Variant report

Variant	esv3320859
Chromosome Location	chr1:179453629-179458627
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:179454141-179454154	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:179454165-179454208	MCF-7	breast:	n/a	n/a
3	FOXA1	chr1:179454199-179454469	T-47D	breast:	n/a	n/a
4	KAP1	chr1:179456091-179456217	U2OS	brain:	n/a	n/a
5	MYC	chr1:179453888-179453972	MCF-7	breast:	n/a	n/a
6	MYC	chr1:179453789-179454367	MCF-7	breast:	n/a	n/a
7	MYC	chr1:179454229-179454294	MCF-7	breast:	n/a	n/a
8	MYC	chr1:179454232-179454262	MCF-7	breast:	n/a	n/a
9	MYC	chr1:179453846-179453887	MCF-7	breast:	n/a	n/a
10	MYC	chr1:179454269-179454270	MCF-7	breast:	n/a	n/a
11	MYC	chr1:179454031-179454312	MCF-7	breast:	n/a	n/a
12	MYC	chr1:179453761-179453785	MCF-7	breast:	n/a	n/a
13	PAX5	chr1:179453618-179453951	GM12878	blood:	n/a	n/a
14	PAX5	chr1:179453602-179454021	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:179453770-179454076	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:179453821-179453906	A549	lung:	n/a	n/a
17	POLR2A	chr1:179454273-179454345	A549	lung:	n/a	n/a
18	POLR2A	chr1:179454106-179454360	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:179453978-179454268	A549	lung:	n/a	n/a
20	POLR2A	chr1:179453690-179454304	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:179454306-179454377	MCF-7	breast:	n/a	n/a
22	SETDB1	chr1:179455933-179456401	U2OS	brain:	n/a	n/a
23	ZNF274	chr1:179456842-179457121	GM08714	blood:	n/a	n/a
24	ZNF274	chr1:179456876-179457125	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF274	chr1:179456740-179457131	NT2-D1	testis:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179452715..179454955-chr1:179456900..179459797,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269064	TF binding region
AXDND1	TF binding region
ENSG00000269064	chromatin interactions

Extended variants
information (count: 89 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:89 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538245830	chr1:179453665-179453666	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs10913795	chr1:179453667-179453668	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs571428580	chr1:179453756-179453757	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs36068644	chr1:179453820-179453821	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs55998153	chr1:179453824-179453825	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs184733865	chr1:179453826-179453827	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs370166320	chr1:179453839-179453840	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs148538849	chr1:179453860-179453861	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs113075905	chr1:179453865-179453866	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs548527606	chr1:179453881-179453882	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs12038148	chr1:179453885-179453886	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs145436302	chr1:179453938-179453939	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs544997770	chr1:179453949-179453950	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs147725999	chr1:179453957-179453958	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs34890906	chr1:179453965-179453966	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs541153527	chr1:179453971-179453972	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs560946747	chr1:179453980-179453981	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs36027796	chr1:179453992-179453993	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs549267491	chr1:179454001-179454002	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs142531557	chr1:179454009-179454010	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs531879338	chr1:179454013-179454014	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs35954891	chr1:179454047-179454048	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs571337097	chr1:179454068-179454069	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs368580737	chr1:179454080-179454081	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs562144085	chr1:179454121-179454122	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs10913796	chr1:179454136-179454137	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs547525447	chr1:179454201-179454202	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs567418850	chr1:179454211-179454212	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs151328047	chr1:179454213-179454214	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs36070349	chr1:179454227-179454228	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs569948223	chr1:179454242-179454243	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs145276411	chr1:179454243-179454244	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs538527832	chr1:179454245-179454246	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs558867458	chr1:179454255-179454256	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs572102903	chr1:179454257-179454258	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs541014773	chr1:179454283-179454284	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs554711005	chr1:179454325-179454326	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs12137397	chr1:179454326-179454327	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
39	rs111932589	chr1:179454365-179454366	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs12134114	chr1:179454370-179454371	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs140578594	chr1:179454371-179454372	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs72704416	chr1:179454379-179454380	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs150093324	chr1:179454389-179454390	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs12138189	chr1:179454544-179454545	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs138362521	chr1:179454609-179454610	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs149280341	chr1:179454674-179454675	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs189412821	chr1:179454686-179454687	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs181053190	chr1:179454716-179454717	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs549969107	chr1:179454739-179454740	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs12138249	chr1:179454751-179454752	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:87)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	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
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	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
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	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
Trisomy 5 syndrome	21098271	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
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Glioblastoma multiforme	17369134	CNVD
Cancer	17440070	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	16397240	CNVD
Mental retardation	17847001	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	23248035	CNVD
Metanephric adenoma	20802469	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179453600-179454000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179454000-179454400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links