Variant report

Variant	nsv1011299
Chromosome Location	chr4:92678001-92836545
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr4:92679711-92680078	HCT-116	colon:	n/a	n/a
2	BATF	chr4:92812540-92812781	GM12878	blood:	n/a	chr4:92812671-92812682
3	BATF	chr4:92812456-92812830	GM12878	blood:	n/a	chr4:92812671-92812682
4	BATF	chr4:92685314-92685539	GM12878	blood:	n/a	n/a
5	BHLHE40	chr4:92767508-92767581	GM12878	blood:	n/a	n/a
6	BHLHE40	chr4:92831092-92831515	GM12878	blood:	n/a	n/a
7	BRCA1	chr4:92695586-92695633	GM12878	blood:	n/a	n/a
8	BRCA1	chr4:92827208-92827254	H1-hESC	embryonic stem cell:	n/a	n/a
9	BRCA1	chr4:92758741-92759534	Hela-S3	cervix:	n/a	n/a
10	CBX3	chr4:92679542-92680072	HCT-116	colon:	n/a	chr4:92679572-92679583
11	CBX3	chr4:92679695-92680141	HCT-116	colon:	n/a	n/a
12	CEBPB	chr4:92833707-92833907	A549	lung:	n/a	chr4:92833836-92833847 chr4:92833838-92833849
13	CEBPB	chr4:92716834-92717409	IMR90	lung:	n/a	chr4:92717222-92717233
14	CEBPB	chr4:92717074-92717365	K562	blood:	n/a	chr4:92717222-92717233
15	CEBPB	chr4:92835356-92835641	MCF-7	breast:	n/a	n/a
16	CEBPB	chr4:92758691-92759082	MCF-7	breast:	n/a	n/a
17	CEBPB	chr4:92777270-92777483	HepG2	liver:	n/a	chr4:92777378-92777389 chr4:92777378-92777391
18	CEBPB	chr4:92835385-92835609	MCF-7	breast:	n/a	n/a
19	CEBPB	chr4:92835366-92835674	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr4:92747311-92748011	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr4:92717046-92717407	HepG2	liver:	n/a	chr4:92717222-92717233
22	CEBPB	chr4:92833703-92833962	HepG2	liver:	n/a	chr4:92833836-92833847 chr4:92833838-92833849
23	CEBPB	chr4:92758787-92759032	A549	lung:	n/a	n/a
24	CEBPB	chr4:92750683-92751085	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr4:92777276-92777573	Hela-S3	cervix:	n/a	chr4:92777378-92777389 chr4:92777378-92777391
26	CEBPB	chr4:92758635-92759377	Hela-S3	cervix:	n/a	chr4:92759191-92759203
27	CEBPB	chr4:92759725-92760073	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr4:92829425-92829558	HepG2	liver:	n/a	chr4:92829491-92829502 chr4:92829535-92829546 chr4:92829535-92829548 chr4:92829490-92829501 chr4:92829535-92829546 chr4:92829490-92829501
29	CEBPB	chr4:92758628-92759069	MCF-7	breast:	n/a	n/a
30	CTCF	chr4:92823816-92823881	GM10266	blood:	n/a	n/a
31	CTCF	chr4:92686140-92686205	Kidney_OC	kidney:	n/a	n/a
32	CTCF	chr4:92735324-92735388	GM13976	blood:	n/a	n/a
33	CTCF	chr4:92756462-92756495	Lung_OC	lung:	n/a	n/a
34	CTCF	chr4:92776900-92777050	AG10803	skin:	n/a	n/a
35	CTCF	chr4:92756060-92756210	HRE	kidney:	n/a	n/a
36	CTCF	chr4:92700823-92700874	GM10248	blood:	n/a	n/a
37	CTCF	chr4:92717995-92718023	Fibrobl	skin:	n/a	n/a
38	CTCF	chr4:92812907-92812923	Kidney_OC	kidney:	n/a	n/a
39	CTCF	chr4:92802290-92802317	LNCaP	prostate:	n/a	n/a
40	CTCF	chr4:92723966-92724043	LNCaP	prostate:	n/a	n/a
41	CTCF	chr4:92806020-92806170	AG10803	skin:	n/a	n/a
42	CTCF	chr4:92813029-92813068	GM13977	blood:	n/a	n/a
43	CTCF	chr4:92703620-92703770	GM12870	blood:	n/a	n/a
44	E2F4	chr4:92758726-92758954	MCF10A-Er-Src	breast:	n/a	n/a
45	E2F4	chr4:92704040-92704230	MCF10A-Er-Src	breast:	n/a	n/a
46	E2F4	chr4:92835437-92835636	MCF10A-Er-Src	breast:	n/a	n/a
47	E2F4	chr4:92738728-92738769	MCF10A-Er-Src	breast:	n/a	n/a
48	E2F4	chr4:92747441-92747608	MCF10A-Er-Src	breast:	n/a	n/a
49	E2F4	chr4:92767017-92767217	MCF10A-Er-Src	breast:	n/a	n/a
50	EBF1	chr4:92831271-92831516	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:92763071..92764755-chr4:92766152..92768101,2	MCF-7	breast:
2	chr4:92733503..92735821-chr4:92736564..92739014,2	K562	blood:
3	chr4:92733503..92735821-chr4:92736564..92739014,2	K562	blood:
4	chr4:92702026..92702759-chr6:57445422..57446224,2	MCF-7	breast:
5	chr2:39076189..39078927-chr4:92754563..92756152,2	MCF-7	breast:
6	chr19:18390428..18392471-chr4:92786104..92787624,2	K562	blood:
7	chr4:92763071..92764755-chr4:92766152..92768101,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM190A-1	chr4:92810110-92810219	XLOC_003610
2	lnc-FAM190A-1	chr4:92816603-92816760	XLOC_003610
3	lnc-FAM190A-1	chr4:92809037-92809255	XLOC_003610
4	lnc-RP11-9B6.1.1-5	chr4:92806197-92806405	NONHSAT097422
5	lnc-FAM190A-1	chr4:92825397-92825486	XLOC_003610

