Variant report
Variant | nsv872634 |
---|---|
Chromosome Location | chr1:188806530-188862962 |
allele | n/a |
Outlinks | Ensembl   UCSC |
- TF binding region (count:157)
- CpG islands (count:123)
- Chromatin interactive region (count:4)
- LncRNA region (count:3)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
No. | Chromosome Location | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr1:188826889-188826939 | IMR90 | lung: | fetal |
2 | chr1:188826889-188826939 | IMR90 | lung: | fetal |
3 | chr1:188826823-188826873 | HCF | heart: | n/a |
4 | chr1:188826823-188826873 | NT2-D1 | testis: | n/a |
5 | chr1:188826823-188826873 | HUVEC | blood vessel: | n/a |
6 | chr1:188826889-188826939 | H1-hESC | embryonic stem cell: | embryo |
7 | chr1:188826889-188826939 | SAEC | small airway: | n/a |
8 | chr1:188826823-188826873 | AG09319 | gingival: | n/a |
9 | chr1:188826823-188826873 | AG04449 | skin: | fetal |
10 | chr1:188826823-188826873 | NH-A | brain: | n/a |
11 | chr1:188826889-188826939 | AoSMC | blood vessel: | n/a |
12 | chr1:188826823-188826873 | U87 | brain: | n/a |
13 | chr1:188826823-188826873 | ovcar-3 | ovarian: | n/a |
14 | chr1:188826889-188826939 | HPAEpiC | pulmonary alveolar: | n/a |
15 | chr1:188826823-188826873 | GM12891 | blood: | n/a |
16 | chr1:188826823-188826873 | SK-N-SH | brain: | n/a |
17 | chr1:188826823-188826873 | LNCaP | prostate: | n/a |
18 | chr1:188826889-188826939 | U87 | brain: | n/a |
19 | chr1:188826823-188826873 | ECC-1 | luminal epithelium: | n/a |
20 | chr1:188826889-188826939 | SK-N-SH_RA | brain: | n/a |
21 | chr1:188826889-188826939 | Jurkat | blood: | n/a |
22 | chr1:188826889-188826939 | MCF-7 | breast: | n/a |
23 | chr1:188826823-188826873 | PrEC | prostate: | n/a |
24 | chr1:188826823-188826873 | HL-60 | blood: | n/a |
25 | chr1:188826823-188826873 | Hela-S3 | cervix: | n/a |
26 | chr1:188826889-188826939 | RPTEC | kidney: | n/a |
27 | chr1:188826823-188826873 | MCF-7 | breast: | n/a |
28 | chr1:188826889-188826939 | AG09319 | gingival: | n/a |
29 | chr1:188826889-188826939 | HCF | heart: | n/a |
30 | chr1:188826889-188826939 | PFSK-1 | brain: | n/a |
31 | chr1:188826889-188826939 | NHDF-neo | bronchial: | n/a |
32 | chr1:188826889-188826939 | SKMC | muscle: | n/a |
33 | chr1:188826889-188826939 | Hela-S3 | cervix: | n/a |
34 | chr1:188826823-188826873 | CMK | blood: | n/a |
35 | chr1:188826823-188826873 | HRE | kidney: | n/a |
36 | chr1:188826889-188826939 | HRCEpiC | kidney: | n/a |
37 | chr1:188826823-188826873 | HCM | heart: | n/a |
38 | chr1:188826889-188826939 | NT2-D1 | testis: | n/a |
39 | chr1:188826889-188826939 | HMEC | breast: | n/a |
40 | chr1:188826889-188826939 | GM12891 | blood: | n/a |
41 | chr1:188826889-188826939 | ovcar-3 | ovarian: | n/a |
42 | chr1:188826823-188826873 | SK-N-MC | brain: | n/a |
43 | chr1:188826823-188826873 | AG04450 | lung: | fetal |
44 | chr1:188826889-188826939 | PANC-1 | pancreas: | n/a |
45 | chr1:188826823-188826873 | H1-hESC | embryonic stem cell: | embryo |
46 | chr1:188826823-188826873 | HCPEpiC | choroid plexus: | n/a |
47 | chr1:188826823-188826873 | HEK293 | kidney: | embryo |
48 | chr1:188826823-188826873 | GM19239 | blood: | n/a |
49 | chr1:188826889-188826939 | HCT-116 | colon: | n/a |
50 | chr1:188826889-188826939 | HNPCEpiC | eye: | n/a |
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No. | Distal block | Cell Line | Cell type | Cell Stage |
---|---|---|---|---|
1 | chr1:188846061..188848491-chr1:188851171..188853585,2 | MCF-7 | breast: | |
2 | chr1:188788862..188791265-chr1:188817309..188819818,2 | MCF-7 | breast: | |
3 | chr1:188401580..188402198-chr1:188862429..188863519,3 | MCF-7 | breast: | |
4 | chr1:188846061..188848491-chr1:188851171..188853585,2 | MCF-7 | breast: |
