Variant report
| Variant | nsv470304 |
|---|---|
| Chromosome Location | chr12:75116030-75163097 |
| allele | n/a |
| Outlinks | Ensembl UCSC |
- TF binding region (count:151)
- CpG islands (count:61)
- Chromatin interactive region (count:7)
- LncRNA region (count:1)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No. | Chromosome Location | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:75116380-75116430 | U87 | brain: | n/a |
| 2 | chr12:75116380-75116430 | BE2_C | brain: | n/a |
| 3 | chr12:75116380-75116430 | MCF-7 | breast: | n/a |
| 4 | chr12:75116380-75116430 | NHDF-neo | bronchial: | n/a |
| 5 | chr12:75116380-75116430 | RPTEC | kidney: | n/a |
| 6 | chr12:75116380-75116430 | HEK293 | kidney: | embryo |
| 7 | chr12:75116380-75116430 | HRCEpiC | kidney: | n/a |
| 8 | chr12:75116380-75116430 | MCF10A-Er-Src | breast: | n/a |
| 9 | chr12:75116380-75116430 | HCM | heart: | n/a |
| 10 | chr12:75116380-75116430 | HCPEpiC | choroid plexus: | n/a |
| 11 | chr12:75116380-75116430 | Hela-S3 | cervix: | n/a |
| 12 | chr12:75116380-75116430 | ECC-1 | luminal epithelium: | n/a |
| 13 | chr12:75116380-75116430 | NHBE | bronchial: | n/a |
| 14 | chr12:75116380-75116430 | ovcar-3 | ovarian: | n/a |
| 15 | chr12:75116380-75116430 | AoSMC | blood vessel: | n/a |
| 16 | chr12:75116380-75116430 | SAEC | small airway: | n/a |
| 17 | chr12:75116380-75116430 | PFSK-1 | brain: | n/a |
| 18 | chr12:75116380-75116430 | HCT-116 | colon: | n/a |
| 19 | chr12:75116380-75116430 | A549 | lung: | n/a |
| 20 | chr12:75116380-75116430 | ProgFib | skin: | n/a |
| 21 | chr12:75116380-75116430 | HRPEpiC | eye: | n/a |
| 22 | chr12:75116380-75116430 | CMK | blood: | n/a |
| 23 | chr12:75116380-75116430 | HUVEC | blood vessel: | n/a |
| 24 | chr12:75116380-75116430 | Hepatocyte | liver: | n/a |
| 25 | chr12:75116380-75116430 | T-47D | breast: | n/a |
| 26 | chr12:75116380-75116430 | AG04449 | skin: | fetal |
| 27 | chr12:75116380-75116430 | H1-hESC | embryonic stem cell: | embryo |
| 28 | chr12:75116380-75116430 | HRE | kidney: | n/a |
| 29 | chr12:75116380-75116430 | GM12891 | blood: | n/a |
| 30 | chr12:75116380-75116430 | SK-N-SH | brain: | n/a |
| 31 | chr12:75116380-75116430 | HL-60 | blood: | n/a |
| 32 | chr12:75116380-75116430 | NT2-D1 | testis: | n/a |
| 33 | chr12:75116380-75116430 | IMR90 | lung: | fetal |
| 34 | chr12:75116380-75116430 | SKMC | muscle: | n/a |
| 35 | chr12:75116380-75116430 | HepG2 | liver: | n/a |
| 36 | chr12:75116380-75116430 | PrEC | prostate: | n/a |
| 37 | chr12:75116380-75116430 | HAEpiC | amniotic membrane: | n/a |
| 38 | chr12:75116380-75116430 | AG10803 | skin: | n/a |
| 39 | chr12:75116380-75116430 | HIPEpiC | eye: | n/a |
| 40 | chr12:75116380-75116430 | HMEC | breast: | n/a |
| 41 | chr12:75116380-75116430 | PANC-1 | pancreas: | n/a |
| 42 | chr12:75116380-75116430 | K562 | blood: | n/a |
| 43 | chr12:75116380-75116430 | SK-N-SH_RA | brain: | n/a |
| 44 | chr12:75116380-75116430 | GM12878 | blood: | n/a |
| 45 | chr12:75116380-75116430 | AG04450 | lung: | fetal |
| 46 | chr12:75116380-75116430 | SK-N-MC | brain: | n/a |
| 47 | chr12:75116380-75116430 | Jurkat | blood: | n/a |
| 48 | chr12:75116380-75116430 | Caco-2 | colon: | n/a |
| 49 | chr12:75116380-75116430 | HEEpiC | esophagus: | n/a |
| 50 | chr12:75116380-75116430 | AG09319 | gingival: | n/a |
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| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr12:75120647..75123375-chr12:75123565..75125151,2 | MCF-7 | breast: | |
| 2 | chr12:75160845..75163008-chr12:75163683..75165464,2 | MCF-7 | breast: | |
| 3 | chr12:75106983..75109185-chr12:75115008..75117745,2 | K562 | blood: | |
| 4 | chr12:75140866..75141740-chr12:75683619..75684268,4 | MCF-7 | breast: | |
