Variant report

Variant	nsv1020742
Chromosome Location	chr9:2281999-2298146
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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2290959..2293717-chr9:2295989..2299437,4	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	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
5	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
6	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:

(count:2 , 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

No data

Variant related genes	Relation type
ENSG00000147852	chromatin interactions
ENSG00000236404	chromatin interactions

Extended variants
information (count: 807 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:807 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10757356	chr9:2281999-2282000	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs139678334	chr9:2282015-2282016	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs565575807	chr9:2282031-2282032	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs35376484	chr9:2282049-2282050	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs369645382	chr9:2282060-2282061	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs149775868	chr9:2282102-2282103	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs78807258	chr9:2282104-2282105	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs200342694	chr9:2282106-2282107	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs567732691	chr9:2282160-2282161	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs139960375	chr9:2282162-2282163	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs374012898	chr9:2282169-2282170	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs549900870	chr9:2282180-2282181	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs570081522	chr9:2282240-2282241	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs187943573	chr9:2282250-2282251	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs538648046	chr9:2282257-2282258	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs558638166	chr9:2282278-2282279	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs577883807	chr9:2282331-2282332	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs533816680	chr9:2282354-2282355	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs56221829	chr9:2282358-2282359	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs573917269	chr9:2282372-2282373	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs542835269	chr9:2282393-2282394	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs556341108	chr9:2282410-2282411	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs576160424	chr9:2282419-2282420	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs545034903	chr9:2282438-2282439	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs540978921	chr9:2282439-2282440	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs190917276	chr9:2282451-2282452	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs528012520	chr9:2282502-2282503	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541393314	chr9:2282550-2282551	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs561615011	chr9:2282573-2282574	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs530275269	chr9:2282592-2282593	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs564361356	chr9:2282606-2282607	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs549913006	chr9:2282643-2282644	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs75270373	chr9:2282648-2282649	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs182472606	chr9:2282651-2282652	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs552561736	chr9:2282704-2282705	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs565966831	chr9:2282779-2282780	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs371070838	chr9:2282783-2282784	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs187999761	chr9:2282785-2282786	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs553822452	chr9:2282818-2282819	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs567563762	chr9:2282819-2282820	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs111920847	chr9:2282876-2282877	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs114462550	chr9:2282939-2282940	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs192675066	chr9:2282942-2282943	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs1324208	chr9:2282951-2282952	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs544751658	chr9:2282955-2282956	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs79836517	chr9:2282960-2282961	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs114619356	chr9:2282961-2282962	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs62530621	chr9:2282981-2282982	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs561423943	chr9:2283038-2283039	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs563467576	chr9:2283044-2283045	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

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
Renal cell carcinoma	21215367	CNVD

Chromatin state (count:223 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2263400-2290400	Weak transcription	Right Atrium	heart
2	chr9:2277000-2288000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:2277400-2286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:2280000-2282000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:2280600-2284200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:2280800-2282000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:2281000-2282200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:2281000-2282600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:2281000-2291200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:2281200-2282200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:2281200-2282200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:2281200-2282800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr9:2281200-2283200	Enhancers	Placenta	Placenta
14	chr9:2281400-2282000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:2281400-2282200	Enhancers	NH-A	brain
16	chr9:2281400-2283000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:2281600-2282200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr9:2281600-2282200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr9:2281600-2283200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
20	chr9:2281600-2283400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr9:2281800-2282000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
22	chr9:2281800-2282200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:2281800-2282200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
24	chr9:2281800-2282200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
25	chr9:2281800-2283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:2281800-2285000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:2282000-2282200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:2282000-2282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:2282000-2283400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:2282000-2283800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr9:2282200-2282400	Flanking Active TSS	NH-A	brain
32	chr9:2282200-2282800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:2282200-2282800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
34	chr9:2282200-2284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:2282200-2284200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr9:2282200-2284600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr9:2282200-2284800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:2282200-2287000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
39	chr9:2282400-2283000	Enhancers	NH-A	brain
40	chr9:2282600-2282800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:2282600-2291800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:2282800-2284000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:2282800-2284200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr9:2283000-2286600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:2283200-2283400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr9:2283200-2284200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:2283400-2283600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr9:2283400-2283600	Enhancers	Esophagus	oesophagus
49	chr9:2283400-2285600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:2283400-2286400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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