Variant report

Variant	esv3415711
Chromosome Location	chr3:87779311-87802607
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr3:87790020-87790221	K562	blood:	n/a	n/a
2	CBX3	chr3:87789999-87790224	K562	blood:	n/a	n/a
3	CEBPB	chr3:87781609-87781831	K562	blood:	n/a	chr3:87781780-87781791 chr3:87781778-87781791 chr3:87781778-87781791 chr3:87781780-87781789
4	CTCF	chr3:87783900-87784050	GM12878	blood:	n/a	n/a
5	CTCF	chr3:87791420-87791570	GM06990	blood:	n/a	n/a
6	CTCF	chr3:87783224-87783327	GM20000	blood:	n/a	n/a
7	FOS	chr3:87781662-87781861	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:87787007-87787323	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:87787001-87787294	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr3:87787032-87787316	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:87781670-87781878	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr3:87790033-87790395	T-47D	breast:	n/a	n/a
13	GATA3	chr3:87781361-87781740	SH-SY5Y	brain:	n/a	n/a
14	GATA3	chr3:87782785-87783199	T-47D	breast:	n/a	n/a
15	GATA3	chr3:87782659-87783453	MCF-7	breast:	n/a	chr3:87782725-87782735
16	GATA3	chr3:87782706-87783314	MCF-7	breast:	n/a	chr3:87782725-87782735
17	JUN	chr3:87801884-87801902	H1-hESC	embryonic stem cell:	n/a	n/a
18	KAP1	chr3:87791373-87791808	HEK293	kidney:	n/a	n/a
19	MAFF	chr3:87779807-87779815	HepG2	liver:	n/a	n/a
20	MAFK	chr3:87779834-87779923	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:87781342-87781882	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr3:87798619-87798819	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:87787032-87787437	U87	brain:	n/a	n/a
24	POLR2A	chr3:87787043-87787445	U87	brain:	n/a	n/a
25	POLR2A	chr3:87781373-87781868	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr3:87787009-87787445	U87	brain:	n/a	n/a
27	POLR2A	chr3:87794073-87794122	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:87787031-87787437	U87	brain:	n/a	n/a
29	POU5F1	chr3:87782820-87783076	H1-hESC	embryonic stem cell:	n/a	n/a
30	REST	chr3:87781381-87781813	H1-neurons	neurons:	n/a	n/a
31	REST	chr3:87781126-87781918	H1-neurons	neurons:	n/a	chr3:87781183-87781192
32	SETDB1	chr3:87791400-87791910	U2OS	brain:	n/a	n/a
33	SP1	chr3:87782840-87783161	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP1	chr3:87782806-87783074	H1-hESC	embryonic stem cell:	n/a	n/a
35	SRF	chr3:87782814-87783099	ECC-1	luminal epithelium:	n/a	n/a
36	STAT3	chr3:87782093-87782293	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr3:87781144-87781311	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr3:87785972-87786172	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr3:87795960-87796144	MCF10A-Er-Src	breast:	n/a	n/a
40	TEAD4	chr3:87782723-87783323	ECC-1	luminal epithelium:	n/a	n/a
41	TEAD4	chr3:87782741-87783291	ECC-1	luminal epithelium:	n/a	n/a
42	TEAD4	chr3:87790115-87790394	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr3:87782764-87783164	H1-hESC	embryonic stem cell:	n/a	n/a
44	TEAD4	chr3:87782814-87783179	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZNF143	chr3:87782783-87783048	H1-hESC	embryonic stem cell:	n/a	n/a
46	ZNF143	chr3:87789970-87790253	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZNF217	chr3:87782849-87783218	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:87774485..87776498-chr3:87777273..87779870,3	MCF-7	breast:
2	chr3:87752670..87754550-chr3:87776800..87779392,2	MCF-7	breast:
3	chr3:87787506..87789179-chr3:87800683..87802189,2	MCF-7	breast:
4	chr3:87773985..87776726-chr3:87783571..87785837,2	MCF-7	breast:
5	chr3:87789321..87792117-chr3:87796229..87798081,2	MCF-7	breast:
6	chr3:87787506..87789179-chr3:87800683..87802189,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-873P	TF binding region
ENSG00000200703	chromatin interactions

Extended variants
information (count: 746 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:746 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546492160	chr3:87779356-87779357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs13071755	chr3:87779384-87779385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs528667448	chr3:87779394-87779395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs547344045	chr3:87779395-87779396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs546333561	chr3:87779401-87779402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs376903677	chr3:87779402-87779403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs149537149	chr3:87779408-87779409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs538666033	chr3:87779410-87779411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs556553395	chr3:87779426-87779427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs115385550	chr3:87779460-87779461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs535950352	chr3:87779477-87779478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs554216970	chr3:87779505-87779506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs572731700	chr3:87779526-87779527	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs533725687	chr3:87779572-87779573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs558466269	chr3:87779628-87779629	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs9820878	chr3:87779635-87779636	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs542018069	chr3:87779700-87779701	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs4519728	chr3:87779738-87779739	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs563543438	chr3:87779767-87779768	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs537623326	chr3:87779803-87779804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs575560952	chr3:87779821-87779822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs185428327	chr3:87779836-87779837	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs561346064	chr3:87779855-87779856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs528730499	chr3:87779872-87779873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs541467288	chr3:87779976-87779977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs565616449	chr3:87779980-87779981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs564459460	chr3:87779991-87779992	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs532695493	chr3:87780001-87780002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs551213179	chr3:87780032-87780033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs533138824	chr3:87780056-87780057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs535825162	chr3:87780147-87780148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs547916312	chr3:87780173-87780174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs189544344	chr3:87780174-87780175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs533787379	chr3:87780188-87780189	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs548812079	chr3:87780247-87780248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs558049075	chr3:87780256-87780257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs550068673	chr3:87780287-87780288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs570587620	chr3:87780373-87780374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs4324484	chr3:87780377-87780378	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs76406890	chr3:87780439-87780440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs529092800	chr3:87780453-87780454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs34655630	chr3:87780454-87780455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs181602856	chr3:87780486-87780487	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs543025343	chr3:87780516-87780517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs145178018	chr3:87780544-87780545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs183618148	chr3:87780554-87780555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs538214272	chr3:87780559-87780560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs148804069	chr3:87780560-87780561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs534391252	chr3:87780594-87780595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs532704954	chr3:87780619-87780620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
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
Acute lymphoblastic leukemia	20435627	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
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87776400-87779600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:87779000-87782800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:87779600-87779800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:87779600-87779800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:87779800-87788600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:87782600-87782800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:87782800-87783000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:87782800-87783400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:87782800-87783400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:87782800-87783600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:87782800-87783600	Enhancers	HMEC	breast
12	chr3:87782800-87783600	Enhancers	NHEK	skin
13	chr3:87783000-87783400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:87783400-87783800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:87783400-87783800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:87783400-87784000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:87783600-87786800	Weak transcription	HMEC	breast
18	chr3:87783800-87787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:87784000-87787400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:87785400-87786200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:87786200-87788600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:87786800-87787400	Enhancers	HMEC	breast
23	chr3:87787200-87787400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:87788600-87789200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
25	chr3:87788600-87789400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:87789200-87789400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:87789800-87794000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:87793000-87793400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr3:87794400-87797800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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