Variant report
Variant | esv3349122 |
---|---|
Chromosome Location | chr3:138739730-138763779 |
allele | n/a |
Outlinks | Ensembl   UCSC |
- TF binding region (count:191)
- CpG islands (count:794)
- Chromatin interactive region (count:5)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No. | Chromosome Location | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr3:138762690-138762740 | LNCaP | prostate: | n/a |
2 | chr3:138762690-138762740 | LNCaP | prostate: | n/a |
3 | chr3:138739807-138739857 | HCPEpiC | choroid plexus: | n/a |
4 | chr3:138762690-138762740 | SKMC | muscle: | n/a |
5 | chr3:138762324-138762374 | Caco-2 | colon: | n/a |
6 | chr3:138739807-138739857 | NT2-D1 | testis: | n/a |
7 | chr3:138739916-138739966 | K562 | blood: | n/a |
8 | chr3:138739722-138739772 | NHDF-neo | bronchial: | n/a |
9 | chr3:138762690-138762740 | Hela-S3 | cervix: | n/a |
10 | chr3:138739916-138739966 | ECC-1 | luminal epithelium: | n/a |
11 | chr3:138739922-138739972 | HL-60 | blood: | n/a |
12 | chr3:138739874-138739924 | HRPEpiC | eye: | n/a |
13 | chr3:138763424-138763474 | MCF-7 | breast: | n/a |
14 | chr3:138740313-138740363 | ProgFib | skin: | n/a |
15 | chr3:138739874-138739924 | HCPEpiC | choroid plexus: | n/a |
16 | chr3:138762324-138762374 | NT2-D1 | testis: | n/a |
17 | chr3:138740022-138740072 | GM12878 | blood: | n/a |
18 | chr3:138740313-138740363 | HCF | heart: | n/a |
19 | chr3:138762324-138762374 | IMR90 | lung: | fetal |
20 | chr3:138739807-138739857 | NB4 | blood: | n/a |
21 | chr3:138740022-138740072 | AG10803 | skin: | n/a |
22 | chr3:138740022-138740072 | HNPCEpiC | eye: | n/a |
23 | chr3:138740313-138740363 | AG10803 | skin: | n/a |
24 | chr3:138739916-138739966 | Caco-2 | colon: | n/a |
25 | chr3:138739722-138739772 | ovcar-3 | ovarian: | n/a |
26 | chr3:138739874-138739924 | LNCaP | prostate: | n/a |
27 | chr3:138739807-138739857 | AG04450 | lung: | fetal |
28 | chr3:138762690-138762740 | NB4 | blood: | n/a |
29 | chr3:138762690-138762740 | SK-N-SH | brain: | n/a |
30 | chr3:138743093-138743143 | AG10803 | skin: | n/a |
31 | chr3:138739900-138739950 | NH-A | brain: | n/a |
32 | chr3:138739922-138739972 | SK-N-SH | brain: | n/a |
33 | chr3:138763670-138763720 | K562 | blood: | n/a |
34 | chr3:138740022-138740072 | HCPEpiC | choroid plexus: | n/a |
35 | chr3:138740313-138740363 | GM12892 | blood: | n/a |
36 | chr3:138739874-138739924 | HCT-116 | colon: | n/a |
37 | chr3:138763670-138763720 | NB4 | blood: | n/a |
38 | chr3:138762324-138762374 | RPTEC | kidney: | n/a |
39 | chr3:138739922-138739972 | Jurkat | blood: | n/a |
40 | chr3:138740022-138740072 | A549 | lung: | n/a |
41 | chr3:138743093-138743143 | HIPEpiC | eye: | n/a |
42 | chr3:138739722-138739772 | Caco-2 | colon: | n/a |
43 | chr3:138739922-138739972 | K562 | blood: | n/a |
44 | chr3:138739807-138739857 | HL-60 | blood: | n/a |
45 | chr3:138739916-138739966 | GM12878 | blood: | n/a |
46 | chr3:138739916-138739966 | NB4 | blood: | n/a |
47 | chr3:138743093-138743143 | AG04450 | lung: | fetal |
48 | chr3:138739922-138739972 | RPTEC | kidney: | n/a |
49 | chr3:138743093-138743143 | Jurkat | blood: | n/a |
50 | chr3:138762324-138762374 | AG04449 | skin: | fetal |
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No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr3:138753495..138756477-chr3:138757359..138759824,2 | MCF-7 | breast: | |
2 | chr3:138660271..138660907-chr3:138754909..138755634,2 | MCF-7 | breast: | |
3 | chr3:138753495..138756477-chr3:138757359..138759824,2 | MCF-7 | breast: | |
4 | chr3:138754418..138756747-chr3:138761779..138763993,2 | K562 | blood: | |
5 | chr3:138712483..138714466-chr3:138755533..138758216,2 | K562 | blood: |
No data |
No data |
No data |
Variant related genes | Relation type |
---|---|
PRR23B | TF binding region |
PRR23C | TF binding region |
PRR23B | CpG island |
PRR23C | CpG island |
ENSG00000233701 | chromatin interactions |
No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | rs560682363 | chr3:138739769-138739770 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
2 | rs574256541 | chr3:138739808-138739809 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