| 5 | chr12:75143585..75146196-chr12:75682282..75684719,2 | MCF-7 | breast: | |
| 6 | chr12:75123651..75124270-chr3:64290669..64291523,2 | MCF-7 | breast: | |
| 7 | chr12:75140910..75141773-chr12:75451603..75452321,3 | MCF-7 | breast: |
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| No. | lncRNA name | Chromosome Location | lncRNA alias |
|---|---|---|---|
| 1 | lnc-KCNC2-7 | chr12:75121818-75122631 | NONHSAT029512 |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| ENSG00000257998 | TF binding region |
| ENSG00000257998 | CpG island |
| ENSG00000257998 | chromatin interactions |
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | rs1396162 | chr12:75116030-75116031 | Enhancers Weak transcription | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | mRNA abundance |
| 2 | rs73361615 | chr12:75116085-75116086 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 3 | rs545068104 | chr12:75116090-75116091 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 4 | rs533504987 | chr12:75116095-75116096 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 5 | rs185319166 | chr12:75116108-75116109 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 6 | rs544567030 | chr12:75116134-75116135 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 7 | rs561122100 | chr12:75116138-75116139 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 8 | rs374434629 | chr12:75116145-75116146 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 9 | rs192113045 | chr12:75116150-75116151 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 10 | rs145966458 | chr12:75116161-75116162 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 11 | rs540397887 | chr12:75116169-75116170 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 12 | rs146138077 | chr12:75116177-75116178 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 13 | rs532530491 | chr12:75116179-75116180 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 14 | rs55928489 | chr12:75116180-75116181 | Enhancers Weak transcription | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
| 15 | rs76628482 | chr12:75116181-75116182 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 16 | rs531685142 | chr12:75116200-75116201 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 17 | rs548482356 | chr12:75116229-75116230 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 18 | rs568381145 | chr12:75116245-75116246 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 19 | rs534147095 | chr12:75116285-75116286 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 20 | rs188645609 | chr12:75116314-75116315 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 21 | rs571012186 | chr12:75116318-75116319 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 22 | rs529126061 | chr12:75116332-75116333 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 23 | rs548884300 | chr12:75116373-75116374 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 24 | rs575138015 | chr12:75116374-75116375 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 25 | rs544190444 | chr12:75116380-75116381 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 26 | rs554922443 | chr12:75116387-75116388 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 27 | rs574811980 | chr12:75116393-75116394 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 28 | rs142467721 | chr12:75116396-75116397 | Enhancers Weak transcription | n/a | n/a | Overlapped CNVs | n/a |
| 29 | rs540517116 | chr12:75116428-75116429 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 30 | rs12308494 | chr12:75116429-75116430 | Weak transcription Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
