Variant report

Variant	nsv967008
Chromosome Location	chr3:42511086-42514663
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:42513974-42514001	HepG2	liver:	n/a	n/a
2	CEBPB	chr3:42513076-42513142	HepG2	liver:	n/a	n/a
3	CTCF	chr3:42514540-42514690	HPAF	blood vessel:	n/a	n/a
4	CTCF	chr3:42514580-42514730	SAEC	small airway:	n/a	n/a
5	EP300	chr3:42514555-42515423	T-47D	breast:	n/a	n/a
6	FOXA1	chr3:42512063-42512392	T-47D	breast:	n/a	n/a
7	FOXA1	chr3:42514019-42514232	T-47D	breast:	n/a	n/a
8	GATA2	chr3:42514329-42515509	HUVEC	blood vessel:	n/a	chr3:42515021-42515029 chr3:42515223-42515240 chr3:42515232-42515241
9	GATA3	chr3:42514556-42515370	T-47D	breast:	n/a	chr3:42515021-42515029 chr3:42515223-42515240 chr3:42515232-42515241
10	MYC	chr3:42514630-42515417	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:42514444-42515572	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr3:42514537-42515581	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:42514596-42515679	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:42514528-42515187	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:42513396-42513452	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:42514603-42515464	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr3:42514592-42514846	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:42513481-42513530	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT3	chr3:42512036-42512220	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42514400..42516657-chr3:42530746..42533400,4	MCF-7	breast:
2	chr3:42513067..42515977-chr3:42516724..42519478,3	MCF-7	breast:
3	chr3:42514438..42520179-chr3:42543715..42548032,5	MCF-7	breast:
4	chr3:42514055..42518453-chr3:42530797..42534377,7	MCF-7	breast:
5	chr3:42509273..42511295-chr3:42641295..42643446,2	MCF-7	breast:
6	chr3:42513786..42515650-chr3:42578967..42581599,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VIPR1-2	chr3:42511132-42511371	NONHSAT089219

No data

Variant related genes	Relation type
ENSG00000235787	TF binding region
ENSG00000093183	chromatin interactions
ENSG00000114812	chromatin interactions
ENSG00000114857	chromatin interactions

Extended variants
information (count: 183 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:183 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs112698945	chr3:42511158-42511159	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs533697562	chr3:42511186-42511187	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs550482124	chr3:42511215-42511216	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs535848129	chr3:42511233-42511234	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs570280466	chr3:42511258-42511259	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs143662873	chr3:42511260-42511261	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs543122304	chr3:42511275-42511276	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs548808271	chr3:42511287-42511288	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs148078686	chr3:42511295-42511296	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs342540	chr3:42511311-42511312	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs557762130	chr3:42511314-42511315	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs141895114	chr3:42511338-42511339	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs536962007	chr3:42511339-42511340	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs556807137	chr3:42511368-42511369	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs573502171	chr3:42511399-42511400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs542764546	chr3:42511400-42511401	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs540505022	chr3:42511408-42511409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs558893739	chr3:42511417-42511418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs552884720	chr3:42511451-42511452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs572549439	chr3:42511470-42511471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs541146300	chr3:42511475-42511476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs146080232	chr3:42511485-42511486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs533332129	chr3:42511498-42511499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs544149684	chr3:42511529-42511530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs563925266	chr3:42511530-42511531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs529552079	chr3:42511537-42511538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs115195382	chr3:42511552-42511553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs62248799	chr3:42511594-42511595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs34945761	chr3:42511602-42511603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs190449584	chr3:42511618-42511619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs181898031	chr3:42511690-42511691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs371988874	chr3:42511711-42511712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs60833050	chr3:42511718-42511719	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs112849154	chr3:42511729-42511730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs372472914	chr3:42511730-42511731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs556843935	chr3:42511732-42511733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs567265395	chr3:42511738-42511739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs111432975	chr3:42511756-42511757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs73067999	chr3:42511805-42511806	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs553161778	chr3:42511807-42511808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs572938406	chr3:42511812-42511813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs186990497	chr3:42511892-42511893	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs558256324	chr3:42511905-42511906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs191115457	chr3:42511920-42511921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs142195593	chr3:42511967-42511968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs34688370	chr3:42511983-42511984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs562709782	chr3:42512012-42512013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs560084831	chr3:42512024-42512025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs529619604	chr3:42512027-42512028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs542934806	chr3:42512028-42512029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42510200-42514200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:42513200-42515800	Enhancers	Placenta	Placenta
3	chr3:42513400-42514400	Enhancers	HUVEC	blood vessel
4	chr3:42513400-42515600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:42513400-42516400	Enhancers	Lung	lung
6	chr3:42513400-42519600	Enhancers	Spleen	Spleen
7	chr3:42514200-42514600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:42514200-42514800	Enhancers	Duodenum Mucosa	Duodenum
9	chr3:42514200-42515600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr3:42514200-42515600	Enhancers	Stomach Mucosa	stomach
11	chr3:42514200-42515800	Enhancers	Fetal Heart	heart
12	chr3:42514400-42514600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:42514400-42514600	Enhancers	HSMMtube	muscle
14	chr3:42514400-42515000	Enhancers	NHEK	skin
15	chr3:42514400-42515200	Enhancers	Left Ventricle	heart
16	chr3:42514400-42515200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr3:42514400-42515200	Flanking Active TSS	HUVEC	blood vessel
18	chr3:42514400-42515400	Enhancers	Colonic Mucosa	Colon
19	chr3:42514400-42515600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:42514400-42515600	Enhancers	HMEC	breast
21	chr3:42514400-42515800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:42514400-42516000	Enhancers	Esophagus	oesophagus
23	chr3:42514400-42519200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:42514600-42514800	Enhancers	Fetal Muscle Leg	muscle
25	chr3:42514600-42515000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:42514600-42515000	Flanking Active TSS	HSMMtube	muscle
27	chr3:42514600-42515200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:42514600-42515200	Enhancers	Pancreas	Pancrea
29	chr3:42514600-42515200	Enhancers	Right Atrium	heart
30	chr3:42514600-42515400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:42514600-42515400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr3:42514600-42515400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:42514600-42515600	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:42514600-42515600	Enhancers	HSMM	muscle
35	chr3:42514600-42516200	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links