3 | rs543345467 | chr3:138739813-138739814 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
4 | rs563157012 | chr3:138739854-138739855 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
5 | rs35509575 | chr3:138739898-138739899 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
6 | rs184579619 | chr3:138739901-138739902 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
7 | rs531649852 | chr3:138739942-138739943 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
8 | rs35471025 | chr3:138739947-138739948 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
9 | rs545383122 | chr3:138740001-138740002 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
10 | rs577128656 | chr3:138740003-138740004 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
11 | rs77452156 | chr3:138740031-138740032 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
12 | rs147555492 | chr3:138740071-138740072 | Inactive region | TF binding regionCpG island | 1 gene(s) | Overlapped CNVs | n/a |
13 | rs567124721 | chr3:138740074-138740075 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
14 | rs116445842 | chr3:138740088-138740089 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
15 | rs549677415 | chr3:138740166-138740167 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
16 | rs1546515 | chr3:138740196-138740197 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
17 | rs569913826 | chr3:138740243-138740244 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
18 | rs567409399 | chr3:138740254-138740255 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
19 | rs188933260 | chr3:138740275-138740276 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
20 | rs534820340 | chr3:138740289-138740290 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
21 | rs4528978 | chr3:138740293-138740294 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
22 | rs72978903 | chr3:138740321-138740322 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
23 | rs145620980 | chr3:138740350-138740351 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
24 | rs559737934 | chr3:138740354-138740355 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
25 | rs553212364 | chr3:138743093-138743094 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
26 | rs539956354 | chr3:138743094-138743095 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
27 | rs553070384 | chr3:138743115-138743116 | Inactive region | CpG island | 1 gene(s) | Overlapped CNVs | n/a |
28 | rs140336455 | chr3:138743761-138743762 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
29 | rs553475169 | chr3:138743871-138743872 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
30 | rs573088394 | chr3:138743874-138743875 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
31 | rs542027995 | chr3:138743893-138743894 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
32 | rs555658931 | chr3:138743933-138743934 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
33 | rs75517612 | chr3:138743954-138743955 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
34 | rs544456369 | chr3:138744017-138744018 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
35 | rs575046286 | chr3:138744054-138744055 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
36 | rs182459904 | chr3:138744105-138744106 | Inactive region | TF binding region | 1 gene(s) | Overlapped CNVs | n/a |
37 | rs530856189 | chr3:138750813-138750814 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
38 | rs190014726 | chr3:138750843-138750844 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
39 | rs570818560 | chr3:138750864-138750865 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
40 | rs75446336 | chr3:138750904-138750905 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
41 | rs115094670 | chr3:138750940-138750941 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
42 | rs142736157 | chr3:138750941-138750942 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
43 | rs566561871 | chr3:138750995-138750996 | Active TSS | n/a | n/a | Overlapped CNVs | n/a |
44 | rs564802229 | chr3:138751001-138751002 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
