Variant report

Variant	nsv1003042
Chromosome Location	chr3:98924486-98949289
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

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	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
6	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
7	CTCF	chr3:98928620-98928770	GM12871	blood:	n/a	n/a
8	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
9	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
10	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
11	CTCF	chr3:98927000-98927150	BJ	skin:	n/a	n/a
12	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
13	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
14	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
15	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
16	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
17	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr3:98931762-98932488	ECC-1	luminal epithelium:	n/a	chr3:98931860-98931869 chr3:98931898-98931912 chr3:98931856-98931870
20	ESR1	chr3:98931860-98932211	ECC-1	luminal epithelium:	n/a	n/a
21	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
22	JUND	chr3:98934719-98934891	HepG2	liver:	n/a	n/a
23	MAFF	chr3:98945658-98945713	K562	blood:	n/a	n/a
24	MYC	chr3:98940915-98940924	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFIC	chr3:98931749-98932441	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr3:98931698-98932658	ECC-1	luminal epithelium:	n/a	n/a
27	RAD21	chr3:98937266-98937737	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr3:98937312-98937696	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr3:98937329-98937669	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr3:98937321-98937733	H1-hESC	embryonic stem cell:	n/a	n/a
31	SETDB1	chr3:98937742-98938197	U2OS	brain:	n/a	n/a
32	SPI1	chr3:98930256-98930475	HL-60	blood:	n/a	n/a
33	SPI1	chr3:98930255-98930434	GM12878	blood:	n/a	n/a
34	SPI1	chr3:98930070-98930726	GM12878	blood:	n/a	n/a
35	SPI1	chr3:98930188-98930458	GM12891	blood:	n/a	n/a
36	SPI1	chr3:98930184-98930576	HL-60	blood:	n/a	n/a
37	SPI1	chr3:98930163-98930506	GM12891	blood:	n/a	n/a
38	SPI1	chr3:98930217-98930451	GM12878	blood:	n/a	n/a
39	STAT3	chr3:98932236-98932436	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr3:98939265-98939457	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF12	chr3:98931648-98932609	ECC-1	luminal epithelium:	n/a	chr3:98931993-98932000
42	TCF12	chr3:98931785-98932399	ECC-1	luminal epithelium:	n/a	chr3:98931993-98932000

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839

No data

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 659 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:659 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs79764696	chr3:98925808-98925809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs576165862	chr3:98925816-98925817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs371126990	chr3:98925844-98925845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs73859870	chr3:98925860-98925861	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs546193861	chr3:98925871-98925872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs561814534	chr3:98925872-98925873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs527333173	chr3:98925923-98925924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs546941854	chr3:98925952-98925953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs560424779	chr3:98925956-98925957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs182168852	chr3:98925979-98925980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs552759214	chr3:98925997-98925998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs62277423	chr3:98926090-98926091	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs116733750	chr3:98926184-98926185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs548433409	chr3:98926322-98926323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs138515676	chr3:98926325-98926326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs527251095	chr3:98926345-98926346	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs78747224	chr3:98926347-98926348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs577223903	chr3:98926358-98926359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs539774309	chr3:98926367-98926368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs574007075	chr3:98926391-98926392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs186134251	chr3:98926411-98926412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs542006947	chr3:98926414-98926415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs561632767	chr3:98926428-98926429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs571768051	chr3:98926484-98926485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs540643329	chr3:98926570-98926571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs544277292	chr3:98926609-98926610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs371572499	chr3:98926670-98926671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs189800939	chr3:98926672-98926673	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs201211857	chr3:98926673-98926674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs147745108	chr3:98926675-98926676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs76786552	chr3:98926686-98926687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs563187682	chr3:98926690-98926691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs531857351	chr3:98926766-98926767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs180763741	chr3:98926770-98926771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs563038289	chr3:98926815-98926816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs185611804	chr3:98926906-98926907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs527749580	chr3:98926913-98926914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs547892935	chr3:98926929-98926930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs570893980	chr3:98926942-98926943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs372706966	chr3:98927001-98927002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs541135683	chr3:98927002-98927003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs377309893	chr3:98927009-98927010	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs114472154	chr3:98927019-98927020	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs143412046	chr3:98927049-98927050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs191147824	chr3:98927055-98927056	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs113176832	chr3:98927057-98927058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs141548169	chr3:98927087-98927088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs2030399	chr3:98927110-98927111	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs557414566	chr3:98927111-98927112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs577258346	chr3:98927113-98927114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
4	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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