Variant report

Variant	nsv508230
Chromosome Location	chr3:98933987-98969536
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	CEBPB	chr3:98965180-98965549	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:98965139-98965653	ECC-1	luminal epithelium:	n/a	n/a
3	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
4	CEBPB	chr3:98965132-98965584	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
6	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
7	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
8	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
10	CTCF	chr3:98958060-98958210	AG04449	skin:	n/a	n/a
11	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
13	CTCF	chr3:98957445-98957519	ProgFib	skin:	n/a	n/a
14	CTCF	chr3:98965300-98965450	HVMF	connective:	n/a	n/a
15	CTCF	chr3:98961260-98961410	AG10803	skin:	n/a	n/a
16	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
17	CTCF	chr3:98961240-98961390	AG10803	skin:	n/a	n/a
18	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
19	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
20	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
21	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
22	E2F4	chr3:98964937-98965413	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr3:98968903-98969461	MCF10A-Er-Src	breast:	n/a	chr3:98969283-98969300
24	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr3:98968956-98969557	ECC-1	luminal epithelium:	n/a	chr3:98969124-98969133 chr3:98969120-98969134
26	EP300	chr3:98964901-98965675	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr3:98967085-98967283	SK-N-SH_RA	brain:	n/a	n/a
28	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
29	FOS	chr3:98969099-98969511	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr3:98967068-98967355	MCF10A-Er-Src	breast:	n/a	chr3:98967211-98967222
31	FOS	chr3:98965067-98965592	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:98967047-98967367	MCF10A-Er-Src	breast:	n/a	chr3:98967211-98967222
33	FOS	chr3:98967084-98967325	MCF10A-Er-Src	breast:	n/a	chr3:98967211-98967222
34	FOS	chr3:98967754-98968123	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:98967053-98967388	HUVEC	blood vessel:	n/a	chr3:98967211-98967222
36	FOS	chr3:98969194-98969525	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:98965053-98965546	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:98965071-98965482	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr3:98967134-98967242	MCF10A-Er-Src	breast:	n/a	chr3:98967211-98967222
40	FOS	chr3:98965053-98965527	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr3:98969100-98969507	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr3:98968004-98968053	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr3:98969106-98969535	MCF10A-Er-Src	breast:	n/a	n/a
44	FOXA1	chr3:98969244-98969472	ECC-1	luminal epithelium:	n/a	n/a
45	FOXA2	chr3:98964348-98964692	A549	lung:	n/a	n/a
46	FOXM1	chr3:98964944-98965618	ECC-1	luminal epithelium:	n/a	n/a
47	FOXM1	chr3:98968955-98969558	ECC-1	luminal epithelium:	n/a	n/a
48	GATA2	chr3:98964829-98965503	HUVEC	blood vessel:	n/a	n/a
49	HMGN3	chr3:98951831-98951978	K562	blood:	n/a	n/a
50	JUN	chr3:98960281-98960354	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98960467..98962608-chr3:98963910..98966387,2	K562	blood:
2	chr3:98960467..98962608-chr3:98963910..98966387,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCBLD2-2	chr3:98934068-98935110	NONHSAT090839

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 1147 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:1147 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569543472	chr3:98933995-98933996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs34368377	chr3:98933997-98933998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs534741687	chr3:98934006-98934007	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs557549653	chr3:98934040-98934041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs372458130	chr3:98934093-98934094	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs577604758	chr3:98934096-98934097	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs371416049	chr3:98934108-98934109	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs536639040	chr3:98934116-98934117	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs545024469	chr3:98934137-98934138	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs556819551	chr3:98934153-98934154	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs560162700	chr3:98934172-98934173	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs576768344	chr3:98934216-98934217	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs16840764	chr3:98934223-98934224	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs562298122	chr3:98934226-98934227	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs572661558	chr3:98934247-98934248	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs183104707	chr3:98934252-98934253	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs188188121	chr3:98934304-98934305	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs138526840	chr3:98934342-98934343	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs367998601	chr3:98934388-98934389	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs533368351	chr3:98934472-98934473	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs549868733	chr3:98934475-98934476	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs142583991	chr3:98934493-98934494	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs529122096	chr3:98934502-98934503	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs548841508	chr3:98934510-98934511	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs6803675	chr3:98934512-98934513	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs528260721	chr3:98934536-98934537	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs146743645	chr3:98934553-98934554	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs73859873	chr3:98934557-98934558	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs532455072	chr3:98934592-98934593	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs368093269	chr3:98934598-98934599	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs567251114	chr3:98934601-98934602	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs6806218	chr3:98934604-98934605	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs556086197	chr3:98934629-98934630	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs572646074	chr3:98934639-98934640	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs114372862	chr3:98934663-98934664	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs541222023	chr3:98934667-98934668	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs531859308	chr3:98934672-98934673	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs138811993	chr3:98934700-98934701	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs578009896	chr3:98934793-98934794	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs115464935	chr3:98934827-98934828	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs192972658	chr3:98934838-98934839	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs116730422	chr3:98934869-98934870	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs16840770	chr3:98934878-98934879	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs559216533	chr3:98934897-98934898	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs57832379	chr3:98934944-98934945	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs376678413	chr3:98934972-98934973	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs528292096	chr3:98934997-98934998	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs142897807	chr3:98935041-98935042	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs184303681	chr3:98935050-98935051	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs114439436	chr3:98935056-98935057	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

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
Pancreatic cancer	17952125	CNVD

Chromatin state (count:137 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98934400-98935000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:98951400-98952800	Enhancers	Osteobl	bone
20	chr3:98951800-98952200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:98951800-98952200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:98952200-98959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:98952200-98959200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:98952800-98959200	Weak transcription	Osteobl	bone
25	chr3:98955600-98955800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:98957400-98959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:98959000-98959400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:98959000-98960600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:98959200-98960400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:98959200-98961800	Enhancers	Osteobl	bone
31	chr3:98959200-98962000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:98959400-98959600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:98959400-98960200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:98959600-98959800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:98959600-98960600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:98959800-98960400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:98959800-98960400	Enhancers	HSMMtube	muscle
38	chr3:98959800-98961600	Enhancers	NHDF-Ad	bronchial
39	chr3:98960200-98961600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:98960200-98961600	Enhancers	Aorta	Aorta
41	chr3:98960200-98961800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:98960400-98961400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:98960400-98966800	Weak transcription	HSMMtube	muscle
44	chr3:98960600-98961600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:98961000-98961600	Enhancers	NHEK	skin
46	chr3:98961200-98961600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:98961200-98961600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:98961400-98964800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:98961600-98964800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:98961600-98964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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