| 31 | rs532331202 | chr12:75116447-75116448 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 32 | rs545984500 | chr12:75116523-75116524 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 33 | rs553251675 | chr12:75116541-75116542 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 34 | rs562959178 | chr12:75116592-75116593 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 35 | rs531612284 | chr12:75116598-75116599 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 36 | rs568797647 | chr12:75116608-75116609 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 37 | rs568093738 | chr12:75116623-75116624 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 38 | rs528013617 | chr12:75116661-75116662 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 39 | rs192955610 | chr12:75116662-75116663 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 40 | rs548061369 | chr12:75116701-75116702 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 41 | rs12319702 | chr12:75116712-75116713 | Weak transcription Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
| 42 | rs6582242 | chr12:75116718-75116719 | Weak transcription Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
| 43 | rs558381423 | chr12:75116737-75116738 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 44 | rs142912900 | chr12:75116743-75116744 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 45 | rs182470271 | chr12:75116761-75116762 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 46 | rs55916036 | chr12:75116793-75116794 | Weak transcription Enhancers | n/a | n/a | LD-proxies of rSNPOverlapped rCNV | n/a |
| 47 | rs186905465 | chr12:75116794-75116795 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 48 | rs534126489 | chr12:75116836-75116837 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 49 | rs553985664 | chr12:75116857-75116858 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
| 50 | rs576973614 | chr12:75116891-75116892 | Weak transcription Enhancers | n/a | n/a | Overlapped CNVs | n/a |
Variant related diseases (count:72)
| Disease | PMID | Source |
|---|---|---|
| Wilms tumour | 21544195 | CNVD |
| Esophageal cancer | 21851588 | CNVD |
| Lung cancer | 20668451 | CNVD |
| Breast cancer | 20668451 | CNVD |
| Cancer | 20668451 | CNVD |
| Ovarian cancer | 20668451 | CNVD |
| Pancreas cancer | 20668451 | CNVD |
| Prostate cancer | 20668451 | CNVD |
| Ewing''s sarcoma | 21437220 | CNVD |
| Testicular germ cell tumor | 18059402 | CNVD |
| Chronic lymphocytic leukemia | 21546498 | CNVD |
| Medulloblastoma | 21979893 | CNVD |
| Malaria | 21533027 | CNVD |
| Chronic lymphocytic leukemia | 22228453 | CNVD |
| Basal cell lymphoma | 17053054 | CNVD |
| Chronic lymphocytic leukemia | 21670202 | CNVD |
| Acute lymphoblastic leukemia | 20435627 | CNVD |
| Hodgkin''s lymphoma | 17606441 | CNVD |
| Autism | 22495311 | CNVD |
| Neurodevelopmental disorder | 22521361 | CNVD |
| T-cell prolymphocytic leukemia | 19278963 | CNVD |
| Breast cancer | 21949216 | CNVD |
| Carcinoma ex pleomorphic adenoma | 18828159 | CNVD |
| Acute myeloid leukemia | 16864856 | CNVD |
| Cancer | 21637783 | CNVD |
| Glioblastoma multiforme | 21080181 | CNVD |
| Renal cell carcinoma | 19461508 | CNVD |
| Burkitt''s lymphoma | 18698080 | CNVD |
| Astrocytoma | 17387387 | CNVD |
| Breast cancer | 21264507 | CNVD |
| Glioblastoma multiforme | 19960244 | CNVD |
| Gastrointestinal stromal cancer | 20470368 | CNVD |
| Adenoid cystic carcinoma | 17372589 | CNVD |
| Lung cancer | 18438408 | CNVD |
| Breast cancer | 17899364 | CNVD |
| Colorectal cancer | 16272173 | CNVD |
| Cancer | 16751803 | CNVD |
| Endometrioid adenocarcinoma | 16974079 | CNVD |
| small cell lung cancer | 20016488 | CNVD |
| Melanoma | 18172304 | CNVD |