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No. | lncRNA name | Chromosome Location | lncRNA alias |
---|---|---|---|
1 | lnc-FAM5C-2 | chr1:188856372-188856565 | XLOC_001129 |
2 | lnc-FAM5C-2 | chr1:188838608-188838879 | XLOC_001129 |
3 | lnc-PLA2G4A-17 | chr1:188860643-188860786 | refGeneNc_416_NR_033922 |
No data |
No data |
Variant related genes | Relation type |
---|---|
ENSG00000238054 | TF binding region |
ENSG00000238054 | CpG island |
KIAA0494 | miRNA target sites |
No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
---|---|---|---|---|---|---|---|
1 | rs545109250 | chr1:188812205-188812206 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
2 | rs7548983 | chr1:188812287-188812288 | Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
3 | rs189570968 | chr1:188812297-188812298 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
4 | rs73068782 | chr1:188812369-188812370 | Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
5 | rs370064266 | chr1:188812459-188812460 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
6 | rs372728864 | chr1:188812460-188812461 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
7 | rs529948246 | chr1:188812549-188812550 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
8 | rs375026532 | chr1:188812557-188812558 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
9 | rs75730299 | chr1:188812564-188812565 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
10 | rs537380735 | chr1:188812571-188812572 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
11 | rs146037269 | chr1:188812606-188812607 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
12 | rs78916713 | chr1:188812631-188812632 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
13 | rs181277902 | chr1:188812640-188812641 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
14 | rs375006964 | chr1:188812649-188812650 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
15 | rs11811064 | chr1:188812655-188812656 | Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
16 | rs34807144 | chr1:188812663-188812664 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
17 | rs548603273 | chr1:188812723-188812724 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
18 | rs568421708 | chr1:188812736-188812737 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
19 | rs534509140 | chr1:188812797-188812798 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
20 | rs118018029 | chr1:188812813-188812814 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
21 | rs11810709 | chr1:188812874-188812875 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
22 | rs75637922 | chr1:188812893-188812894 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
23 | rs76440077 | chr1:188812920-188812921 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
24 | rs76812487 | chr1:188812986-188812987 | Enhancers | n/a | n/a | Overlapped CNVs | n/a |
25 | rs184322551 | chr1:188813097-188813098 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
26 | rs372911301 | chr1:188813121-188813122 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
27 | rs188924345 | chr1:188813142-188813143 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
28 | rs181616614 | chr1:188813154-188813155 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
29 | rs539823312 | chr1:188813221-188813222 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
30 | rs560223729 | chr1:188813234-188813235 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
31 | rs532429955 | chr1:188813260-188813261 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
32 | rs552136587 | chr1:188813304-188813305 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
33 | rs562653512 | chr1:188813350-188813351 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
34 | rs187236120 | chr1:188813378-188813379 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
