Variant report

Variant	nsv1020101
Chromosome Location	chr9:3060187-3099009
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62477919..62478756-chr9:3062250..3062792,2	MCF-7	breast:

Extended variants
information (count: 284 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:284 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs150509378	chr9:3060227-3060228	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs575956843	chr9:3060238-3060239	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs540567099	chr9:3060243-3060244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs560295706	chr9:3060248-3060249	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs535749341	chr9:3060251-3060252	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs10738843	chr9:3060291-3060292	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs139478075	chr9:3060314-3060315	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs562457070	chr9:3060359-3060360	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs144910746	chr9:3060371-3060372	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs73391587	chr9:3062008-3062009	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs550167477	chr9:3062011-3062012	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs369282003	chr9:3062054-3062055	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs570368428	chr9:3062066-3062067	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs539387741	chr9:3062089-3062090	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs7041084	chr9:3062092-3062093	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs572713909	chr9:3062106-3062107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs534687558	chr9:3062118-3062119	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs554673269	chr9:3062127-3062128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs189149791	chr9:3062153-3062154	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs192538244	chr9:3062169-3062170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs563387338	chr9:3062171-3062172	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs56020201	chr9:3062185-3062186	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs140426644	chr9:3062189-3062190	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs145648943	chr9:3062190-3062191	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs181017705	chr9:3070659-3070660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs568440880	chr9:3070690-3070691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs534409611	chr9:3070716-3070717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs554120281	chr9:3070724-3070725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs573773535	chr9:3070727-3070728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs76505451	chr9:3070753-3070754	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs554326092	chr9:3070756-3070757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs34667647	chr9:3070808-3070809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs573035606	chr9:3070817-3070818	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs575426816	chr9:3070838-3070839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs147133949	chr9:3070881-3070882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs185080310	chr9:3070894-3070895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs558889831	chr9:3070895-3070896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs368289613	chr9:3070911-3070912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs565195940	chr9:3070922-3070923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs116370101	chr9:3070942-3070943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs138025567	chr9:3070965-3070966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs560781231	chr9:3071010-3071011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs543844086	chr9:3071041-3071042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs56105985	chr9:3071085-3071086	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs560963705	chr9:3071155-3071156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs188377444	chr9:3071184-3071185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs568876665	chr9:3071190-3071191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs146988831	chr9:3073414-3073415	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs3904472	chr9:3073429-3073430	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs559932844	chr9:3073430-3073431	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

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
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
Ovarian cancer	22355333	CNVD
Autism	20808228	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3058000-3060400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:3058200-3060400	Enhancers	NHEK	skin
3	chr9:3058400-3060400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:3058400-3060400	Enhancers	HMEC	breast
5	chr9:3059200-3060400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr9:3059600-3060200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:3059600-3060200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:3059600-3060200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr9:3059600-3060400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:3059600-3060400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr9:3059600-3060400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:3059600-3060400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:3059800-3060200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:3059800-3060200	Enhancers	HepG2	liver
15	chr9:3059800-3060400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:3060000-3060400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:3062000-3062200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:3070600-3071200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:3073400-3074800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:3073400-3074800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:3074000-3074600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr9:3074000-3074800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:3074200-3074600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr9:3074400-3074800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:3080400-3080800	Enhancers	Primary hematopoietic stem cells	blood
26	chr9:3087600-3088800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:3087600-3088800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr9:3088000-3088400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr9:3088000-3088800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr9:3088800-3090000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:3090000-3090200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:3099000-3100800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:3099000-3100800	Enhancers	Fetal Brain Male	brain

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