Variant report

Variant	nsv550292
Chromosome Location	chr10:28660603-28665041
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:28591043..28593687-chr10:28664623..28666439,2	MCF-7	breast:
2	chr10:28591813..28593697-chr10:28661899..28664079,2	MCF-7	breast:
3	chr10:28663936..28666501-chr10:28668438..28671380,2	MCF-7	breast:
4	chr10:28591610..28593155-chr10:28664575..28666519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	chromatin interactions

Extended variants
information (count: 205 )
Associated
traits (count: 41 )

Variant overlapped rSNPs/rCNVs (count:205 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1249271	chr10:28660603-28660604	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs114319304	chr10:28660613-28660614	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs187779367	chr10:28660655-28660656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs192342567	chr10:28660684-28660685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs528179529	chr10:28660730-28660731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs546150177	chr10:28660738-28660739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs370467660	chr10:28660741-28660742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs1262020	chr10:28660755-28660756	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs535154161	chr10:28660761-28660762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs183609246	chr10:28660769-28660770	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs566385145	chr10:28660776-28660777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs201021809	chr10:28660779-28660780	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs1273096	chr10:28660799-28660800	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs569091656	chr10:28660822-28660823	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs529753176	chr10:28660831-28660832	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs116222965	chr10:28660851-28660852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs4525118	chr10:28660857-28660858	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs555224285	chr10:28660880-28660881	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs148086959	chr10:28660906-28660907	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs566923864	chr10:28660937-28660938	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs1249272	chr10:28660953-28660954	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs555936692	chr10:28660963-28660964	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs573973883	chr10:28660975-28660976	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs544305831	chr10:28660984-28660985	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs11007060	chr10:28661016-28661017	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs141863080	chr10:28661027-28661028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs192763798	chr10:28661065-28661066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs553141443	chr10:28661110-28661111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs560326140	chr10:28661127-28661128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs527923199	chr10:28661132-28661133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs539938435	chr10:28661181-28661182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs561660311	chr10:28661199-28661200	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs200758404	chr10:28661201-28661202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs201867935	chr10:28661202-28661203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs397743796	chr10:28661210-28661211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs118134664	chr10:28661242-28661243	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs116870143	chr10:28661246-28661247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200085000	chr10:28661262-28661263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569105322	chr10:28661265-28661266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs184824713	chr10:28661266-28661267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs533268728	chr10:28661308-28661309	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556027248	chr10:28661321-28661322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs118146167	chr10:28661378-28661379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs566660651	chr10:28661383-28661384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs146526628	chr10:28661385-28661386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs12763338	chr10:28661406-28661407	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs187046399	chr10:28661433-28661434	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs116202597	chr10:28661436-28661437	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs74127209	chr10:28661470-28661471	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs556288921	chr10:28661478-28661479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:41)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Phyllodes tumor	17334353	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Lung cancer	18438408	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
T-cell lymphomas	19863542	CNVD
Esophageal cancer	21851588	CNVD
Behavioral abnormalities	21522184	CNVD
Dysmorphic features	21522184	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22048815	CNVD
Myelofibrosis	22110671	CNVD
Chronic lymphocytic leukemia	21546498	CNVD

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28644400-28665000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28656200-28661800	Weak transcription	Colonic Mucosa	Colon
3	chr10:28657200-28662600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:28657800-28661400	Weak transcription	Placenta	Placenta
5	chr10:28658600-28660800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr10:28659400-28664400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr10:28659600-28667800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:28659800-28663200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:28659800-28667800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr10:28660000-28668200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr10:28660200-28663800	Weak transcription	HepG2	liver
12	chr10:28660400-28664400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:28660400-28664400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:28660400-28667600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:28660800-28661000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:28661400-28662200	Enhancers	Placenta	Placenta
17	chr10:28662200-28663600	Weak transcription	Placenta	Placenta
18	chr10:28662600-28662800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr10:28662600-28664000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr10:28662800-28664200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr10:28663200-28663400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:28663400-28663800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:28663600-28664000	Enhancers	Placenta	Placenta
24	chr10:28663800-28664000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:28663800-28664000	Enhancers	Pancreas	Pancrea
26	chr10:28663800-28665400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:28663800-28665400	Enhancers	HMEC	breast
28	chr10:28663800-28666000	Enhancers	HepG2	liver
29	chr10:28664000-28664800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr10:28664000-28665000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr10:28664000-28665000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr10:28664000-28665000	Weak transcription	Placenta	Placenta
33	chr10:28664000-28665200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:28664200-28665000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr10:28664200-28665000	Enhancers	HSMMtube	muscle
36	chr10:28664200-28665200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:28664200-28665200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:28664200-28665200	Weak transcription	Pancreas	Pancrea
39	chr10:28664200-28665200	Enhancers	NHEK	skin
40	chr10:28664400-28664800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr10:28664400-28664800	Enhancers	HSMM	muscle
42	chr10:28664400-28665000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:28664400-28665000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr10:28664400-28665000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr10:28664400-28665000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr10:28664400-28665000	Enhancers	Duodenum Mucosa	Duodenum
47	chr10:28664400-28665000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr10:28664400-28665200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:28664400-28665200	Enhancers	Fetal Heart	heart
50	chr10:28664400-28665200	Enhancers	A549	lung

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