Variant report

Variant	nsv1008663
Chromosome Location	chr3:98867385-98953749
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	chr3:98895292-98895657	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
5	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
6	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
7	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
8	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
9	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
10	CEBPB	chr3:98888891-98889173	A549	lung:	n/a	chr3:98889001-98889012
11	CEBPB	chr3:98888858-98889087	HepG2	liver:	n/a	chr3:98889001-98889012
12	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
13	CHD2	chr3:98891868-98891881	HepG2	liver:	n/a	n/a
14	CTCF	chr3:98892030-98892141	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:98891936-98892226	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr3:98891960-98892110	HFF-Myc	foreskin:	n/a	n/a
17	CTCF	chr3:98867940-98868090	GM12864	blood:	n/a	n/a
18	CTCF	chr3:98892020-98892170	GM12864	blood:	n/a	n/a
19	CTCF	chr3:98891700-98891810	GM19238	blood:	n/a	n/a
20	CTCF	chr3:98891942-98892195	A549	lung:	n/a	n/a
21	CTCF	chr3:98892020-98892170	HRE	kidney:	n/a	n/a
22	CTCF	chr3:98891960-98892110	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr3:98892040-98892190	HVMF	connective:	n/a	n/a
24	CTCF	chr3:98891960-98892162	Spleen_OC	spleen:	n/a	n/a
25	CTCF	chr3:98891960-98892110	AG04450	lung:	n/a	n/a
26	CTCF	chr3:98891865-98892364	HCT-116	colon:	n/a	n/a
27	CTCF	chr3:98892000-98892150	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr3:98891980-98892130	HBMEC	blood vessel:	n/a	n/a
29	CTCF	chr3:98891960-98892110	RPTEC	kidney:	n/a	n/a
30	CTCF	chr3:98891888-98892222	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr3:98891960-98892110	HAc	cerebellar:	n/a	n/a
32	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
33	CTCF	chr3:98891960-98892110	HVMF	connective:	n/a	n/a
34	CTCF	chr3:98891649-98892476	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr3:98891580-98891730	GM12874	blood:	n/a	n/a
36	CTCF	chr3:98891967-98892175	GM20000	blood:	n/a	n/a
37	CTCF	chr3:98891980-98892130	AG09309	skin:	n/a	n/a
38	CTCF	chr3:98892000-98892150	GM12878	blood:	n/a	n/a
39	CTCF	chr3:98892020-98892170	HPAF	blood vessel:	n/a	n/a
40	CTCF	chr3:98892000-98892150	HL-60	blood:	n/a	n/a
41	CTCF	chr3:98892020-98892170	HEK293	kidney:	n/a	n/a
42	CTCF	chr3:98891960-98892110	HMEC	breast:	n/a	n/a
43	CTCF	chr3:98891940-98892090	GM12878	blood:	n/a	n/a
44	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
45	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
46	CTCF	chr3:98891898-98892165	A549	lung:	n/a	n/a
47	CTCF	chr3:98891719-98891860	GM12892	blood:	n/a	n/a
48	CTCF	chr3:98892000-98892150	HPF	lung:	n/a	n/a
49	CTCF	chr3:98891953-98892185	GM12892	blood:	n/a	n/a
50	CTCF	chr3:98891960-98892110	GM12869	blood:	n/a	n/a

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

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

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 2653 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2653 , 50 per page) page: 1 2 3 4 5 6 7 ... 54

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533905051	chr3:98867439-98867440	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs111644776	chr3:98867473-98867474	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs145422885	chr3:98867538-98867539	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs573250632	chr3:98867546-98867547	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs7646463	chr3:98867574-98867575	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs185932515	chr3:98867575-98867576	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs149215838	chr3:98867605-98867606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs6802620	chr3:98867641-98867642	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs113716882	chr3:98867646-98867647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs528668378	chr3:98867652-98867653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs529838837	chr3:98867671-98867672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs543354538	chr3:98867682-98867683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs191577437	chr3:98867720-98867721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs774935	chr3:98867753-98867754	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs560495392	chr3:98867754-98867755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs550954133	chr3:98867765-98867766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs567657923	chr3:98867771-98867772	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs181302605	chr3:98867776-98867777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs549341926	chr3:98867785-98867786	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs75026113	chr3:98867803-98867804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs572990033	chr3:98867812-98867813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538796285	chr3:98867821-98867822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs558369618	chr3:98867831-98867832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs561253115	chr3:98867881-98867882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs78569547	chr3:98867890-98867891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs185514574	chr3:98867897-98867898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs574071641	chr3:98867907-98867908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs148338562	chr3:98867913-98867914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs147038453	chr3:98867927-98867928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs528700619	chr3:98867928-98867929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs545538243	chr3:98867930-98867931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs114252852	chr3:98867941-98867942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566416640	chr3:98867950-98867951	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs145672026	chr3:98867971-98867972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs190719225	chr3:98867972-98867973	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs567693804	chr3:98867984-98867985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs530103678	chr3:98867986-98867987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs546595924	chr3:98867997-98867998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs78055231	chr3:98868011-98868012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs566709224	chr3:98868026-98868027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372514943	chr3:98868028-98868029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs538462488	chr3:98868033-98868034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs558755368	chr3:98868036-98868037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs533583059	chr3:98868051-98868052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs568706611	chr3:98868088-98868089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs116449810	chr3:98868107-98868108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs367647231	chr3:98868162-98868163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs7649157	chr3:98868166-98868167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs376617297	chr3:98868173-98868174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs182909848	chr3:98868181-98868182	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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98865000-98868400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:98865000-98876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98867000-98867600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:98867600-98875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:98868400-98869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:98875400-98875600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:98875600-98877000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:98875600-98877600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:98876800-98879200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:98877000-98879000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:98877200-98878600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:98877600-98878200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:98877800-98878400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:98878000-98878200	ZNF genes & repeats	Aorta	Aorta
15	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:98878400-98882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:98879200-98879400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:98879400-98891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:98882200-98882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:98885400-98886400	Enhancers	NHDF-Ad	bronchial
22	chr3:98885600-98886000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:98885600-98886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:98886400-98891400	Weak transcription	NHDF-Ad	bronchial
25	chr3:98891400-98892000	Enhancers	Fetal Thymus	thymus
26	chr3:98891400-98892000	Enhancers	NHDF-Ad	bronchial
27	chr3:98891600-98891800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:98891600-98892000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:98891600-98892000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:98891600-98892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:98891600-98892000	Enhancers	HSMM	muscle
32	chr3:98891800-98892000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:98891800-98892000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:98891800-98892400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
38	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:98899200-98899600	Enhancers	NHEK	skin
42	chr3:98899200-98900200	Enhancers	HMEC	breast
43	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
45	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
46	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
48	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus

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