Variant report

Variant	nsv524090
Chromosome Location	chr3:28631124-28645278
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28615082..28617679-chr3:28638478..28641059,2	MCF-7	breast:
2	chr3:28645073..28647922-chr3:28738651..28741431,2	MCF-7	breast:
3	chr3:28622132..28623707-chr3:28628901..28631452,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZCWPW2-1	chr3:28632042-28632276	XLOC_002605

Variant related genes	Relation type
ENSG00000228214	chromatin interactions
RGS12	miRNA target sites

Extended variants
information (count: 304 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:304 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4521182	chr3:28631124-28631125	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs372774676	chr3:28631139-28631140	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs4356777	chr3:28631155-28631156	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs551407218	chr3:28631266-28631267	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs571115707	chr3:28631306-28631307	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs189519319	chr3:28631376-28631377	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs147746723	chr3:28631414-28631415	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs539615200	chr3:28631432-28631433	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs142600284	chr3:28631469-28631470	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs535490053	chr3:28631480-28631481	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs180769219	chr3:28631501-28631502	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs575548545	chr3:28631505-28631506	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs35397523	chr3:28631658-28631659	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs116180700	chr3:28631664-28631665	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs146861350	chr3:28631666-28631667	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs576312814	chr3:28631714-28631715	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs78213207	chr3:28631728-28631729	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs185214050	chr3:28631818-28631819	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs529631435	chr3:28631832-28631833	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs543274931	chr3:28631859-28631860	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs562344943	chr3:28631895-28631896	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs189977195	chr3:28631897-28631898	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs183097784	chr3:28631946-28631947	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs571006704	chr3:28632004-28632005	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs527510894	chr3:28632018-28632019	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs547173487	chr3:28632132-28632133	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
27	rs540264449	chr3:28632150-28632151	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
28	rs72894714	chr3:28632182-28632183	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs74498135	chr3:28632188-28632189	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
30	rs186782260	chr3:28632208-28632209	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
31	rs191619135	chr3:28632215-28632216	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
32	rs558315317	chr3:28632216-28632217	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
33	rs34046306	chr3:28632225-28632226	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs540945601	chr3:28632250-28632251	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
35	rs140792044	chr3:28632271-28632272	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
36	rs554430342	chr3:28632297-28632298	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs150110369	chr3:28632415-28632416	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs542959353	chr3:28632443-28632444	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs183820753	chr3:28632446-28632447	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs531255001	chr3:28632448-28632449	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs544967073	chr3:28632497-28632498	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs72894716	chr3:28632498-28632499	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs527399356	chr3:28632505-28632506	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs116451277	chr3:28632509-28632510	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs541425603	chr3:28632511-28632512	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs560758631	chr3:28632612-28632613	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs4522734	chr3:28632664-28632665	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs549854359	chr3:28632689-28632690	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs578159423	chr3:28632695-28632696	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs569913838	chr3:28632696-28632697	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	16618734	CNVD
Cancer	20164919	CNVD
Developmental delay	21147756	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28618200-28631200	Weak transcription	Psoas Muscle	Psoas
2	chr3:28627600-28631600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:28627800-28631600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:28627800-28631800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:28628400-28631800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:28628600-28631800	Weak transcription	Aorta	Aorta
7	chr3:28628800-28633600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:28629400-28631200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:28631000-28632400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:28631200-28631400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:28631200-28631400	Enhancers	Psoas Muscle	Psoas
12	chr3:28631200-28634000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:28631400-28632400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:28631600-28631800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr3:28631600-28632000	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:28631600-28632200	Active TSS	NHLF	lung
17	chr3:28631600-28632600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:28631600-28632800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:28631600-28632800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:28631600-28633000	Enhancers	HSMM	muscle
21	chr3:28631800-28632000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:28631800-28632000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:28631800-28632000	Enhancers	Aorta	Aorta
24	chr3:28631800-28632000	Active TSS	HSMMtube	muscle
25	chr3:28631800-28632200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr3:28631800-28632200	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr3:28631800-28632400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:28631800-28632600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr3:28631800-28632600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:28631800-28632600	Enhancers	Osteobl	bone
31	chr3:28632000-28632200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:28632000-28632200	Flanking Active TSS	HSMMtube	muscle
33	chr3:28632000-28632400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:28632000-28632600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr3:28632000-28632600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:28632000-28632600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:28632000-28632600	Weak transcription	Aorta	Aorta
38	chr3:28632200-28632400	Enhancers	Brain Anterior Caudate	brain
39	chr3:28632200-28632400	Flanking Active TSS	NHLF	lung
40	chr3:28632200-28632800	Enhancers	HSMMtube	muscle
41	chr3:28632200-28632800	Enhancers	NH-A	brain
42	chr3:28632400-28632800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:28632600-28632800	Enhancers	Aorta	Aorta
44	chr3:28632600-28633000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:28632600-28634600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:28633600-28633800	Enhancers	Brain Substantia Nigra	brain
47	chr3:28634800-28635000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:28635000-28635400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:28639200-28640200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:28639600-28640000	Enhancers	NHEK	skin

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