Variant report

Variant	nsv1012359
Chromosome Location	chr3:98893510-98965013
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	BRCA1	chr3:98930300-98930345	GM12878	blood:	n/a	n/a
2	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
3	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
4	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
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	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
7	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
8	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
9	CTCF	chr3:98928620-98928770	GM12871	blood:	n/a	n/a
10	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
11	CTCF	chr3:98958060-98958210	AG04449	skin:	n/a	n/a
12	CTCF	chr3:98904800-98904950	WI-38	lung:	n/a	n/a
13	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
14	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
15	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
17	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr3:98927000-98927150	BJ	skin:	n/a	n/a
19	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
20	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:98961260-98961410	AG10803	skin:	n/a	n/a
22	CTCF	chr3:98961240-98961390	AG10803	skin:	n/a	n/a
23	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
24	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
25	CTCF	chr3:98957445-98957519	ProgFib	skin:	n/a	n/a
26	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
27	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
28	E2F4	chr3:98903417-98903604	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F4	chr3:98964937-98965413	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr3:98895870-98896330	MCF10A-Er-Src	breast:	n/a	n/a
32	EP300	chr3:98964901-98965675	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr3:98931762-98932488	ECC-1	luminal epithelium:	n/a	chr3:98931860-98931869 chr3:98931898-98931912 chr3:98931856-98931870
34	ESR1	chr3:98931860-98932211	ECC-1	luminal epithelium:	n/a	n/a
35	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
36	FOXA2	chr3:98964348-98964692	A549	lung:	n/a	n/a
37	FOXM1	chr3:98964944-98965618	ECC-1	luminal epithelium:	n/a	n/a
38	GATA2	chr3:98964829-98965503	HUVEC	blood vessel:	n/a	n/a
39	HMGN3	chr3:98951831-98951978	K562	blood:	n/a	n/a
40	JUN	chr3:98960281-98960354	H1-hESC	embryonic stem cell:	n/a	n/a
41	JUND	chr3:98934719-98934891	HepG2	liver:	n/a	n/a
42	MAFF	chr3:98895059-98895353	K562	blood:	n/a	chr3:98895199-98895217
43	MAFF	chr3:98895023-98895385	HepG2	liver:	n/a	chr3:98895199-98895217
44	MAFF	chr3:98945658-98945713	K562	blood:	n/a	n/a
45	MAFK	chr3:98895068-98895372	H1-hESC	embryonic stem cell:	n/a	chr3:98895200-98895215
46	MAFK	chr3:98894912-98895526	GM12878	blood:	n/a	chr3:98895200-98895215
47	MAFK	chr3:98895021-98895388	HepG2	liver:	n/a	chr3:98895200-98895215
48	MAFK	chr3:98895059-98895387	HepG2	liver:	n/a	chr3:98895200-98895215
49	MAFK	chr3:98895024-98895369	K562	blood:	n/a	chr3:98895200-98895215
50	MAFK	chr3:98895012-98895403	IMR90	lung:	n/a	chr3:98895200-98895215

No.	Distal block	Cell Line	Cell type
1	chr3:98960467..98962608-chr3:98963910..98966387,2	K562	blood:
2	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
3	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
4	chr3:98960467..98962608-chr3:98963910..98966387,2	K562	blood:

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: 2046 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2046 , 50 per page) page: 1 2 3 4 5 6 7 ... 41

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2461791	chr3:98893510-98893511	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs374166800	chr3:98893521-98893522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs191112193	chr3:98893555-98893556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs60066948	chr3:98893600-98893601	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs375907297	chr3:98893630-98893631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539764960	chr3:98893647-98893648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs556402557	chr3:98893675-98893676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs115801559	chr3:98893698-98893699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs542083453	chr3:98893712-98893713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs555927661	chr3:98893751-98893752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs549484874	chr3:98893759-98893760	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs183814858	chr3:98893793-98893794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs2461792	chr3:98893852-98893853	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs188358739	chr3:98893853-98893854	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs543484760	chr3:98893887-98893888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537268345	chr3:98893975-98893976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs543756494	chr3:98893984-98893985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2687672	chr3:98894016-98894017	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs191629683	chr3:98894026-98894027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs116731968	chr3:98894075-98894076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs144053774	chr3:98894119-98894120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs112210211	chr3:98894122-98894123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs528176045	chr3:98894163-98894164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs532254081	chr3:98894169-98894170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs146767526	chr3:98894175-98894176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs570924769	chr3:98894192-98894193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs536679365	chr3:98894224-98894225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs2687671	chr3:98894234-98894235	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs114698199	chr3:98894241-98894242	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs2687670	chr3:98894246-98894247	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs139218173	chr3:98894279-98894280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs541815437	chr3:98894285-98894286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs572555483	chr3:98894395-98894396	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs375046276	chr3:98894442-98894443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs548368344	chr3:98894449-98894450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs183455113	chr3:98894471-98894472	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs143127851	chr3:98894495-98894496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs368802925	chr3:98894564-98894565	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs111927671	chr3:98894590-98894591	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs563663936	chr3:98894594-98894595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs61031480	chr3:98894624-98894625	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs570277407	chr3:98894647-98894648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542858963	chr3:98894660-98894661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs148108512	chr3:98894667-98894668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs9830015	chr3:98894721-98894722	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs187795259	chr3:98894741-98894742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs141864994	chr3:98894747-98894748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs191545748	chr3:98894761-98894762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs535137127	chr3:98894782-98894783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs372543819	chr3:98894803-98894804	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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
6	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98899200-98899600	Enhancers	NHEK	skin
10	chr3:98899200-98900200	Enhancers	HMEC	breast
11	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
13	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
14	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
16	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
19	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus
20	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
23	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:98951400-98952800	Enhancers	Osteobl	bone
42	chr3:98951800-98952200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:98951800-98952200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:98952200-98959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:98952200-98959200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:98952800-98959200	Weak transcription	Osteobl	bone
47	chr3:98955600-98955800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:98957400-98959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:98959000-98959400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:98959000-98960600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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