45 | rs538770594 | chr3:138751009-138751010 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
46 | rs71838895 | chr3:138751010-138751011 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
47 | rs76149997 | chr3:138751020-138751021 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
48 | rs77986128 | chr3:138751022-138751023 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
49 | rs75667031 | chr3:138751023-138751024 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
50 | rs533501093 | chr3:138751049-138751050 | Active TSS Enhancers | n/a | n/a | Overlapped CNVs | n/a |
Disease | PMID | Source |
---|---|---|
Basal cell lymphoma | 17053054 | CNVD |
Esophageal cancer | 21851588 | CNVD |
Uveal melanoma | 21693616 | CNVD |
Glioblastoma multiforme | 21080181 | CNVD |
Retinoblastoma | 21504564 | CNVD |
Medulloblastoma | 21979893 | CNVD |
Thoracic aortic aneurysm | 21092924 | CNVD |
Intellectual disability | 22102821 | CNVD |
Autism | 22495311 | CNVD |
Lung cancer | 18438408 | CNVD |
Cancer | 21129771 | CNVD |
Congenital diaphragmatic hernia | 21085971 | CNVD |
Cervical cancer | 21062161 | CNVD |
Squamous cell cancer | 20885788 | CNVD |
Melanoma | 18172304 | CNVD |
T-cell prolymphocytic leukemia | 19278963 | CNVD |
Bipolar disorder | 18458673 | CNVD |
Breast cancer | 22032731 | CNVD |
Breast cancer | 16461572 | CNVD |
Neuroblastoma | 17533364 | CNVD |
Cervical Cancer | 21857958 | CNVD |
Melanoma | 21693616 | CNVD |
Lung cancer | 21426551 | CNVD |
Cancer | 21637783 | CNVD |
Cervical cancer | 21063398 | CNVD |
Esophageal squamous carcinoma | 21637470 | CNVD |
Liposarcoma | 21253554 | CNVD |
Oral cancer | 21386901 | CNVD |
Renal cell carcinoma | 19461508 | CNVD |
Cancer | 22065749 | CNVD |
Endometrial cancer | 22040021 | CNVD |
Breast cancer | 21264507 | CNVD |
Chronic lymphocytic leukemia | 21546498 | CNVD |
microdeletion syndrome | 22180640 | CNVD |
T-cell prolymphocytic leukemia | 17713554 | CNVD |
Multiple myeloma | 17550852 | CNVD |
Basal cell lymphoma | 21115979 | CNVD |
Ovarian cancer | 22174824 | CNVD |
Colorectal cancer | 18645599 | CNVD |
head and neck squamous cell carcinoma | 17671120 | CNVD |
High-grade prostatic intraepithelial neoplasia | 16573809 | CNVD |
Hepatocellular carcinoma | 16750200 | CNVD |
Lung cancer | 16740712 | CNVD |
Esophageal squamous carcinoma | 18350619 | CNVD |
Myelodysplastic syndrome | 21251322 | CNVD |
Blepharophimosis-ptosis-epicanthus inversus syndrome | 22067867 | CNVD |
small cell lung cancer | 20016488 | CNVD |
Acute lymphoblastic leukemia | 21339820 | CNVD |
Developmental delay | 21147756 | CNVD |
lymphocytic leukemia | 21291569 | CNVD |
Myelofibrosis | 22110671 | CNVD |
abnormal development | 18461090 | CNVD |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr3:138750800-138751800 | Active TSS | Rectal Mucosa Donor 29 | rectum |
2 | chr3:138751000-138751800 | Enhancers | Rectal Mucosa Donor 31 | rectum |
3 | chr3:138751400-138752200 | Enhancers | Stomach Mucosa | stomach |
4 | chr3:138751800-138752000 | Flanking Active TSS | Rectal Mucosa Donor 31 | rectum |
5 | chr3:138752000-138752600 | Enhancers | Rectal Mucosa Donor 31 | rectum |
6 | chr3:138752600-138756200 | Weak transcription | Rectal Mucosa Donor 31 | rectum |
7 | chr3:138756200-138756800 | Enhancers | Rectal Mucosa Donor 31 | rectum |
8 | chr3:138756400-138757000 | Enhancers | Rectal Mucosa Donor 29 | rectum |
9 | chr3:138757000-138757800 | Enhancers | ES-I3 Cell Line | embryonic stem cell |
10 | chr3:138757200-138757400 | Enhancers | iPS DF 6.9 Cell Line | embryonic stem cell |
11 | chr3:138757200-138757600 | Enhancers | iPS-20b Cell Line | embryonic stem cell |
12 | chr3:138757200-138757800 | Enhancers | HUES6 Cell Line | embryonic stem cell |
13 | chr3:138757400-138765200 | Weak transcription | iPS DF 6.9 Cell Line | embryonic stem cell |
14 | chr3:138757600-138757800 | Enhancers | Brain Germinal Matrix | brain |
15 | chr3:138758400-138758600 | Enhancers | Brain Germinal Matrix | brain |
16 | chr3:138762800-138764200 | ZNF genes & repeats | iPS DF 19.11 Cell Line | embryonic stem cell |
17 | chr3:138763200-138763600 | ZNF genes & repeats | Foreskin Fibroblast Primary Cells skin01 | Skin |