Variant report

Variant	nsv1016677
Chromosome Location	chr9:2253741-2415423
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:28)
LncRNA
region (count:9)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
2	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
3	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
4	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
5	chr9:2257367..2260216-chr9:2810940..2813820,2	MCF-7	breast:
6	chr9:2321723..2322570-chr9:2728160..2728820,2	MCF-7	breast:
7	chr9:2333652..2336415-chr9:2621221..2622791,2	MCF-7	breast:
8	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
9	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
10	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
11	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
12	chr9:2334689..2336340-chr9:2621369..2623518,2	MCF-7	breast:
13	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
14	chr9:2335749..2336338-chr9:2727775..2728597,3	MCF-7	breast:
15	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
16	chr9:2255030..2255773-chr9:2600478..2601011,2	MCF-7	breast:
17	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
18	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
19	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
20	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
21	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
22	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
23	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
24	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
25	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
26	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
27	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
28	chr9:2244966..2246945-chr9:2263682..2266605,2	MCF-7	breast:

(count:9 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2415397-2415540	l_3727_chr9:2411588-2611526_ovary
2	lnc-VLDLR-2	chr9:2390027-2390054	XLOC_007266
3	lnc-VLDLR-2	chr9:2408820-2408888	XLOC_007266
4	lnc-SMARCA2-5	chr9:2264485-2264628	NONHSAT129991
5	lnc-SMARCA2-5	chr9:2273475-2274167	NONHSAT129991
6	lnc-SMARCA2-6	chr9:2276007-2276253	NONHSAT129989
7	lnc-SMARCA2-6	chr9:2291976-2293037	NONHSAT129989
8	lnc-KIAA0020-1	chr9:2411589-2414510	l_3727_chr9:2411588-2611526_ovary
9	lnc-SMARCA2-6	chr9:2287708-2288332	NONHSAT129989

No data

Variant related genes	Relation type
ENSG00000236404	chromatin interactions
ENSG00000147852	chromatin interactions

Extended variants
information (count: 7734 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:7734 , 50 per page) page: 1 2 3 4 5 6 7 ... 155

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10965354	chr9:2253741-2253742	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs559084984	chr9:2253763-2253764	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs572480646	chr9:2253778-2253779	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs376089643	chr9:2253779-2253780	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs575762564	chr9:2253821-2253822	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs369730498	chr9:2253834-2253835	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs554049517	chr9:2253842-2253843	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs573885998	chr9:2253846-2253847	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs397812082	chr9:2253851-2253852	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs397761068	chr9:2253852-2253853	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs542885267	chr9:2253858-2253859	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs74786604	chr9:2253921-2253922	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs575819480	chr9:2253928-2253929	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs9697002	chr9:2253943-2253944	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs386731658	chr9:2253994-2253995	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs2376224	chr9:2253996-2253997	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs547045462	chr9:2254015-2254016	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs560926468	chr9:2254035-2254036	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs187352747	chr9:2254080-2254081	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs146342335	chr9:2254106-2254107	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs570303895	chr9:2254119-2254120	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs192114097	chr9:2254122-2254123	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs552709096	chr9:2254123-2254124	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs75366486	chr9:2254125-2254126	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs535100468	chr9:2254127-2254128	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs139478629	chr9:2254131-2254132	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs36006041	chr9:2254185-2254186	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs398068382	chr9:2254188-2254189	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs185405797	chr9:2254203-2254204	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs564603991	chr9:2254237-2254238	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs7041763	chr9:2254245-2254246	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs376931309	chr9:2254249-2254250	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs575833429	chr9:2254273-2254274	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs572137264	chr9:2254288-2254289	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs565538964	chr9:2254291-2254292	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs541063599	chr9:2254316-2254317	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs533440222	chr9:2254317-2254318	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs190700449	chr9:2254337-2254338	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs142785846	chr9:2254362-2254363	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs370377408	chr9:2254365-2254366	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs114655912	chr9:2254366-2254367	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs34859419	chr9:2254367-2254368	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs374124912	chr9:2254368-2254369	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs115214324	chr9:2254400-2254401	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs564049802	chr9:2254405-2254406	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs73641018	chr9:2254408-2254409	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs550507096	chr9:2254413-2254414	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs148484393	chr9:2254471-2254472	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs7042935	chr9:2254498-2254499	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs16938139	chr9:2254508-2254509	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:103)

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
Non-syndromic sensorineural hearing loss	18451855	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:963 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2248600-2263800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:2248800-2257000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:2249000-2253800	Weak transcription	Stomach Mucosa	stomach
4	chr9:2252200-2260400	Weak transcription	A549	lung
5	chr9:2252800-2254400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr9:2253200-2254200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:2253600-2253800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:2253600-2254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:2253600-2254600	Enhancers	Ovary	ovary
10	chr9:2253600-2255400	Enhancers	Fetal Muscle Leg	muscle
11	chr9:2253600-2255800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:2253800-2254200	Enhancers	Stomach Mucosa	stomach
13	chr9:2254000-2254200	Enhancers	Fetal Heart	heart
14	chr9:2254000-2254200	Enhancers	Fetal Kidney	kidney
15	chr9:2254000-2255000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:2254000-2255600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:2254200-2254400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:2254200-2254600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:2254200-2254800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:2254200-2255200	Weak transcription	Fetal Heart	heart
21	chr9:2254400-2255200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:2254400-2255800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:2254600-2255400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:2254600-2257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:2254600-2262800	Weak transcription	Ovary	ovary
26	chr9:2254800-2255200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr9:2254800-2255400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr9:2255000-2255600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:2255200-2255400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:2255200-2255400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr9:2255200-2255600	Enhancers	Fetal Heart	heart
32	chr9:2255400-2255600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr9:2255400-2260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:2255400-2262800	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:2255600-2255800	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr9:2255600-2257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:2255800-2256200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr9:2255800-2257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:2256200-2263200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:2257000-2257400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:2257000-2258000	Enhancers	Primary B cells from peripheral blood	blood
42	chr9:2257000-2258200	Enhancers	Primary B cells from cord blood	blood
43	chr9:2257200-2257400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:2257400-2257600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:2257400-2257800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:2257400-2257800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:2257400-2257800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr9:2257400-2257800	Enhancers	GM12878-XiMat	blood
49	chr9:2257400-2258000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:2257400-2275000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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