:C
71
24
32
1
EIF2AK1:7:6033669:A:G|EIF2AK1:7:6033671:G:A
observed
EIF2AK1
7
EIF2AK1:7:6033669:A:G
EIF2AK1:7:6033671:G:A
2
9
9
9
ABCD2:12:39556615:C:T|ABCD2:12:39556680:T:C
observed
ABCD2
12
ABCD2:12:39556615:C:T
ABCD2:12:39556680:T:C
65
89
84
4
SMCO1:3:196512284:G:T|SMCO1:3:196512320:T:C
observed
SMCO1
3
SMCO1:3:196512284:G:T
SMCO1:3:196512320:T:C
36
121
48
1
SCCPDH:1:246748996:C:T|SCCPDH:1:246749077:T:C
observed
SCCPDH
1
SCCPDH:1:246748996:C:T
SCCPDH:1:246749077:T:C
81
25
13
1
DNM1L:12:32733738:A:G|DNM1L:12:32733803:T:C
observed
DNM1L
12
DNM1L:12:32733738:A:G
DNM1L:12:32733803:T:C
65
28
3
1
TMC5:16:19451911:G:A|TMC5:16:19451986:A:G
observed
TMC5
16
TMC5:16:19451911:G:A
TMC5:16:19451986:A:G
75
8
201
1
EFCAB8:20:32888051:A:G|EFCAB8:20:32888148:C:T
observed
EFCAB8
20
EFCAB8:20:32888051:A:G
EFCAB8:20:32888148:C:T
97
182
24
6
TRIM49B:11:49029395:C:A|TRIM49B:11:49029396:A:T
observed
TRIM49B
11
TRIM49B:11:49029395:C:A
TRIM49B:11:49029396:A:T
1
4
4
4
OR4K5:14:19920801:C:A|OR4K5:14:19920810:T:C
observed
OR4K5
14
OR4K5:14:19920801:C:A
OR4K5:14:19920810:T:C
9
80
6
1
ABHD14B:3:51974826:G:T|ABHD14B:3:51974867:A:G
observed
ABHD14B
3
ABHD14B:3:51974826:G:T
ABHD14B:3:51974867:A:G
41
74
11
1
KCNJ16:17:70105172:T:C|KCNJ16:17:70105213:T:C
observed
KCNJ16
17
KCNJ16:17:70105172:T:C
KCNJ16:17:70105213:T:C
41
28
150
1
SCYL3:1:169884590:G:C|SCYL3:1:169884616:T:C
observed
SCYL3
1
SCYL3:1:169884590:G:C
SCYL3:1:169884616:T:C
26
199
71
9
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Splicing epistasis — non-cancer 1000-gene control set

167,322 cis-double SNV pairs (83,661 observed + 83,661 unobserved-matched) in 1000 Genomes, enumerated within a 1000-gene random sample of protein-coding genes excluding all OncoKB entries.

Built as a control comparator for the OncoKB-987-driver dataset to test whether the splicing-epistasis depletion signal (Lynn et al., Section 2 ¶1-5) is panel-specific or generalizes to non-cancer genes.

Same methodology as paper §2: ≤100 nt window, ≥3 carriers/variant, TopLD r² ≥ 0.2 dropped, greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt. seed=42.

Constraint (pLI) distribution of the 1000 sampled genes:

  • pLI < 0.1 (LoF-tolerant): 727
  • pLI ≥ 0.9 (LoF-intolerant): 141
  • 0.5 ≤ pLI < 0.9: 53
  • 0.1 ≤ pLI < 0.5: 79

Same columns as nicolynnvila/splicing_epistasis_okgp_test and ..._okgp_oncokb987.
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