Variant report

Variant	nsv946481
Chromosome Location	chr1:165639060-165646269
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	CEBPB	chr1:165640895-165641153	A549	lung:	n/a	chr1:165640996-165641009
2	CTCF	chr1:165642000-165642121	GM10248	blood:	n/a	n/a
3	E2F4	chr1:165644766-165644966	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F4	chr1:165640814-165641190	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F4	chr1:165645402-165645602	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:165645061-165645303	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:165640776-165641108	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:165645051-165645338	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:165640765-165641170	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:165645103-165645365	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:165640760-165641144	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:165643817-165644144	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr1:165640766-165641171	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:165645080-165645376	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA2	chr1:165643901-165644256	HUVEC	blood vessel:	n/a	n/a
16	GATA3	chr1:165640682-165640905	SH-SY5Y	brain:	n/a	n/a
17	MYC	chr1:165640804-165641099	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr1:165640860-165641171	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:165645168-165645312	K562	blood:	n/a	n/a
20	POLR2A	chr1:165644913-165645042	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:165644053-165644064	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:165646139-165646168	K562	blood:	n/a	n/a
23	POLR2A	chr1:165644082-165644132	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr1:165644292-165644395	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:165640877-165641098	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr1:165644943-165645053	HUVEC	blood vessel:	n/a	n/a
27	STAT3	chr1:165640839-165641180	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
28	STAT3	chr1:165640722-165641256	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
29	STAT3	chr1:165640775-165641100	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
30	STAT3	chr1:165640840-165641099	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991

No.	Distal block	Cell Line	Cell type
1	chr1:165637022..165639402-chr1:165664990..165667855,2	K562	blood:
2	chr1:165636460..165640030-chr1:165641604..165644830,4	K562	blood:
3	chr1:165636460..165640030-chr1:165641604..165644830,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGST3-3	chr1:165640493-165640962	NONHSAT007330
2	lnc-MGST3-4	chr1:165645547-165646018	NONHSAT007331

Variant related genes	Relation type
ENSG00000230175	TF binding region
ALDH9A1	TF binding region
ENSG00000225272	TF binding region
ENSG00000143149	chromatin interactions

Extended variants
information (count: 313 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:313 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs551705476	chr1:165639085-165639086	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs544939614	chr1:165639124-165639125	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs551171189	chr1:165639134-165639135	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs185249012	chr1:165639159-165639160	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs540013907	chr1:165639189-165639190	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs12065621	chr1:165639264-165639265	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs570325967	chr1:165639296-165639297	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs536147760	chr1:165639298-165639299	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs76051990	chr1:165639323-165639324	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs572328175	chr1:165639396-165639397	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs188983278	chr1:165639402-165639403	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs557941661	chr1:165639407-165639408	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs182425385	chr1:165639444-165639445	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs577419571	chr1:165639445-165639446	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs543171175	chr1:165639476-165639477	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs12123278	chr1:165639490-165639491	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs529195498	chr1:165639533-165639534	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs77438524	chr1:165639554-165639555	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs34304173	chr1:165639569-165639570	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs560673961	chr1:165639589-165639590	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs376755798	chr1:165639599-165639600	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs542489634	chr1:165639600-165639601	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs187048920	chr1:165639617-165639618	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs1890080	chr1:165639630-165639631	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs552567901	chr1:165639635-165639636	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs559637067	chr1:165639638-165639639	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs191965906	chr1:165639651-165639652	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs372658578	chr1:165639666-165639667	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs533827239	chr1:165639667-165639668	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs79110777	chr1:165639676-165639677	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs1890079	chr1:165639677-165639678	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs571209248	chr1:165639678-165639679	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs533577149	chr1:165639742-165639743	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs181710559	chr1:165639841-165639842	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs570261978	chr1:165639857-165639858	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs186057431	chr1:165639870-165639871	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs140287321	chr1:165639922-165639923	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs190435237	chr1:165639952-165639953	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs566086727	chr1:165639997-165639998	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs145390737	chr1:165639998-165639999	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs558239544	chr1:165640134-165640135	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs79933726	chr1:165640135-165640136	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs537143169	chr1:165640157-165640158	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs884121	chr1:165640178-165640179	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs148053085	chr1:165640199-165640200	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs376806846	chr1:165640200-165640201	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs182510403	chr1:165640257-165640258	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs186830580	chr1:165640263-165640264	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs199831384	chr1:165640325-165640326	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs559360516	chr1:165640399-165640400	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Lung cancer	18438408	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	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
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
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21509527	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
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	22522925	CNVD
Myelofibrosis	22110671	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Williams-beuren syndrome	16971481	CNVD

Chromatin state (count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165618200-165652400	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:165619000-165642600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:165619000-165643600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:165619200-165648800	Strong transcription	Liver	Liver
6	chr1:165619600-165642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
9	chr1:165628000-165646600	Strong transcription	Primary T cells from cord blood	blood
10	chr1:165628800-165640200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:165628800-165642000	Strong transcription	HSMM	muscle
12	chr1:165628800-165642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:165628800-165644000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:165628800-165646800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:165628800-165646800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:165629000-165639400	Strong transcription	Placenta	Placenta
17	chr1:165629000-165653600	Strong transcription	Dnd41	blood
18	chr1:165629200-165641600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:165629200-165642800	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:165629200-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:165629400-165642200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:165629400-165642600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:165629400-165652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:165629400-165654200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:165629400-165656000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:165629600-165641800	Strong transcription	Fetal Lung	lung
27	chr1:165629600-165643000	Strong transcription	Primary B cells from cord blood	blood
28	chr1:165629600-165654800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr1:165629800-165642000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:165629800-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:165629800-165654800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:165630000-165642200	Strong transcription	Fetal Thymus	thymus
33	chr1:165630000-165642200	Strong transcription	Thymus	Thymus
34	chr1:165630000-165654400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:165631000-165639400	Strong transcription	NH-A	brain
36	chr1:165631000-165643400	Strong transcription	Hela-S3	cervix
37	chr1:165632200-165645400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:165632400-165649400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:165633600-165651200	Weak transcription	Pancreas	Pancrea
40	chr1:165633600-165651400	Weak transcription	Gastric	stomach
41	chr1:165633800-165651000	Weak transcription	Small Intestine	intestine
42	chr1:165634400-165644600	Weak transcription	Fetal Brain Male	brain
43	chr1:165634400-165651800	Weak transcription	Fetal Heart	heart
44	chr1:165634600-165644800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:165635200-165647800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:165635600-165639400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:165635600-165640600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:165635800-165640800	Strong transcription	GM12878-XiMat	blood
49	chr1:165635800-165645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:165635800-165648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links