Variant report

Variant	nsv613129
Chromosome Location	chr9:2256092-2330907
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:12)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2244966..2246945-chr9:2263682..2266605,2	MCF-7	breast:
2	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
3	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
4	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
5	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
6	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
7	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
8	chr9:2257367..2260216-chr9:2810940..2813820,2	MCF-7	breast:
9	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
10	chr9:2321723..2322570-chr9:2728160..2728820,2	MCF-7	breast:
11	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
12	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCA2-6	chr9:2287708-2288332	NONHSAT129989
2	lnc-SMARCA2-6	chr9:2291976-2293037	NONHSAT129989
3	lnc-SMARCA2-6	chr9:2276007-2276253	NONHSAT129989
4	lnc-SMARCA2-5	chr9:2264485-2264628	NONHSAT129991
5	lnc-SMARCA2-5	chr9:2273475-2274167	NONHSAT129991

No data

Variant related genes	Relation type
ENSG00000236404	chromatin interactions
ENSG00000147852	chromatin interactions

Extended variants
information (count: 3708 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:3708 , 50 per page) page: 1 2 3 4 5 6 7 ... 75

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs16938145	chr9:2256092-2256093	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	disease
2	rs77529977	chr9:2256140-2256141	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs186620144	chr9:2256151-2256152	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs369076308	chr9:2256155-2256156	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs560573891	chr9:2256167-2256168	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs189893991	chr9:2256184-2256185	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs535424176	chr9:2256231-2256232	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs542146254	chr9:2256245-2256246	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs530958243	chr9:2256250-2256251	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs7039694	chr9:2256269-2256270	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs567984916	chr9:2256317-2256318	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs530740357	chr9:2256320-2256321	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs550829154	chr9:2256355-2256356	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs7019812	chr9:2256356-2256357	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs536524027	chr9:2256360-2256361	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546369027	chr9:2256386-2256387	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs182371214	chr9:2256402-2256403	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs535060866	chr9:2256422-2256423	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555662092	chr9:2256424-2256425	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs138323120	chr9:2256441-2256442	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs187050213	chr9:2256449-2256450	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs192837128	chr9:2256516-2256517	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs6475647	chr9:2256529-2256530	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs185374054	chr9:2256535-2256536	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs553928489	chr9:2256540-2256541	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs188489749	chr9:2256541-2256542	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs193240834	chr9:2256542-2256543	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs6475648	chr9:2256575-2256576	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs530453400	chr9:2256618-2256619	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs530853059	chr9:2256623-2256624	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs80306634	chr9:2256645-2256646	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs564347052	chr9:2256653-2256654	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs74526637	chr9:2256664-2256665	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs77026464	chr9:2256665-2256666	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs141819457	chr9:2256670-2256671	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs7020176	chr9:2256676-2256677	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs7040265	chr9:2256677-2256678	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs117554916	chr9:2256694-2256695	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs543439092	chr9:2256713-2256714	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs548606513	chr9:2256717-2256718	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs568492304	chr9:2256718-2256719	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs538196046	chr9:2256736-2256737	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188282687	chr9:2256752-2256753	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs150612859	chr9:2256766-2256767	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs534102587	chr9:2256773-2256774	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs554254051	chr9:2256799-2256800	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs139722767	chr9:2256840-2256841	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs55662811	chr9:2256869-2256870	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs180898446	chr9:2256870-2256871	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs200752717	chr9:2256879-2256880	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	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:583 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

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	chr9:2252200-2260400	Weak transcription	A549	lung
4	chr9:2254600-2257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:2254600-2262800	Weak transcription	Ovary	ovary
6	chr9:2255400-2260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:2255400-2262800	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:2255600-2257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:2255800-2256200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
10	chr9:2255800-2257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:2256200-2263200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:2257000-2257400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:2257000-2258000	Enhancers	Primary B cells from peripheral blood	blood
14	chr9:2257000-2258200	Enhancers	Primary B cells from cord blood	blood
15	chr9:2257200-2257400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:2257400-2257600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:2257400-2257800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:2257400-2257800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:2257400-2257800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr9:2257400-2257800	Enhancers	GM12878-XiMat	blood
21	chr9:2257400-2258000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:2257400-2275000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:2257600-2262800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:2257800-2258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:2257800-2260200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:2257800-2260600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:2258000-2260400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:2258000-2263000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr9:2258200-2258400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr9:2258200-2263000	Weak transcription	Primary B cells from cord blood	blood
31	chr9:2258400-2266200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:2259400-2259800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:2259600-2261400	Enhancers	Brain Germinal Matrix	brain
34	chr9:2259800-2260200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:2259800-2261200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:2259800-2261200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr9:2260200-2260600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:2260200-2260800	Enhancers	Fetal Brain Male	brain
39	chr9:2260200-2261000	Enhancers	Brain Hippocampus Middle	brain
40	chr9:2260200-2261000	Enhancers	Fetal Brain Female	brain
41	chr9:2260200-2261200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:2260200-2261200	Enhancers	Brain Anterior Caudate	brain
43	chr9:2260200-2261400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:2260200-2261600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:2260200-2261800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:2260400-2260800	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:2260400-2260800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:2260400-2260800	Enhancers	Esophagus	oesophagus
49	chr9:2260400-2260800	Enhancers	Pancreas	Pancrea
50	chr9:2260400-2261000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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