35 | rs542006204 | chr1:188813389-188813390 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
36 | rs548666650 | chr1:188813420-188813421 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
37 | rs191904732 | chr1:188813436-188813437 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
38 | rs6692124 | chr1:188813513-188813514 | Weak transcription | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
39 | rs182491057 | chr1:188813524-188813525 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
40 | rs571098497 | chr1:188813538-188813539 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
41 | rs540122311 | chr1:188813544-188813545 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
42 | rs138826557 | chr1:188813558-188813559 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
43 | rs185934427 | chr1:188813575-188813576 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
44 | rs570197371 | chr1:188813594-188813595 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
45 | rs537573785 | chr1:188813599-188813600 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
46 | rs562139713 | chr1:188813621-188813622 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
47 | rs189872213 | chr1:188813656-188813657 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
48 | rs574181092 | chr1:188813683-188813684 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
49 | rs559683289 | chr1:188813701-188813702 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
50 | rs553727462 | chr1:188813744-188813745 | Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
Disease | PMID | Source |
---|---|---|
Breast cancer | 17603634 | CNVD |
Esophageal squamous carcinoma | 21637470 | CNVD |
HIV/AIDS | 22032296 | CNVD |
Schizophrenia | 19415332 | CNVD |
Autism | 22495311 | CNVD |
Liposarcoma | 21253554 | CNVD |
Burkitt''s lymphoma | 18698080 | CNVD |
Melanoma | 18172304 | CNVD |
Rett syndrome | 21593744 | CNVD |
Cancer | 20164919 | CNVD |
Medulloblastoma | 21979893 | CNVD |
Acute lymphoblastic leukemia | 17443227 | CNVD |
Wilms tumour | 21544195 | CNVD |
Breast cancer | 17133270 | CNVD |
Carcinoma ex pleomorphic adenoma | 18828159 | CNVD |
Non-small cell lung cancer | 21044232 | CNVD |
Cervical cancer | 21063398 | CNVD |
Acute lymphoblastic leukemia | 20435627 | CNVD |
Astrocytoma | 17387387 | CNVD |
Breast cancer | 20632083 | CNVD |
Endometrial cancer | 22040021 | CNVD |
Ewing''s sarcoma | 21437220 | CNVD |
Gastrointestinal stromal cancer | 20470368 | CNVD |
Glioblastoma multiforme | 19960244 | CNVD |
Glioblastoma multiforme | 21080181 | CNVD |
Hepatocellular carcinoma | 22174799 | CNVD |
Medulloblastoma | 21292688 | CNVD |
Phyllodes tumor | 17334353 | CNVD |
Breast cancer | 21264507 | CNVD |
Multiple myeloma | 21628407 | CNVD |
Cancer | 16751803 | CNVD |
Prostate cancer | 16705090 | CNVD |
Neuroblastoma | 19435921 | CNVD |
Breast cancer | 17850661 | CNVD |
Breast cancer | 16461572 | CNVD |
Intracranial tumor | 16823260 | CNVD |
Medulloblastoma | 18056178 | CNVD |
Monoclonal gammopathy of undetermined significance | 17077331 | CNVD |
Primary mediastinal b-cell lymphoma | 17728785 | CNVD |
Colorectal cancer | 16272173 | CNVD |
Acute lymphoblastic leukemia | 21098271 | CNVD |
Neuroblastoma | 21899760 | CNVD |
Ovarian neoplasms | 16753589 | CNVD |
Glioblastoma multiforme | 17002787 | CNVD |
Breast cancer | 21858162 | CNVD |
Non-small cell lung cancer | 21385341 | CNVD |
Acute lymphoblastic leukemia | 21980252 | CNVD |
Breast cancer | 16608533 | CNVD |
Ewing''s sarcoma | 22429812 | CNVD |
Acute promyelocytic leukemia | 19109227 | CNVD |
Hepatocellular carcinoma | 18803288 | CNVD |
Basal cell lymphoma | 16317097 | CNVD |
Diffuse large b-cell lymphoma | 16317097 | CNVD |
Breast cancer | 17001317 | CNVD |
