Variant report

Variant	nsv1014172
Chromosome Location	chr3:98900805-98949302
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

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	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
3	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
4	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
5	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
6	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
7	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
9	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
10	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
11	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
12	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
14	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
15	CTCF	chr3:98904800-98904950	WI-38	lung:	n/a	n/a
16	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
17	CTCF	chr3:98927000-98927150	BJ	skin:	n/a	n/a
18	CTCF	chr3:98928620-98928770	GM12871	blood:	n/a	n/a
19	E2F4	chr3:98903417-98903604	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
21	EP300	chr3:98931762-98932488	ECC-1	luminal epithelium:	n/a	chr3:98931860-98931869 chr3:98931898-98931912 chr3:98931856-98931870
22	ESR1	chr3:98931860-98932211	ECC-1	luminal epithelium:	n/a	n/a
23	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
24	JUND	chr3:98934719-98934891	HepG2	liver:	n/a	n/a
25	MAFF	chr3:98945658-98945713	K562	blood:	n/a	n/a
26	MYC	chr3:98916015-98916133	MCF10A-Er-Src	breast:	n/a	n/a
27	MYC	chr3:98909815-98909957	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr3:98940915-98940924	H1-hESC	embryonic stem cell:	n/a	n/a
29	MYC	chr3:98906109-98906137	GM12878	blood:	n/a	n/a
30	MYC	chr3:98906100-98906193	MCF-7	breast:	n/a	n/a
31	MYC	chr3:98909845-98909901	MCF10A-Er-Src	breast:	n/a	n/a
32	NFIC	chr3:98931749-98932441	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr3:98931698-98932658	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr3:98921032-98921057	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr3:98906141-98906151	MCF-7	breast:	n/a	n/a
36	POLR2A	chr3:98911266-98911341	Gliobla	brain:	n/a	n/a
37	POLR2A	chr3:98908405-98908583	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:98906072-98906183	A549	lung:	n/a	n/a
39	POLR2A	chr3:98907602-98908258	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr3:98903633-98903647	MCF10A-Er-Src	breast:	n/a	n/a
41	RAD21	chr3:98937266-98937737	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr3:98937312-98937696	ECC-1	luminal epithelium:	n/a	n/a
43	RAD21	chr3:98937321-98937733	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr3:98937329-98937669	H1-hESC	embryonic stem cell:	n/a	n/a
45	SETDB1	chr3:98937742-98938197	U2OS	brain:	n/a	n/a
46	SPI1	chr3:98930184-98930576	HL-60	blood:	n/a	n/a
47	SPI1	chr3:98930163-98930506	GM12891	blood:	n/a	n/a
48	SPI1	chr3:98930188-98930458	GM12891	blood:	n/a	n/a
49	SPI1	chr3:98930256-98930475	HL-60	blood:	n/a	n/a
50	SPI1	chr3:98930255-98930434	GM12878	blood:	n/a	n/a

No data

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

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

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839
2	lnc-ST3GAL6-6	chr3:98904502-98904611	NONHSAT090838

No data

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 1204 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:1204 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547684921	chr3:98902330-98902331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs371249884	chr3:98902389-98902390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs7641092	chr3:98902395-98902396	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs774973	chr3:98902416-98902417	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs76157764	chr3:98902432-98902433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs398091671	chr3:98902437-98902438	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs200556058	chr3:98902438-98902439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs116192946	chr3:98902456-98902457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs188148368	chr3:98902505-98902506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs201886641	chr3:98902519-98902520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs9857240	chr3:98902532-98902533	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs535526680	chr3:98902540-98902541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs555078196	chr3:98902578-98902579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs7629965	chr3:98902589-98902590	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs139406779	chr3:98902620-98902621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs184276535	chr3:98902631-98902632	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs577098774	chr3:98902636-98902637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs142637360	chr3:98902657-98902658	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs112881503	chr3:98902667-98902668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs189479857	chr3:98902693-98902694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs150550873	chr3:98902703-98902704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs192472979	chr3:98902725-98902726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs185494076	chr3:98902736-98902737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs139515859	chr3:98902777-98902778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs573463374	chr3:98902792-98902793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs114482462	chr3:98902851-98902852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs774972	chr3:98902911-98902912	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs529333938	chr3:98903002-98903003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs149684757	chr3:98903098-98903099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs147775016	chr3:98903116-98903117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs141164362	chr3:98903220-98903221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs115910103	chr3:98903255-98903256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs565420111	chr3:98903267-98903268	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs534342624	chr3:98903287-98903288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs189198550	chr3:98903309-98903310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs570850163	chr3:98903342-98903343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs78077131	chr3:98903392-98903393	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs812305	chr3:98903440-98903441	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs576550365	chr3:98903441-98903442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs529069966	chr3:98903483-98903484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76720787	chr3:98903496-98903497	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs59080898	chr3:98903544-98903545	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs35912178	chr3:98903556-98903557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs572550642	chr3:98903564-98903565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs180782624	chr3:98903567-98903568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs186487437	chr3:98903589-98903590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs145009018	chr3:98903598-98903599	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs188623439	chr3:98903633-98903634	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs543655036	chr3:98903660-98903661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs563361112	chr3:98903667-98903668	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
3	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
4	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
6	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
9	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus
10	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
13	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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