Variant report

Variant	nsv1012264
Chromosome Location	chr3:98855069-98949409
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	ARID3A	chr3:98892032-98892087	HepG2	liver:	n/a	n/a
2	BRCA1	chr3:98869565-98869661	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr3:98930300-98930345	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:98888891-98889173	A549	lung:	n/a	chr3:98889001-98889012
5	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
6	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
7	CEBPB	chr3:98888858-98889087	HepG2	liver:	n/a	chr3:98889001-98889012
8	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
9	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
10	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
11	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
12	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
13	CHD2	chr3:98891868-98891881	HepG2	liver:	n/a	n/a
14	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
15	CTCF	chr3:98863935-98863991	HUVEC	blood vessel:	n/a	chr3:98863976-98863984 chr3:98863973-98863991
16	CTCF	chr3:98891980-98892130	AG09309	skin:	n/a	n/a
17	CTCF	chr3:98891862-98891865	GM12892	blood:	n/a	n/a
18	CTCF	chr3:98892000-98892150	GM12865	blood:	n/a	n/a
19	CTCF	chr3:98891917-98892161	K562	blood:	n/a	n/a
20	CTCF	chr3:98891960-98892110	BE2_C	brain:	n/a	n/a
21	CTCF	chr3:98892000-98892150	HRPEpiC	eye:	n/a	n/a
22	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
23	CTCF	chr3:98892000-98892150	HCFaa	heart:	n/a	n/a
24	CTCF	chr3:98891960-98892110	HCT-116	colon:	n/a	n/a
25	CTCF	chr3:98891980-98892130	GM12874	blood:	n/a	n/a
26	CTCF	chr3:98891953-98892185	GM12892	blood:	n/a	n/a
27	CTCF	chr3:98892000-98892150	GM06990	blood:	n/a	n/a
28	CTCF	chr3:98867940-98868090	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr3:98891649-98892476	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr3:98867980-98868130	HAc	cerebellar:	n/a	n/a
31	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:98891955-98892200	Fibrobl	skin:	n/a	n/a
33	CTCF	chr3:98891960-98892110	A549	lung:	n/a	n/a
34	CTCF	chr3:98891948-98892216	HepG2	liver:	n/a	n/a
35	CTCF	chr3:98928620-98928770	GM12871	blood:	n/a	n/a
36	CTCF	chr3:98891967-98892175	GM20000	blood:	n/a	n/a
37	CTCF	chr3:98892020-98892170	AG09309	skin:	n/a	n/a
38	CTCF	chr3:98891963-98892190	GM10248	blood:	n/a	n/a
39	CTCF	chr3:98891961-98892166	K562	blood:	n/a	n/a
40	CTCF	chr3:98891888-98892222	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr3:98891808-98892220	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:98891963-98892196	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr3:98891700-98891850	AG04449	skin:	n/a	n/a
44	CTCF	chr3:98891960-98892110	GM12868	blood:	n/a	n/a
45	CTCF	chr3:98891954-98892202	HepG2	liver:	n/a	n/a
46	CTCF	chr3:98891960-98892110	NB4	blood:	n/a	n/a
47	CTCF	chr3:98892020-98892170	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr3:98891949-98892173	Lung_OC	lung:	n/a	n/a
49	CTCF	chr3:98891936-98892217	Gliobla	brain:	n/a	n/a
50	CTCF	chr3:98891812-98892196	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98742090..98742958-chr3:98891307..98892432,5	MCF-7	breast:
2	chr3:98742225..98743062-chr3:98891577..98892142,2	MCF-7	breast:
3	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
4	chr3:98833031..98833794-chr3:98891585..98892473,5	MCF-7	breast:
5	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:

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

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 3177 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:3177 , 50 per page) page: 1 2 3 4 5 6 7 ... 64

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12635777	chr3:98855069-98855070	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs35482774	chr3:98855082-98855083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs137857646	chr3:98855090-98855091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs565263696	chr3:98855102-98855103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs186903594	chr3:98855160-98855161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs532785374	chr3:98855168-98855169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs142268104	chr3:98855183-98855184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs192160439	chr3:98855196-98855197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs35270409	chr3:98855226-98855227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs12635825	chr3:98855269-98855270	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs549306296	chr3:98855279-98855280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs72932802	chr3:98855302-98855303	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs112594123	chr3:98855349-98855350	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs548576096	chr3:98855362-98855363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs114177042	chr3:98855371-98855372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs534196358	chr3:98855379-98855380	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs2690239	chr3:98855430-98855431	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs184284930	chr3:98855481-98855482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs112782135	chr3:98855522-98855523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs539269684	chr3:98855539-98855540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs555893323	chr3:98855604-98855605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs575740960	chr3:98855605-98855606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535236695	chr3:98855646-98855647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs150914214	chr3:98855654-98855655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs116219234	chr3:98855717-98855718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2690240	chr3:98855841-98855842	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs560780533	chr3:98855866-98855867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs555728852	chr3:98855874-98855875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs190502329	chr3:98855926-98855927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs2690241	chr3:98855939-98855940	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs563033330	chr3:98855949-98855950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2682414	chr3:98855954-98855955	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs2690242	chr3:98855962-98855963	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs56968045	chr3:98855967-98855968	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs150048299	chr3:98855984-98855985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs112814975	chr3:98856013-98856014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs77182754	chr3:98856023-98856024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs539307403	chr3:98856029-98856030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs549654827	chr3:98856034-98856035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs374191384	chr3:98856035-98856036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs397947035	chr3:98856039-98856040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs182394396	chr3:98856047-98856048	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs147883330	chr3:98856049-98856050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs371083950	chr3:98856062-98856063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs141506099	chr3:98856063-98856064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs145340028	chr3:98856090-98856091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs114377914	chr3:98856099-98856100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs2690243	chr3:98856143-98856144	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs151016875	chr3:98856221-98856222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs368325275	chr3:98856236-98856237	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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98849000-98863800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98862200-98862800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:98862200-98863200	Enhancers	Fetal Brain Male	brain
4	chr3:98862400-98863800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:98863800-98864400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:98864000-98864600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:98864000-98865000	Enhancers	NHEK	skin
8	chr3:98864400-98864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98864600-98865000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:98864800-98865000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:98865000-98868400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:98865000-98876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:98867000-98867600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:98867600-98875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:98868400-98869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:98875400-98875600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:98875600-98877000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98875600-98877600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:98876800-98879200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:98877000-98879000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:98877200-98878600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:98877600-98878200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:98877800-98878400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:98878000-98878200	ZNF genes & repeats	Aorta	Aorta
25	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:98878400-98882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:98879200-98879400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98879400-98891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:98882200-98882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:98885400-98886400	Enhancers	NHDF-Ad	bronchial
32	chr3:98885600-98886000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:98885600-98886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:98886400-98891400	Weak transcription	NHDF-Ad	bronchial
35	chr3:98891400-98892000	Enhancers	Fetal Thymus	thymus
36	chr3:98891400-98892000	Enhancers	NHDF-Ad	bronchial
37	chr3:98891600-98891800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:98891600-98892000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:98891600-98892000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:98891600-98892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:98891600-98892000	Enhancers	HSMM	muscle
42	chr3:98891800-98892000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:98891800-98892000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:98891800-98892400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
48	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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