Variant report

Variant	nsv1004438
Chromosome Location	chr3:98863348-98949409
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	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
5	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
6	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
7	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
8	CEBPB	chr3:98888858-98889087	HepG2	liver:	n/a	chr3:98889001-98889012
9	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
10	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
11	CEBPB	chr3:98888891-98889173	A549	lung:	n/a	chr3:98889001-98889012
12	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
13	CHD2	chr3:98891868-98891881	HepG2	liver:	n/a	n/a
14	CTCF	chr3:98863935-98863991	HUVEC	blood vessel:	n/a	chr3:98863976-98863984 chr3:98863973-98863991
15	CTCF	chr3:98892020-98892170	GM12871	blood:	n/a	n/a
16	CTCF	chr3:98891963-98892196	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr3:98891942-98892195	A549	lung:	n/a	n/a
18	CTCF	chr3:98891936-98892217	Gliobla	brain:	n/a	n/a
19	CTCF	chr3:98891825-98892287	IMR90	lung:	n/a	n/a
20	CTCF	chr3:98891917-98892161	K562	blood:	n/a	n/a
21	CTCF	chr3:98892000-98892150	GM12801	blood:	n/a	n/a
22	CTCF	chr3:98891960-98892110	GM12870	blood:	n/a	n/a
23	CTCF	chr3:98891862-98891865	GM12892	blood:	n/a	n/a
24	CTCF	chr3:98891888-98892222	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr3:98891940-98892090	GM12869	blood:	n/a	n/a
26	CTCF	chr3:98891860-98892010	WI-38	lung:	n/a	n/a
27	CTCF	chr3:98891767-98892334	HCT-116	colon:	n/a	n/a
28	CTCF	chr3:98892020-98892170	HEK293	kidney:	n/a	n/a
29	CTCF	chr3:98863920-98864070	NHEK	skin:	n/a	chr3:98863975-98863996 chr3:98863976-98863984 chr3:98863973-98863991
30	CTCF	chr3:98891967-98892175	GM20000	blood:	n/a	n/a
31	CTCF	chr3:98891918-98892214	GM10266	blood:	n/a	n/a
32	CTCF	chr3:98891694-98892423	A549	lung:	n/a	n/a
33	CTCF	chr3:98892000-98892150	GM12873	blood:	n/a	n/a
34	CTCF	chr3:98892000-98892150	GM12865	blood:	n/a	n/a
35	CTCF	chr3:98891960-98892110	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:98891940-98892090	GM12875	blood:	n/a	n/a
37	CTCF	chr3:98892000-98892150	HCFaa	heart:	n/a	n/a
38	CTCF	chr3:98891988-98892188	GM13976	blood:	n/a	n/a
39	CTCF	chr3:98892000-98892150	K562	blood:	n/a	n/a
40	CTCF	chr3:98892000-98892150	HMEC	breast:	n/a	n/a
41	CTCF	chr3:98891800-98891950	HAc	cerebellar:	n/a	n/a
42	CTCF	chr3:98891480-98891630	WI-38	lung:	n/a	n/a
43	CTCF	chr3:98892000-98892150	GM06990	blood:	n/a	n/a
44	CTCF	chr3:98892000-98892150	Caco-2	colon:	n/a	n/a
45	CTCF	chr3:98891812-98892196	K562	blood:	n/a	n/a
46	CTCF	chr3:98891960-98892110	GM12872	blood:	n/a	n/a
47	CTCF	chr3:98891973-98892185	GM19239	blood:	n/a	n/a
48	CTCF	chr3:98891960-98892110	AG04450	lung:	n/a	n/a
49	CTCF	chr3:98887620-98887770	NHDF-neo	bronchial:	n/a	n/a
50	CTCF	chr3:98891960-98892110	GM12868	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	chr3:98833031..98833794-chr3:98891585..98892473,5	MCF-7	breast:
4	chr3:98898412..98900467-chr3:98901353..98902956,2	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	chr3:98896222-98896357	NONHSAT090838
2	lnc-ST3GAL6-6	chr3:98899387-98899480	NONHSAT090838
3	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839
4	lnc-ST3GAL6-6	chr3:98904502-98904611	NONHSAT090838