Variant related genes	Relation type
KRT19P6	TF binding region
ENSG00000249052	TF binding region
ENSG00000130522	chromatin interactions
SERTAD4	miRNA target sites
UBXN2A	miRNA target sites
IL6ST	miRNA target sites

Extended variants
information (count: 1203 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:1203 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543080326	chr4:92678016-92678017	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs562951064	chr4:92678038-92678039	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs531804358	chr4:92678060-92678061	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs551861226	chr4:92678075-92678076	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs372020883	chr4:92678093-92678094	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs74681648	chr4:92678094-92678095	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs570767049	chr4:92678102-92678103	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs533200036	chr4:92678103-92678104	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs199785282	chr4:92678109-92678110	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs546566882	chr4:92678164-92678165	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs17018705	chr4:92678177-92678178	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs74395732	chr4:92678196-92678197	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs139169278	chr4:92678203-92678204	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs141459724	chr4:92678207-92678208	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs542161831	chr4:92678240-92678241	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537507282	chr4:92678307-92678308	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs190589685	chr4:92678412-92678413	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs563877630	chr4:92678445-92678446	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs557837745	chr4:92678487-92678488	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs58112141	chr4:92678495-92678496	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs369902053	chr4:92678572-92678573	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs17287631	chr4:92678634-92678635	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs376721455	chr4:92678665-92678666	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs554156832	chr4:92678666-92678667	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs114254186	chr4:92678686-92678687	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs543356961	chr4:92678748-92678749	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs370190711	chr4:92678750-92678751	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs562827867	chr4:92678756-92678757	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs531737992	chr4:92678782-92678783	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs150841954	chr4:92678821-92678822	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs183312155	chr4:92678827-92678828	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs187048290	chr4:92678887-92678888	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs139265303	chr4:92678891-92678892	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs377179416	chr4:92678904-92678905	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs566349623	chr4:92678950-92678951	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs529119832	chr4:92678955-92678956	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs17018706	chr4:92678964-92678965	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs568468905	chr4:92678966-92678967	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs537893109	chr4:92679024-92679025	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547408839	chr4:92679025-92679026	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs60650720	chr4:92679167-92679168	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs192258881	chr4:92679203-92679204	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs149549623	chr4:92679220-92679221	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs143946307	chr4:92679254-92679255	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs534111499	chr4:92679280-92679281	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs184459207	chr4:92679282-92679283	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs188031766	chr4:92679283-92679284	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs543294265	chr4:92679286-92679287	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs146155364	chr4:92679293-92679294	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs11937231	chr4:92679356-92679357	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Acute monocytic leukemia	16498392	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myelofibrosis	22110671	CNVD
Parkinson disease	20877625	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Obesity	20622171	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cancer	20164920	CNVD
Cancer	20164919	CNVD
Esophageal cancer	21851588	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:92677000-92678200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:92677400-92679200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:92677800-92680600	Enhancers	HUVEC	blood vessel
4	chr4:92678200-92679800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:92679000-92680200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:92679200-92680600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:92679600-92680200	Enhancers	NH-A	brain
8	chr4:92679800-92680200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:92679800-92680200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:92680000-92680400	Enhancers	Hela-S3	cervix
11	chr4:92680200-92680600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:92686200-92686800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:92686400-92687000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:92686600-92687000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:92686800-92687200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr4:92696200-92696800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
17	chr4:92712400-92713200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:92712600-92713000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr4:92712600-92713000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:92712600-92713200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:92712600-92713200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr4:92712600-92713200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:92712600-92713200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:92712600-92713200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:92712600-92713200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:92712600-92713200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:92712600-92713200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:92712600-92713200	Active TSS	Liver	Liver
29	chr4:92712600-92713200	Active TSS	Brain Germinal Matrix	brain
30	chr4:92712600-92713200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr4:92712600-92713200	Active TSS	Fetal Stomach	stomach
32	chr4:92712600-92713200	Active TSS	Pancreas	Pancrea
33	chr4:92712600-92713400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr4:92712600-92713400	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr4:92712600-92713400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:92712600-92713400	Active TSS	Fetal Brain Female	brain
37	chr4:92712800-92713200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:92712800-92713200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:92712800-92713200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:92712800-92713200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:92712800-92713200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:92712800-92713200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr4:92712800-92713200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:92712800-92713200	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr4:92712800-92713200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:92712800-92713200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:92712800-92713200	Active TSS	Colonic Mucosa	Colon
48	chr4:92712800-92713200	Active TSS	Fetal Intestine Large	intestine
49	chr4:92712800-92713200	Active TSS	Fetal Intestine Small	intestine
50	chr4:92712800-92713200	Active TSS	Pancreatic Islets	Pancreatic Islet

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