Acute myeloid leukemia | 21251322 | CNVD |
Multiple myeloma | 17550852 | CNVD |
Prostate cancer | 18632612 | CNVD |
Acute myeloid leukemia | 20729466 | CNVD |
Hodgkin''s lymphoma | 17606441 | CNVD |
Testicular germ cell tumor | 18059402 | CNVD |
Ependymoma | 18628472 | CNVD |
Leukemia | 18628472 | CNVD |
Neuroblastoma | 18923191 | CNVD |
Chronic lymphocytic leukemia | 21546498 | CNVD |
Ewing''s sarcoma | 17952124 | CNVD |
Acute lymphoblastic leukemia | 19100363 | CNVD |
Lung cancer | 18438408 | CNVD |
Breast cancer | 21509527 | CNVD |
Endometrioid adenocarcinoma | 16974079 | CNVD |
Metanephric adenoma | 20802469 | CNVD |
Melanoma | 20688739 | CNVD |
small cell lung cancer | 20016488 | CNVD |
Breast cancer | 21611746 | CNVD |
Myelofibrosis | 22110671 | CNVD |
primary effusion lymphomas | 17116491 | CNVD |
Breast cancer | 17393978 | CNVD |
Hepatocellular carcinoma | 16750200 | CNVD |
Acute lymphoblastic leukemia | 22237106 | CNVD |
Breast cancer | 17899364 | CNVD |
Non-small cell lung cancer | 19010865 | CNVD |
Mental retardation | 17847001 | CNVD |
Basal cell lymphoma | 17170743 | CNVD |
Follicular lymphoma | 17170743 | CNVD |
Trisomy 5 syndrome | 21098271 | CNVD |
early-passage human iPS cells | 21368824 | CNVD |
Non-syndromic sensorineural hearing loss | 22037309 | CNVD |
Pancreatic cancer | 17952125 | CNVD |
No. | Chromosome Location | Chromatin state | Cell line | Tissue |
---|---|---|---|---|
1 | chr1:188812200-188812600 | Enhancers | iPS-15b Cell Line | embryonic stem cell |
2 | chr1:188812200-188813000 | Enhancers | HUES48 Cell Line | embryonic stem cell |
3 | chr1:188812400-188813000 | Enhancers | ES-I3 Cell Line | embryonic stem cell |
4 | chr1:188812800-188813000 | Enhancers | Pancreas | Pancrea |
5 | chr1:188813000-188815600 | Weak transcription | Pancreas | Pancrea |
6 | chr1:188815600-188816000 | ZNF genes & repeats | Pancreas | Pancrea |
7 | chr1:188815800-188816000 | Enhancers | H1 Derived Mesenchymal Stem Cells | ES cell derived |
8 | chr1:188819600-188820400 | Enhancers | Pancreatic Islets | Pancreatic Islet |
9 | chr1:188820400-188821400 | Active TSS | Pancreatic Islets | Pancreatic Islet |
10 | chr1:188820600-188820800 | Enhancers | H1 BMP4 Derived Mesendoderm Cultured Cells | ES cell derived |
11 | chr1:188823800-188824200 | Enhancers | iPS-20b Cell Line | embryonic stem cell |
12 | chr1:188823800-188824600 | Enhancers | iPS-15b Cell Line | embryonic stem cell |
13 | chr1:188824200-188824600 | Enhancers | HUES6 Cell Line | embryonic stem cell |
14 | chr1:188826600-188826800 | Enhancers | H1 Derived Mesenchymal Stem Cells | ES cell derived |
15 | chr1:188826600-188827000 | ZNF genes & repeats | iPS DF 19.11 Cell Line | embryonic stem cell |
16 | chr1:188826600-188827200 | ZNF genes & repeats | ES-UCSF4 Cell Line | embryonic stem cell |
17 | chr1:188826800-188827000 | Weak transcription | H1 Derived Mesenchymal Stem Cells | ES cell derived |
18 | chr1:188827000-188827200 | ZNF genes & repeats | H1 Derived Mesenchymal Stem Cells | ES cell derived |
19 | chr1:188835000-188835400 | Enhancers | H1 BMP4 Derived Trophoblast Cultured Cells | ES cell derived |
20 | chr1:188846600-188847200 | Enhancers | H9 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
21 | chr1:188846600-188847600 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
22 | chr1:188854400-188855000 | Enhancers | Hela-S3 | cervix |
23 | chr1:188855000-188855800 | Weak transcription | Hela-S3 | cervix |
24 | chr1:188855800-188856400 | Enhancers | Hela-S3 | cervix |
25 | chr1:188856400-188857600 | Flanking Active TSS | Hela-S3 | cervix |
26 | chr1:188857200-188858000 | Enhancers | Foreskin Melanocyte Primary Cells skin03 | Skin |
27 | chr1:188857600-188859200 | Weak transcription | Hela-S3 | cervix |
28 | chr1:188859200-188859600 | Enhancers | Hela-S3 | cervix |