Variant report

Variant	nsv1019572
Chromosome Location	chr9:2273780-2349950
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
2	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
3	chr9:2335749..2336338-chr9:2727775..2728597,3	MCF-7	breast:
4	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
5	chr9:2334689..2336340-chr9:2621369..2623518,2	MCF-7	breast:
6	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
7	chr9:2333652..2336415-chr9:2621221..2622791,2	MCF-7	breast:
8	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
9	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
10	chr9:2321723..2322570-chr9:2728160..2728820,2	MCF-7	breast:
11	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
12	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
13	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
14	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCA2-6	chr9:2287708-2288332	NONHSAT129989
2	lnc-SMARCA2-6	chr9:2276007-2276253	NONHSAT129989
3	lnc-SMARCA2-6	chr9:2291976-2293037	NONHSAT129989
4	lnc-SMARCA2-5	chr9:2273475-2274167	NONHSAT129991

No data

Variant related genes	Relation type
ENSG00000147852	chromatin interactions
ENSG00000236404	chromatin interactions

Extended variants
information (count: 3573 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:3573 , 50 per page) page: 1 2 3 4 5 6 7 ... 72

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575648781	chr9:2273785-2273786	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs189001665	chr9:2273804-2273805	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs559106568	chr9:2273812-2273813	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs572452871	chr9:2273820-2273821	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs541478296	chr9:2273822-2273823	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs560959966	chr9:2273870-2273871	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs574461858	chr9:2273871-2273872	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs551797326	chr9:2273901-2273902	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs562444354	chr9:2273908-2273909	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs16938218	chr9:2273915-2273916	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs550997828	chr9:2273925-2273926	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs551332950	chr9:2273931-2273932	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs180969543	chr9:2273943-2273944	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs4741667	chr9:2273963-2273964	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs186234911	chr9:2273967-2273968	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs536288832	chr9:2273968-2273969	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs191332314	chr9:2273992-2273993	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs570302420	chr9:2274002-2274003	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs147559905	chr9:2274060-2274061	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs10123832	chr9:2274082-2274083	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs181386549	chr9:2274114-2274115	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs534811374	chr9:2274153-2274154	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs554668501	chr9:2274181-2274182	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs575991728	chr9:2274202-2274203	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs370327968	chr9:2274207-2274208	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs556931870	chr9:2274244-2274245	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs186061586	chr9:2274246-2274247	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs141969613	chr9:2274278-2274279	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs370404582	chr9:2274298-2274299	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs564955789	chr9:2274305-2274306	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs16938219	chr9:2274355-2274356	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs536853951	chr9:2274374-2274375	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs541212955	chr9:2274383-2274384	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs561007793	chr9:2274390-2274391	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs529813429	chr9:2274415-2274416	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs544644858	chr9:2274420-2274421	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs541939751	chr9:2274422-2274423	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs190822913	chr9:2274434-2274435	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs183220074	chr9:2274437-2274438	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs552806156	chr9:2274440-2274441	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs561870520	chr9:2274472-2274473	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs200649714	chr9:2274474-2274475	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs547201621	chr9:2274491-2274492	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs10123928	chr9:2274492-2274493	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs189102249	chr9:2274496-2274497	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs10123949	chr9:2274506-2274507	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs568260297	chr9:2274518-2274519	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs190657781	chr9:2274529-2274530	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs372793005	chr9:2274558-2274559	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs182944017	chr9:2274605-2274606	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Renal cell carcinoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:443 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2257400-2275000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:2263400-2290400	Weak transcription	Right Atrium	heart
3	chr9:2265800-2276000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:2271200-2275200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:2272400-2275200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:2272600-2275200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:2273400-2274400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:2273400-2274400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:2273400-2275000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr9:2273400-2275000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:2273600-2274400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr9:2273600-2274400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:2273800-2276000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:2274200-2274400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:2274400-2275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:2274400-2275200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:2274400-2275400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:2274400-2275400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:2274400-2276200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:2274800-2275800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:2275000-2275400	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr9:2275000-2275600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:2275000-2275800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr9:2275200-2275400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:2275200-2275800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:2275200-2275800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr9:2275200-2275800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr9:2275200-2276000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:2275400-2275800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr9:2275400-2275800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr9:2275400-2275800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr9:2275400-2277000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr9:2275400-2278400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:2275600-2276600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:2275600-2276800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr9:2275800-2276000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr9:2275800-2276000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:2275800-2276400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:2275800-2276600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:2275800-2276800	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr9:2275800-2280000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr9:2275800-2281600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:2276000-2276200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr9:2276000-2276200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:2276000-2277200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:2276000-2277400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:2276000-2278800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr9:2276000-2280000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:2276200-2276600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:2276200-2278200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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