Variant report

Variant	nsv615017
Chromosome Location	chr9:104874984-104994909
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:3)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:104973156..104974681-chr9:104986450..104988784,2	MCF-7	breast:
2	chr9:104973156..104974681-chr9:104986450..104988784,2	MCF-7	breast:
3	chr11:118868629..118869144-chr9:104880609..104881109,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIN3A-3	chr9:104946414-104946469	NONHSAT133756
2	lnc-GRIN3A-3	chr9:104946414-104946469	ucscGeneNc_uc004bbt_2
3	lnc-GRIN3A-3	chr9:104942626-104945366	NONHSAT133756
4	lnc-GRIN3A-3	chr9:104990149-104990219	NONHSAT133756
5	lnc-GRIN3A-3	chr9:104942631-104945366	ucscGeneNc_uc004bbt_2
6	lnc-GRIN3A-3	chr9:104990149-104990219	ucscGeneNc_uc004bbt_2

No data

Variant related genes	Relation type
ENSG00000255121	chromatin interactions
ENSG00000186166	chromatin interactions

Extended variants
information (count: 1001 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:1001 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545426665	chr9:104875805-104875806	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs542225777	chr9:104875821-104875822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs112734801	chr9:104875841-104875842	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs567843824	chr9:104875845-104875846	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs536971043	chr9:104875850-104875851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs372547496	chr9:104875916-104875917	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs189263946	chr9:104875956-104875957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs545237549	chr9:104876025-104876026	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs182186045	chr9:104876026-104876027	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs560303390	chr9:104876104-104876105	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs148580507	chr9:104876126-104876127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs369543292	chr9:104876141-104876142	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs34447661	chr9:104876177-104876178	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs386415670	chr9:104876178-104876179	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs35552628	chr9:104876179-104876180	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs554722556	chr9:104876180-104876181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs575967904	chr9:104876181-104876182	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs565608295	chr9:104876190-104876191	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs12380477	chr9:104876647-104876648	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs554266038	chr9:104876670-104876671	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs12380493	chr9:104876691-104876692	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs112872396	chr9:104876723-104876724	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs373371253	chr9:104876761-104876762	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs141932808	chr9:104876793-104876794	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs145769761	chr9:104876794-104876795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs577107587	chr9:104876870-104876871	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs373590130	chr9:104876884-104876885	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs12380515	chr9:104876930-104876931	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs534463068	chr9:104876948-104876949	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs117985146	chr9:104876965-104876966	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs561374947	chr9:104876977-104876978	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs371479871	chr9:104876996-104876997	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs147786920	chr9:104877007-104877008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs550398548	chr9:104877026-104877027	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs570143424	chr9:104877032-104877033	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs373352326	chr9:104877055-104877056	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs12377882	chr9:104877111-104877112	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs320166	chr9:104877144-104877145	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs191596687	chr9:104877179-104877180	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs12377893	chr9:104877180-104877181	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs113403798	chr9:104877186-104877187	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs7034610	chr9:104877235-104877236	Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs73659244	chr9:104877268-104877269	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs79585279	chr9:104877296-104877297	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs576938229	chr9:104877299-104877300	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs12379341	chr9:104877313-104877314	Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs141269382	chr9:104877332-104877333	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs554090555	chr9:104877387-104877388	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs543342288	chr9:104877408-104877409	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs76234070	chr9:104877413-104877414	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Neuroblastoma	20406844	CNVD
Schizophrenia	23813976	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104875800-104876200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:104876600-104877200	Enhancers	Adipose Nuclei	Adipose
3	chr9:104877200-104877600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr9:104878600-104879600	Enhancers	Fetal Heart	heart
5	chr9:104886400-104886800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:104886600-104887400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:104893200-104893800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:104897000-104897600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:104897600-104898400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr9:104897800-104899000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:104898000-104898400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:104904600-104905000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:104915600-104916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr9:104940400-104941800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr9:104940600-104941400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:104947400-104950200	Enhancers	Fetal Heart	heart
17	chr9:104947800-104948000	Enhancers	Ovary	ovary
18	chr9:104947800-104948400	Enhancers	Stomach Smooth Muscle	stomach
19	chr9:104947800-104948800	Enhancers	Adipose Nuclei	Adipose
20	chr9:104948000-104948800	Enhancers	Fetal Kidney	kidney
21	chr9:104948200-104948800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:104948600-104949200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr9:104948800-104949800	Weak transcription	Fetal Kidney	kidney
24	chr9:104949200-104949600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:104949600-104950400	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr9:104950000-104950200	Enhancers	Fetal Kidney	kidney
27	chr9:104950000-104950800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:104950000-104950800	Enhancers	Ovary	ovary
29	chr9:104971400-104971800	Active TSS	Aorta	Aorta
30	chr9:104985600-104986200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr9:104985600-104986200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr9:104985600-104986200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr9:104985600-104986200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr9:104985600-104986200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr9:104985600-104986200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:104985600-104986200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:104985600-104986400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr9:104985600-104986400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:104985600-104986600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:104985600-104986600	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr9:104985800-104986200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:104985800-104986200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:104985800-104986200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:104985800-104986400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:104985800-104986400	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr9:104985800-104986400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:104985800-104986400	Active TSS	Liver	Liver
48	chr9:104985800-104986400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr9:104985800-104986400	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr9:104985800-104986600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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