Variant report

Variant	nsv3915
Chromosome Location	chr3:98892668-98940053
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr3:98930300-98930345	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:98895381-98895526	Hela-S3	cervix:	n/a	chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895480-98895491 chr3:98895479-98895490 chr3:98895479-98895492 chr3:98895479-98895490
3	CEBPB	chr3:98895351-98895574	A549	lung:	n/a	chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895480-98895491 chr3:98895479-98895490 chr3:98895479-98895492 chr3:98895479-98895490
4	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
5	CEBPB	chr3:98895292-98895657	IMR90	lung:	n/a	chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895480-98895491 chr3:98895479-98895490 chr3:98895479-98895492 chr3:98895479-98895490
6	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
7	CEBPB	chr3:98895313-98895658	HepG2	liver:	n/a	chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895481-98895490 chr3:98895481-98895490 chr3:98895479-98895492 chr3:98895480-98895491 chr3:98895479-98895490 chr3:98895479-98895492 chr3:98895479-98895490
8	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
9	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
10	CTCF	chr3:98927000-98927150	BJ	skin:	n/a	n/a
11	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
12	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
13	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
16	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
17	CTCF	chr3:98904800-98904950	WI-38	lung:	n/a	n/a
18	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
19	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
20	CTCF	chr3:98928620-98928770	GM12871	blood:	n/a	n/a
21	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F4	chr3:98895870-98896330	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr3:98903417-98903604	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr3:98931762-98932488	ECC-1	luminal epithelium:	n/a	chr3:98931860-98931869 chr3:98931898-98931912 chr3:98931856-98931870
26	ESR1	chr3:98931860-98932211	ECC-1	luminal epithelium:	n/a	n/a
27	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
28	JUND	chr3:98934719-98934891	HepG2	liver:	n/a	n/a
29	MAFF	chr3:98895059-98895353	K562	blood:	n/a	chr3:98895199-98895217
30	MAFF	chr3:98895023-98895385	HepG2	liver:	n/a	chr3:98895199-98895217
31	MAFK	chr3:98895068-98895372	H1-hESC	embryonic stem cell:	n/a	chr3:98895200-98895215
32	MAFK	chr3:98895049-98895381	Hela-S3	cervix:	n/a	chr3:98895200-98895215
33	MAFK	chr3:98894912-98895526	GM12878	blood:	n/a	chr3:98895200-98895215
34	MAFK	chr3:98895012-98895403	IMR90	lung:	n/a	chr3:98895200-98895215
35	MAFK	chr3:98895024-98895369	K562	blood:	n/a	chr3:98895200-98895215
36	MAFK	chr3:98895021-98895388	HepG2	liver:	n/a	chr3:98895200-98895215
37	MAFK	chr3:98895059-98895387	HepG2	liver:	n/a	chr3:98895200-98895215
38	MYC	chr3:98895222-98895335	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr3:98906109-98906137	GM12878	blood:	n/a	n/a
40	MYC	chr3:98895321-98895640	MCF10A-Er-Src	breast:	n/a	n/a
41	MYC	chr3:98916015-98916133	MCF10A-Er-Src	breast:	n/a	n/a
42	MYC	chr3:98906100-98906193	MCF-7	breast:	n/a	n/a
43	MYC	chr3:98909815-98909957	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr3:98909845-98909901	MCF10A-Er-Src	breast:	n/a	n/a
45	NFIC	chr3:98931698-98932658	ECC-1	luminal epithelium:	n/a	n/a
46	NFIC	chr3:98931749-98932441	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr3:98911266-98911341	Gliobla	brain:	n/a	n/a
48	POLR2A	chr3:98893669-98893705	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr3:98898216-98898345	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr3:98903633-98903647	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
2	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-6	chr3:98896222-98896357	NONHSAT090838
2	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839
3	lnc-ST3GAL6-6	chr3:98904502-98904611	NONHSAT090838
4	lnc-ST3GAL6-6	chr3:98899387-98899480	NONHSAT090838

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 1385 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:1385 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs114034202	chr3:98892736-98892737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs13086695	chr3:98892742-98892743	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs562731736	chr3:98892774-98892775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs375655064	chr3:98892798-98892799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs56937182	chr3:98892808-98892809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs181889377	chr3:98892821-98892822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs186099302	chr3:98892831-98892832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs145310814	chr3:98892849-98892850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs527649321	chr3:98892858-98892859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs547751189	chr3:98892898-98892899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs570790243	chr3:98892923-98892924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs539744197	chr3:98892946-98892947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs537091847	chr3:98892963-98892964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs370270662	chr3:98892966-98892967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs114880988	chr3:98892971-98892972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs535548101	chr3:98892974-98892975	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189771688	chr3:98892991-98892992	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs541978578	chr3:98892999-98893000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs150953395	chr3:98893026-98893027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs112805875	chr3:98893069-98893070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs78979327	chr3:98893070-98893071	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs376437181	chr3:98893092-98893093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs9823917	chr3:98893174-98893175	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs140736120	chr3:98893237-98893238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs115675784	chr3:98893247-98893248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs114679178	chr3:98893251-98893252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs76830625	chr3:98893266-98893267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs180737849	chr3:98893323-98893324	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs562073132	chr3:98893342-98893343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs527767284	chr3:98893358-98893359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs541115906	chr3:98893397-98893398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs564467168	chr3:98893418-98893419	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs533276966	chr3:98893422-98893423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs550055116	chr3:98893428-98893429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs186666384	chr3:98893433-98893434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs138348398	chr3:98893445-98893446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs529045927	chr3:98893446-98893447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs117869197	chr3:98893454-98893455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs35595599	chr3:98893473-98893474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs565684208	chr3:98893492-98893493	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs2461791	chr3:98893510-98893511	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs374166800	chr3:98893521-98893522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs191112193	chr3:98893555-98893556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs60066948	chr3:98893600-98893601	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs375907297	chr3:98893630-98893631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs539764960	chr3:98893647-98893648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs556402557	chr3:98893675-98893676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs115801559	chr3:98893698-98893699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs542083453	chr3:98893712-98893713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs555927661	chr3:98893751-98893752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
6	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98899200-98899600	Enhancers	NHEK	skin
10	chr3:98899200-98900200	Enhancers	HMEC	breast
11	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
13	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
14	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
16	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
19	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus
20	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
23	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum

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