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ICD-10
HPO
Compare GWAS
Super Class
Secondary malignant neoplasm of respiratory and digestive organs
Sub Class
Secondary malignant neoplasm of liver
C78.7
Case/Control GWAS
ⓘ
Links
Sex Split
Interactive Plot
Statistics
Case
Control
3962
456243
Top SNP Information
Show Table
Location
SNP
Gene
Ref>Alt
Alt in Case
Alt in Control
Chi-square
P-value
Odds Ratio
chr5:33951693
rs16891982
SLC45A2
G>C
414
66647
44.24
2.903e-11
0.7154
chr5:33958959
rs28777
SLC45A2
A>C
357
56638
34.5
4.266e-09
0.728
chr5:33955326
rs35390
SLC45A2
A>C
242
40907
33.82
6.054e-09
0.685
chr5:33955673
rs35391
SLC45A2
C>T
242
40740
33.09
8.815e-09
0.6878
chr5:33951116
rs35397
SLC45A2
T>G
628
89483
25.73
3.918e-07
0.8098
chr3:184689554
rs9831190
VPS8
T>A
304
26796
25.67
4.059e-07
1.345
chr14:64700739
rs1256064
ESR2
A>G
717
100722
25.24
5.054e-07
0.8214
chr17:6630436
rs11654002
-
A>T
969
132127
25.12
5.399e-07
0.8421
chr17:73236124
rs28641831
GGA3
A>G
52
12024
25.07
5.532e-07
0.5043
chr11:4661285
rs905871
OR51D1
A>G
2911
316714
24.55
7.239e-07
1.122
chr17:865499
rs333635
NXN
C>T
173
29292
24.1
9.164e-07
0.6865
chr11:61690405
rs12420625
-
T>G
162
27621
23.46
1.277e-06
0.6817
chr1:150551327
rs11580946
MCL1
G>A
181
14879
23.38
1.331e-06
1.438
chr13:57885104
rs7981559
-
C>T
188
31182
23.31
1.379e-06
0.7009
chr4:155063969
rs56135637
-
G>A
619
60143
23.2
1.459e-06
1.224
chr11:88557991
rs10831496
GRM5
A>G
2289
292917
22.88
1.725e-06
0.8886
chr7:78169182
rs10243724
MAGI2
G>C
88
17060
22.82
1.776e-06
0.6018
chr3:184884820
rs114277344
-
A>T
304
27237
22.8
1.795e-06
1.323
chr16:73382744
rs4889000
ZFHX3
T>C
115
20871
22.54
2.06e-06
0.6418
chr10:133475164
rs11156539
-
T>G
461
66819
22.17
2.497e-06
0.7977
chr1:150551327
rs11580946
MCL1
G>A
180
14699
21.67
3.241e-06
1.421
chr3:184689554
rs9831190
VPS8
T>A
296
26395
19.95
7.933e-06
1.304
chr4:155063969
rs56135637
-
G>A
610
59100
19.15
1.208e-05
1.203
chr7:11231025
rs79835933
-
G>A
476
45152
18.71
1.522e-05
1.228
chr11:114063061
rs591242
ZBTB16
T>C
3747
409199
18.67
1.55e-05
1.103
chr20:33849179
rs1555322
MMP24OS
G>A
1196
122472
18.58
1.63e-05
1.145
chr10:77767972
rs7913317
LRMDA
C>G
736
98416
18.42
1.774e-05
0.8466
chr1:150292561
rs11581793
-
C>T
170
14147
18.14
2.052e-05
1.392
chr3:184884820
rs114277344
-
A>T
297
26840
17.97
2.238e-05
1.286
chr14:55071322
rs4901524
SAMD4A
T>C
1055
136876
17.92
2.306e-05
0.869
chr20:1092806
rs6039915
-
T>C
1071
109109
17.91
2.313e-05
1.15
chr20:32903687
rs819167
-
G>A
408
57586
17.86
2.378e-05
0.8064
chr13:45305925
rs9533954
-
C>T
1934
204821
17.83
2.422e-05
1.117
chr5:126736642
rs75033426
MEGF10
A>G
292
26337
17.59
2.746e-05
1.285
chr4:56162059
rs7681432
-
C>T
2088
259159
17.58
2.752e-05
0.898
chr13:91862011
rs74371587
-
T>C
326
29819
17.57
2.763e-05
1.269
chr20:58235648
rs6015543
PHACTR3
T>C
433
40954
17.38
3.061e-05
1.23
chr8:14879392
rs7846057
SGCZ
C>G
416
58451
17.31
3.181e-05
0.8106
chr18:70536900
rs79449915
-
C>T
106
18176
17.22
3.338e-05
0.6675
chr4:91844237
rs72665427
CCSER1
A>G
2254
278982
17.19
3.385e-05
0.9015
Associated Phenotypes
ⓘ
Shared SNP phenotypes
No shared SNP phenotypes
ID
Name
Top Correlation
HP: 0000118
Phenotypic abnormality
1/20
HP: 0002242
Abnormal intestine morphology
2/20
HP: 0002250
Abnormal large intestine morphology
3/20
HP: 0002664
Neoplasm
2/20
HP: 0003003
Colon cancer
5/20
HP: 0005207
Gastric hypertrophy
19/20
HP: 0007378
Neoplasm of the gastrointestinal tract
2/20
HP: 0011121
Abnormality of skin morphology
3/20
HP: 0011355
Localized skin lesion
3/20
HP: 0011793
Neoplasm by anatomical site
2/20
HP: 0030146
Abnormal liver parenchyma morphology
20/20
HP: 0031492
Epithelial neoplasm
7/20
HP: 0031493
Glandular cell neoplasm
7/20
HP: 0031495
Mucinous neoplasm
7/20
HP: 0031498
Mucinous gastric carcinoma
20/20
HP: 0032021
Eosinophilic liver infiltration
20/20
HP: 0032217
Indurated nodule
1/20
HP: 0100273
Neoplasm of the colon
5/20
HP: 0100834
Neoplasm of the large intestine
5/20
HP: 0200036
Skin nodule
5/20
ID
Name
Top Correlation
HP: 0000951
Abnormality of the skin
0/20
HP: 0001392
Abnormality of the liver
0/20
HP: 0001574
Abnormality of the integument
0/20
HP: 0002012
Abnormality of the abdominal organs
0/20
HP: 0002577
Abnormality of the stomach
0/20
HP: 0011024
Abnormality of the gastrointestinal tract
0/20
HP: 0011792
Neoplasm by histology
0/20
HP: 0012718
Morphological abnormality of the gastrointestinal tract
0/20
HP: 0025031
Abnormality of the digestive system
0/20
HP: 0025033
Abnormality of digestive system morphology
0/20
HP: 0031071
Abnormal endocrine morphology
0/20
HP: 0032064
Gastrointestinal eosinophilia
0/20
HP: 0410042
Abnormal liver morphology
0/20