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 2751 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2751 , 50 per page) page: 1 2 3 4 5 6 7 ... 56

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149714380	chr3:98863379-98863380	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs774945	chr3:98863406-98863407	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs561372959	chr3:98863409-98863410	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs560653667	chr3:98863431-98863432	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs201592650	chr3:98863477-98863478	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs181850638	chr3:98863481-98863482	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs72356310	chr3:98863490-98863491	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs531691748	chr3:98863491-98863492	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs532127821	chr3:98863497-98863498	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs374005808	chr3:98863498-98863499	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs570015633	chr3:98863499-98863500	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs529957827	chr3:98863500-98863501	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs78354826	chr3:98863501-98863502	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs536739971	chr3:98863503-98863504	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs79155818	chr3:98863506-98863507	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs371844031	chr3:98863520-98863521	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs112779737	chr3:98863536-98863537	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs528170835	chr3:98863539-98863540	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs569105194	chr3:98863544-98863545	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs115557026	chr3:98863563-98863564	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs774944	chr3:98863604-98863605	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs574283918	chr3:98863629-98863630	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs533688403	chr3:98863642-98863643	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs149146984	chr3:98863660-98863661	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs369958427	chr3:98863694-98863695	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs186105123	chr3:98863706-98863707	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs114256820	chr3:98863708-98863709	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs545752853	chr3:98863724-98863725	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs559012048	chr3:98863791-98863792	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs368104384	chr3:98863793-98863794	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs371566859	chr3:98863807-98863808	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs140185174	chr3:98863808-98863809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs369270738	chr3:98863809-98863810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs368052820	chr3:98863810-98863811	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs76018549	chr3:98863811-98863812	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs60341617	chr3:98863812-98863813	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs9837998	chr3:98863813-98863814	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs200863418	chr3:98863832-98863833	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs71124026	chr3:98863834-98863835	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs57188522	chr3:98863835-98863836	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs3053147	chr3:98863836-98863837	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs374584019	chr3:98863840-98863841	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530292646	chr3:98863851-98863852	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs540762949	chr3:98863922-98863923	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs34794139	chr3:98863960-98863961	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs529590783	chr3:98863992-98863993	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs550965482	chr3:98863995-98863996	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs189734038	chr3:98864091-98864092	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs78439209	chr3:98864127-98864128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs552495873	chr3:98864253-98864254	Enhancers	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:80 , 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	chr3:98862400-98863800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:98863800-98864400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:98864000-98864600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:98864000-98865000	Enhancers	NHEK	skin
6	chr3:98864400-98864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:98864600-98865000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:98864800-98865000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98865000-98868400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:98865000-98876800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:98867000-98867600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98867600-98875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:98868400-98869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:98875400-98875600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:98875600-98877000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:98875600-98877600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:98876800-98879200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:98877000-98879000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:98877200-98878600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:98877600-98878200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:98877800-98878400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:98878000-98878200	ZNF genes & repeats	Aorta	Aorta
23	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:98878400-98882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:98879200-98879400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:98879400-98891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:98882200-98882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:98885400-98886400	Enhancers	NHDF-Ad	bronchial
30	chr3:98885600-98886000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:98885600-98886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:98886400-98891400	Weak transcription	NHDF-Ad	bronchial
33	chr3:98891400-98892000	Enhancers	Fetal Thymus	thymus
34	chr3:98891400-98892000	Enhancers	NHDF-Ad	bronchial
35	chr3:98891600-98891800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:98891600-98892000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:98891600-98892000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:98891600-98892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:98891600-98892000	Enhancers	HSMM	muscle
40	chr3:98891800-98892000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:98891800-98892000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:98891800-98892400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
46	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:98899200-98899600	Enhancers	NHEK	skin
50	chr3:98899200-98900200	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links