| Glioblastoma multiforme | 21390271 | CNVD |
| Cancer | 20164919 | CNVD |
| Metanephric adenoma | 20802469 | CNVD |
| Breast cancer | 21785460 | CNVD |
| Acute myeloid leukemia | 21251322 | CNVD |
| Gastrointestinal stromal cancer | 20877625 | CNVD |
| Burkitt''s lymphoma | 20823134 | CNVD |
| abnormal development | 18461090 | CNVD |
| Prostate cancer | 18632612 | CNVD |
| High-grade prostatic intraepithelial neoplasia | 16573809 | CNVD |
| craniofacial dysmorphism | 21918468 | CNVD |
| Breast cancer | 17133270 | CNVD |
| Myeloproliferative neoplasm | 20015882 | CNVD |
| Breast cancer | 22032731 | CNVD |
| Biliary cancer | 20360734 | CNVD |
| Breast cancer | 20360734 | CNVD |
| Coronary artery disease | 20360734 | CNVD |
| Crohn''s disease | 20360734 | CNVD |
| Hypertension | 20360734 | CNVD |
| Rheumatoid arthritis | 20360734 | CNVD |
| Type 1 diabetes | 20360734 | CNVD |
| Type 2 diabetes | 20360734 | CNVD |
| Hodgkin''s lymphoma | 18641027 | CNVD |
| Malignant peripheral nerve sheath tumor | 18522746 | CNVD |
| Urothelial cell carcinoma | 18451213 | CNVD |
| Myelofibrosis | 22110671 | CNVD |
| Ovarian cancer | 21720365 | CNVD |
| Non-syndromic sensorineural hearing loss | 18496225 | CNVD |
| Breast cancer | 21509527 | CNVD |
| Breast cancer | 21364760 | CNVD |
| Non-syndromic sensorineural hearing loss | 21987784 | CNVD |
| Non-syndromic sensorineural hearing loss | 22037309 | CNVD |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr12:75110800-75116600 | Weak transcription | iPS-20b Cell Line | embryonic stem cell |
| 2 | chr12:75115000-75116800 | Enhancers | hESC Derived CD184+ Endoderm Cultured Cells | ES cell derived |
| 3 | chr12:75115800-75116200 | Enhancers | Left Ventricle | heart |
| 4 | chr12:75115800-75116400 | Enhancers | H1 Derived Neuronal Progenitor Cultured Cells | ES cell derived |
| 5 | chr12:75116000-75116200 | Enhancers | H9 Cell Line | embryonic stem cell |
| 6 | chr12:75116000-75116400 | Enhancers | ES-I3 Cell Line | embryonic stem cell |
| 7 | chr12:75116000-75116400 | Enhancers | ES-UCSF4 Cell Line | embryonic stem cell |
| 8 | chr12:75116400-75117000 | Enhancers | iPS-18 Cell Line | embryonic stem cell |
| 9 | chr12:75116400-75117400 | Weak transcription | H9 Cell Line | embryonic stem cell |
| 10 | chr12:75116400-75117400 | Weak transcription | ES-UCSF4 Cell Line | embryonic stem cell |
| 11 | chr12:75116600-75118000 | Enhancers | iPS-20b Cell Line | embryonic stem cell |
| 12 | chr12:75117400-75117800 | Enhancers | H9 Cell Line | embryonic stem cell |
| 13 | chr12:75117600-75117800 | Enhancers | ES-UCSF4 Cell Line | embryonic stem cell |
| 14 | chr12:75117600-75120000 | Enhancers | Bone Marrow Derived Cultured Mesenchymal Stem Cells | Bone marrow |
| 15 | chr12:75119000-75119400 | Enhancers | Muscle Satellite Cultured Cells | -- |
| 16 | chr12:75126400-75126600 | Enhancers | Pancreatic Islets | Pancreatic Islet |
| 17 | chr12:75126600-75127000 | Flanking Active TSS | Pancreatic Islets | Pancreatic Islet |
| 18 | chr12:75127000-75127200 | Enhancers | Pancreatic Islets | Pancreatic Islet |
| 19 | chr12:75127200-75134200 | Weak transcription | Pancreatic Islets | Pancreatic Islet |
| 20 | chr12:75134200-75134600 | Enhancers | Fetal Heart | heart |
| 21 | chr12:75134200-75135800 | Enhancers | Pancreatic Islets | Pancreatic Islet |
| 22 | chr12:75134600-75135000 | Weak transcription | Fetal Heart | heart |
| 23 | chr12:75135000-75135800 | Enhancers | Fetal Heart | heart |
| 24 | chr12:75155200-75155400 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
| 25 | chr12:75155400-75156400 | Weak transcription | H9 Derived Neuron Cultured Cells | ES cell derived |
| 26 | chr12:75156400-75156800 | Enhancers | H9 Derived Neuron Cultured Cells | ES cell derived |
