Variant report

Variant	nsv998521
Chromosome Location	chr3:98877662-98949409
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	chr3:98930300-98930345	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:98927039-98927064	HepG2	liver:	n/a	n/a
4	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
5	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
6	CEBPB	chr3:98897865-98898056	IMR90	lung:	n/a	n/a
7	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
8	CEBPB	chr3:98888858-98889087	HepG2	liver:	n/a	chr3:98889001-98889012
9	CEBPB	chr3:98888891-98889173	A549	lung:	n/a	chr3:98889001-98889012
10	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
11	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
12	CHD2	chr3:98891868-98891881	HepG2	liver:	n/a	n/a
13	CTCF	chr3:98891887-98892230	K562	blood:	n/a	n/a
14	CTCF	chr3:98891931-98892222	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr3:98891980-98892130	GM12872	blood:	n/a	n/a
16	CTCF	chr3:98891931-98892206	GM13977	blood:	n/a	n/a
17	CTCF	chr3:98892120-98892270	WI-38	lung:	n/a	n/a
18	CTCF	chr3:98891649-98892476	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr3:98891923-98892227	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:98891961-98892201	K562	blood:	n/a	n/a
21	CTCF	chr3:98927000-98927150	BJ	skin:	n/a	n/a
22	CTCF	chr3:98891960-98892110	HAc	cerebellar:	n/a	n/a
23	CTCF	chr3:98891960-98892110	GM12873	blood:	n/a	n/a
24	CTCF	chr3:98892000-98892150	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr3:98891960-98892110	NHDF-neo	bronchial:	n/a	n/a
26	CTCF	chr3:98891960-98892110	HA-sp	spinal cord:	n/a	n/a
27	CTCF	chr3:98892000-98892150	Caco-2	colon:	n/a	n/a
28	CTCF	chr3:98892020-98892170	NHEK	skin:	n/a	n/a
29	CTCF	chr3:98891862-98892167	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr3:98891580-98891730	GM12874	blood:	n/a	n/a
31	CTCF	chr3:98891865-98892364	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:98891906-98892156	T-47D	breast:	n/a	n/a
33	CTCF	chr3:98891960-98892110	HRPEpiC	eye:	n/a	n/a
34	CTCF	chr3:98891960-98892110	NB4	blood:	n/a	n/a
35	CTCF	chr3:98891700-98891810	GM19238	blood:	n/a	n/a
36	CTCF	chr3:98891960-98892110	RPTEC	kidney:	n/a	n/a
37	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
38	CTCF	chr3:98891960-98892110	GM12866	blood:	n/a	n/a
39	CTCF	chr3:98891900-98892050	A549	lung:	n/a	n/a
40	CTCF	chr3:98891939-98892181	GM19238	blood:	n/a	n/a
41	CTCF	chr3:98891938-98892211	GM12878	blood:	n/a	n/a
42	CTCF	chr3:98891980-98892130	HBMEC	blood vessel:	n/a	n/a
43	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
44	CTCF	chr3:98904800-98904950	WI-38	lung:	n/a	n/a
45	CTCF	chr3:98891953-98892185	GM12892	blood:	n/a	n/a
46	CTCF	chr3:98891920-98892146	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr3:98891960-98892110	BE2_C	brain:	n/a	n/a
48	CTCF	chr3:98892020-98892170	AG09309	skin:	n/a	n/a
49	CTCF	chr3:98891967-98892183	Pancreas_OC	pancreas:	n/a	n/a
50	CTCF	chr3:98891800-98891950	HAc	cerebellar:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
2	chr3:98833031..98833794-chr3:98891585..98892473,5	MCF-7	breast:
3	chr3:98742225..98743062-chr3:98891577..98892142,2	MCF-7	breast:
4	chr3:98742090..98742958-chr3:98891307..98892432,5	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	chr3:98896222-98896357	NONHSAT090838
2	lnc-ST3GAL6-6	chr3:98904502-98904611	NONHSAT090838
3	lnc-ST3GAL6-6	chr3:98899387-98899480	NONHSAT090838
4	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 2068 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2068 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1066373	chr3:98877662-98877663	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs567462477	chr3:98877663-98877664	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs536011237	chr3:98877718-98877719	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs142396331	chr3:98877758-98877759	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs566194220	chr3:98877771-98877772	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs116725645	chr3:98877793-98877794	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs151281971	chr3:98877813-98877814	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs575124030	chr3:98877831-98877832	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs537761913	chr3:98877843-98877844	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs112517921	chr3:98877848-98877849	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs557325492	chr3:98877853-98877854	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs140496849	chr3:98877901-98877902	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs28896543	chr3:98877914-98877915	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs559972983	chr3:98877929-98877930	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs573401299	chr3:98877985-98877986	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs545515260	chr3:98877986-98877987	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs565318440	chr3:98878084-98878085	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs183603399	chr3:98878102-98878103	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs34209875	chr3:98878109-98878110	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs7640939	chr3:98878121-98878122	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs560994637	chr3:98878159-98878160	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs115916822	chr3:98878173-98878174	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs546422801	chr3:98878231-98878232	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs535967368	chr3:98878234-98878235	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs188647360	chr3:98878259-98878260	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs28781585	chr3:98878275-98878276	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs568840673	chr3:98878276-98878277	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs28822211	chr3:98878310-98878311	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs78106300	chr3:98878363-98878364	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs567899418	chr3:98878364-98878365	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs72934756	chr3:98878424-98878425	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs371153756	chr3:98878427-98878428	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs190452997	chr3:98878454-98878455	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs372446779	chr3:98878517-98878518	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs558735409	chr3:98878533-98878534	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs575613812	chr3:98878555-98878556	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs544244363	chr3:98878557-98878558	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs561318391	chr3:98878562-98878563	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs558773526	chr3:98878576-98878577	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs529964167	chr3:98878588-98878589	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs540129268	chr3:98878591-98878592	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs559927246	chr3:98878592-98878593	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs532131765	chr3:98878594-98878595	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs551875705	chr3:98878604-98878605	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs183399920	chr3:98878608-98878609	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs531421438	chr3:98878612-98878613	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs577073984	chr3:98878625-98878626	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs115419987	chr3:98878629-98878630	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs567495542	chr3:98878646-98878647	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs147655105	chr3:98878673-98878674	Weak transcription ZNF genes & repeats	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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98876800-98879200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98877000-98879000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:98877200-98878600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:98877600-98878200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:98877800-98878400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:98878000-98878200	ZNF genes & repeats	Aorta	Aorta
7	chr3:98878200-98893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:98878400-98882200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:98879200-98879400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:98879400-98891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98882200-98882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:98885400-98886400	Enhancers	NHDF-Ad	bronchial
14	chr3:98885600-98886000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:98885600-98886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:98886400-98891400	Weak transcription	NHDF-Ad	bronchial
17	chr3:98891400-98892000	Enhancers	Fetal Thymus	thymus
18	chr3:98891400-98892000	Enhancers	NHDF-Ad	bronchial
19	chr3:98891600-98891800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:98891600-98892000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:98891600-98892000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:98891600-98892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:98891600-98892000	Enhancers	HSMM	muscle
24	chr3:98891800-98892000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:98891800-98892000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:98891800-98892400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
30	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:98899200-98899600	Enhancers	NHEK	skin
34	chr3:98899200-98900200	Enhancers	HMEC	breast
35	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
37	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
38	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
40	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
43	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus
44	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:98931000-98932400	Enhancers	Fetal Kidney	kidney
47	chr3:98932000-98932400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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