Variant report

Variant	nsv1008312
Chromosome Location	chr3:98929420-98953749
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 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	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
4	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
5	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
7	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
9	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
10	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
11	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
12	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
14	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
15	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr3:98931762-98932488	ECC-1	luminal epithelium:	n/a	chr3:98931860-98931869 chr3:98931898-98931912 chr3:98931856-98931870
17	ESR1	chr3:98931860-98932211	ECC-1	luminal epithelium:	n/a	n/a
18	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
19	HMGN3	chr3:98951831-98951978	K562	blood:	n/a	n/a
20	JUND	chr3:98934719-98934891	HepG2	liver:	n/a	n/a
21	MAFF	chr3:98945658-98945713	K562	blood:	n/a	n/a
22	MYC	chr3:98940915-98940924	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFIC	chr3:98931749-98932441	ECC-1	luminal epithelium:	n/a	n/a
24	NFIC	chr3:98931698-98932658	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:98952025-98952068	ProgFib	skin:	n/a	n/a
26	RAD21	chr3:98937266-98937737	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr3:98937329-98937669	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr3:98937321-98937733	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr3:98937312-98937696	ECC-1	luminal epithelium:	n/a	n/a
30	SETDB1	chr3:98937742-98938197	U2OS	brain:	n/a	n/a
31	SPI1	chr3:98930070-98930726	GM12878	blood:	n/a	n/a
32	SPI1	chr3:98930255-98930434	GM12878	blood:	n/a	n/a
33	SPI1	chr3:98930256-98930475	HL-60	blood:	n/a	n/a
34	SPI1	chr3:98930188-98930458	GM12891	blood:	n/a	n/a
35	SPI1	chr3:98930217-98930451	GM12878	blood:	n/a	n/a
36	SPI1	chr3:98930163-98930506	GM12891	blood:	n/a	n/a
37	SPI1	chr3:98930184-98930576	HL-60	blood:	n/a	n/a
38	STAT3	chr3:98939265-98939457	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr3:98932236-98932436	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF12	chr3:98931785-98932399	ECC-1	luminal epithelium:	n/a	chr3:98931993-98932000
41	TCF12	chr3:98931648-98932609	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: 595 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:595 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1589346	chr3:98929420-98929421	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs148994641	chr3:98929421-98929422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs367679907	chr3:98929466-98929467	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs192718320	chr3:98929595-98929596	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs529900350	chr3:98929609-98929610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs113364182	chr3:98929634-98929635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs551526448	chr3:98929653-98929654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs566568642	chr3:98929662-98929663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs546760070	chr3:98929664-98929665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs566568442	chr3:98929672-98929673	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs532147218	chr3:98929735-98929736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs201726212	chr3:98929765-98929766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs184727287	chr3:98929806-98929807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs113354069	chr3:98929809-98929810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs371649316	chr3:98929827-98929828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs549556175	chr3:98929843-98929844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557609045	chr3:98929900-98929901	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs567551447	chr3:98929920-98929921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs536436747	chr3:98929932-98929933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs553055634	chr3:98929987-98929988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs138449485	chr3:98930046-98930047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs117251458	chr3:98930088-98930089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs143972979	chr3:98930221-98930222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs575573042	chr3:98930234-98930235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs370789008	chr3:98930236-98930237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs567950509	chr3:98930258-98930259	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs574733987	chr3:98930274-98930275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs190061750	chr3:98930299-98930300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs193059235	chr3:98930313-98930314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs532075392	chr3:98930335-98930336	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs552172227	chr3:98930338-98930339	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs556537861	chr3:98930345-98930346	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs147279304	chr3:98930356-98930357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs531319161	chr3:98930372-98930373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs571585878	chr3:98930373-98930374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs551028756	chr3:98930419-98930420	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs529235216	chr3:98930421-98930422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs567615008	chr3:98930430-98930431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs9681261	chr3:98930445-98930446	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs546759532	chr3:98930451-98930452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs566648460	chr3:98930465-98930466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs72928611	chr3:98930481-98930482	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs572201717	chr3:98930495-98930496	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs372351362	chr3:98930545-98930546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs558994941	chr3:98930566-98930567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs375488329	chr3:98930646-98930647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs115077964	chr3:98930699-98930700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs148323595	chr3:98930727-98930728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs371683583	chr3:98930742-98930743	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs184801700	chr3:98930760-98930761	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:26 , 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	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
3	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:98951400-98952800	Enhancers	Osteobl	bone
22	chr3:98951800-98952200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:98951800-98952200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:98952200-98959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:98952200-98959200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:98952800-98959200	Weak transcription	Osteobl	bone

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