Variant report

Variant	nsv878781
Chromosome Location	chr4:28568780-28680520
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:11)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:28654800..28656998-chr4:28661413..28663386,2	MCF-7	breast:
2	chr4:28666962..28669631-chr4:28671140..28674094,2	K562	blood:
3	chr4:28599052..28601001-chr4:28607450..28609596,2	MCF-7	breast:
4	chr4:28619270..28620926-chr4:28622787..28624765,2	MCF-7	breast:
5	chr2:19310340..19311108-chr4:28646906..28647846,2	MCF-7	breast:
6	chr4:28642172..28644284-chr4:28671364..28674142,2	MCF-7	breast:
7	chr4:28654800..28656998-chr4:28661413..28663386,2	MCF-7	breast:
8	chr4:28599052..28601001-chr4:28607450..28609596,2	MCF-7	breast:
9	chr4:28642172..28644284-chr4:28671364..28674142,2	MCF-7	breast:
10	chr4:28666962..28669631-chr4:28671140..28674094,2	K562	blood:
11	chr4:28619270..28620926-chr4:28622787..28624765,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIM2-4	chr4:28601669-28601897	ENSG00000250064
2	lnc-STIM2-4	chr4:28579538-28579618	ENSG00000250064
3	lnc-RP11-180C1.1.1-3	chr4:28586520-28586645	NONHSAT095913
4	lnc-RP11-180C1.1.1-3	chr4:28586781-28586911	NONHSAT095913

No data

Extended variants
information (count: 2969 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:2969 , 50 per page) page: 1 2 3 4 5 6 7 ... 60

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6818548	chr4:28568780-28568781	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs151208063	chr4:28568803-28568804	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs527790761	chr4:28568838-28568839	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs547961922	chr4:28568864-28568865	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs570951011	chr4:28568870-28568871	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539878929	chr4:28568871-28568872	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs550129581	chr4:28568896-28568897	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs187213950	chr4:28568971-28568972	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs140273878	chr4:28568982-28568983	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs192795270	chr4:28568999-28569000	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs184846300	chr4:28569010-28569011	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs189300464	chr4:28569030-28569031	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs534879830	chr4:28569040-28569041	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545278079	chr4:28569045-28569046	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs557463788	chr4:28569050-28569051	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs547822312	chr4:28569076-28569077	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs118052094	chr4:28569087-28569088	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs150018508	chr4:28569113-28569114	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs76130797	chr4:28569136-28569137	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs192637348	chr4:28569139-28569140	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs542860827	chr4:28569155-28569156	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs56908066	chr4:28569177-28569178	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs13111564	chr4:28569217-28569218	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs145255243	chr4:28569228-28569229	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs540617056	chr4:28569241-28569242	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs142401049	chr4:28569258-28569259	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs183674138	chr4:28569264-28569265	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549915504	chr4:28569269-28569270	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs569985473	chr4:28569352-28569353	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs529266985	chr4:28569359-28569360	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576652164	chr4:28569397-28569398	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs146361319	chr4:28569506-28569507	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs4692329	chr4:28569507-28569508	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs534914449	chr4:28569579-28569580	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs557900803	chr4:28569633-28569634	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs571027006	chr4:28569652-28569653	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs537110808	chr4:28569690-28569691	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs115871417	chr4:28569696-28569697	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs147865362	chr4:28569706-28569707	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs189516509	chr4:28569749-28569750	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs2458622	chr4:28569807-28569808	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs2471717	chr4:28569819-28569820	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs573154900	chr4:28569871-28569872	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545247208	chr4:28569872-28569873	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs141897784	chr4:28569878-28569879	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs181780366	chr4:28569883-28569884	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs79090293	chr4:28569884-28569885	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs2458623	chr4:28569887-28569888	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs186284848	chr4:28569933-28569934	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs548944081	chr4:28569937-28569938	Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Prostate cancer	16573809	CNVD
Myelofibrosis	22110671	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28568000-28570600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:28570600-28587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:28583600-28583800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:28587400-28588200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:28588200-28623400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:28590400-28591000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:28590600-28591200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:28602000-28602600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:28602200-28602600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:28602400-28602800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:28602600-28603600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:28602800-28603800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:28603800-28604000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:28603800-28604000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:28611400-28611800	Enhancers	Fetal Heart	heart
16	chr4:28622800-28623800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:28623000-28623600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:28623400-28623800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:28623800-28641200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:28629800-28630200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:28632800-28641400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:28641200-28641400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:28641400-28641600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr4:28655800-28656400	Enhancers	HMEC	breast
25	chr4:28655800-28656600	Enhancers	HUVEC	blood vessel
26	chr4:28656000-28656600	Enhancers	NHEK	skin
27	chr4:28661600-28662200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:28669600-28669800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:28673200-28674000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr4:28673400-28673800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr4:28673800-28674800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:28675000-28675200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr4:28676800-28677000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:28678200-28678800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:28678600-28679200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:28678800-28682000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:28679200-28679600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:28679200-28679800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:28679400-28680000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:28679600-28679800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:28679600-28679800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:28679600-28680400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:28679800-28680000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:28680000-28681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:28680000-28682600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:28680400-28681800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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