Variant report

Variant	nsv1013485
Chromosome Location	chr3:533150-578974
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:232)
CpG islands
(count:183)
Chromatin interactive
region (count:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:232 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:534692-534822	HepG2	liver:	n/a	n/a
2	BACH1	chr3:541423-541496	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr3:577662-577951	H1-hESC	embryonic stem cell:	n/a	n/a
4	BHLHE40	chr3:543200-543216	GM12878	blood:	n/a	n/a
5	CEBPB	chr3:544911-545212	IMR90	lung:	n/a	chr3:545063-545076 chr3:545064-545075
6	CEBPB	chr3:544919-545200	A549	lung:	n/a	chr3:545063-545076 chr3:545064-545075
7	CEBPB	chr3:560581-560882	A549	lung:	n/a	chr3:560731-560742
8	CEBPB	chr3:560575-560880	HepG2	liver:	n/a	chr3:560731-560742
9	CEBPB	chr3:534600-534964	HepG2	liver:	n/a	chr3:534767-534778
10	CEBPB	chr3:575781-576057	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr3:544957-545231	H1-hESC	embryonic stem cell:	n/a	chr3:545063-545076 chr3:545064-545075
12	CEBPB	chr3:544910-545217	Hela-S3	cervix:	n/a	chr3:545063-545076 chr3:545064-545075
13	CEBPB	chr3:534354-535027	Hela-S3	cervix:	n/a	chr3:534767-534778
14	CEBPB	chr3:544942-545225	HepG2	liver:	n/a	chr3:545063-545076 chr3:545064-545075
15	CEBPB	chr3:555007-555386	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr3:545112-545116	K562	blood:	n/a	n/a
17	CHD2	chr3:577375-577868	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr3:577614-578025	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:577737-577955	ProgFib	skin:	n/a	n/a
20	CTCF	chr3:577740-577890	GM12871	blood:	n/a	n/a
21	CTCF	chr3:577820-577970	NHLF	lung:	n/a	n/a
22	CTCF	chr3:577720-577870	GM12867	blood:	n/a	n/a
23	CTCF	chr3:577780-577930	GM12868	blood:	n/a	n/a
24	CTCF	chr3:577782-577919	LNCaP	prostate:	n/a	n/a
25	CTCF	chr3:577820-577970	GM12874	blood:	n/a	n/a
26	CTCF	chr3:577825-577874	K562	blood:	n/a	n/a
27	CTCF	chr3:577820-577970	GM12873	blood:	n/a	n/a
28	CTCF	chr3:577800-577950	HRE	kidney:	n/a	n/a
29	CTCF	chr3:538348-538423	LNCaP	prostate:	n/a	n/a
30	CTCF	chr3:577733-577949	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr3:577780-577930	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr3:534896-535014	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr3:577816-577821	K562	blood:	n/a	n/a
34	CTCF	chr3:577760-577910	HRPEpiC	eye:	n/a	n/a
35	CTCF	chr3:577780-577930	HBMEC	blood vessel:	n/a	n/a
36	CTCF	chr3:577780-577930	HPF	lung:	n/a	n/a
37	CTCF	chr3:577720-577870	GM12875	blood:	n/a	n/a
38	CTCF	chr3:577740-577890	AG04450	lung:	n/a	n/a
39	CTCF	chr3:577032-577110	GM13976	blood:	n/a	n/a
40	CTCF	chr3:577780-577930	GM12870	blood:	n/a	n/a
41	CTCF	chr3:577760-577910	GM12869	blood:	n/a	n/a
42	CTCF	chr3:577800-577950	HMEC	breast:	n/a	n/a
43	CTCF	chr3:577740-577890	HAc	cerebellar:	n/a	n/a
44	CTCF	chr3:577740-577890	NHDF-neo	bronchial:	n/a	n/a
45	CTCF	chr3:567460-567610	HEEpiC	esophagus:	n/a	n/a
46	CTCF	chr3:577720-577870	AG09319	gingival:	n/a	n/a
47	CTCF	chr3:577780-577930	AoAF	blood vessel:	n/a	n/a
48	CTCF	chr3:540673-540732	Spleen_OC	spleen:	n/a	n/a
49	CTCF	chr3:577760-577910	AG04449	skin:	n/a	n/a
50	CTCF	chr3:577760-577910	SK-N-SH_RA	brain:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:577821-577871	Caco-2	colon:	n/a
2	chr3:577629-577679	K562	blood:	n/a
3	chr3:577629-577679	HL-60	blood:	n/a
4	chr3:577964-578014	BE2_C	brain:	n/a
5	chr3:577629-577679	AG04449	skin:	fetal
6	chr3:577964-578014	AG09309	skin:	n/a
7	chr3:577629-577679	HAEpiC	amniotic membrane:	n/a
8	chr3:577821-577871	HRCEpiC	kidney:	n/a
9	chr3:577964-578014	HMEC	breast:	n/a
10	chr3:577629-577679	HEEpiC	esophagus:	n/a
11	chr3:577629-577679	HCT-116	colon:	n/a
12	chr3:577629-577679	MCF10A-Er-Src	breast:	n/a
13	chr3:577964-578014	BJ	skin:	n/a
14	chr3:577964-578014	AG10803	skin:	n/a
15	chr3:577629-577679	Caco-2	colon:	n/a
16	chr3:577821-577871	PrEC	prostate:	n/a
17	chr3:577821-577871	AG04450	lung:	fetal
18	chr3:577629-577679	HCF	heart:	n/a
19	chr3:577821-577871	A549	lung:	n/a
20	chr3:577964-578014	HL-60	blood:	n/a
21	chr3:577629-577679	Jurkat	blood:	n/a
22	chr3:577821-577871	ECC-1	luminal epithelium:	n/a
23	chr3:577964-578014	GM12878	blood:	n/a
24	chr3:577821-577871	HEEpiC	esophagus:	n/a
25	chr3:577821-577871	Hela-S3	cervix:	n/a
26	chr3:577629-577679	ovcar-3	ovarian:	n/a
27	chr3:577964-578014	Hepatocyte	liver:	n/a
28	chr3:577821-577871	HUVEC	blood vessel:	n/a
29	chr3:577629-577679	IMR90	lung:	fetal
30	chr3:577821-577871	HRPEpiC	eye:	n/a
31	chr3:577629-577679	AG09309	skin:	n/a
32	chr3:577629-577679	NB4	blood:	n/a
33	chr3:577629-577679	ECC-1	luminal epithelium:	n/a
34	chr3:577821-577871	HL-60	blood:	n/a
35	chr3:577964-578014	SK-N-SH_RA	brain:	n/a
36	chr3:577821-577871	HEK293	kidney:	embryo
37	chr3:577821-577871	U87	brain:	n/a
38	chr3:577821-577871	GM12878	blood:	n/a
39	chr3:577629-577679	SK-N-SH_RA	brain:	n/a
40	chr3:577629-577679	BJ	skin:	n/a
41	chr3:577629-577679	AG04450	lung:	fetal
42	chr3:577964-578014	NHDF-neo	bronchial:	n/a
43	chr3:577821-577871	AG04449	skin:	fetal
44	chr3:577629-577679	HIPEpiC	eye:	n/a
45	chr3:577964-578014	CMK	blood:	n/a
46	chr3:577629-577679	HRE	kidney:	n/a
47	chr3:577629-577679	AG09319	gingival:	n/a
48	chr3:577629-577679	PANC-1	pancreas:	n/a
49	chr3:577629-577679	T-47D	breast:	n/a
50	chr3:577821-577871	ovcar-3	ovarian:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:556350..557928-chr3:558208..559835,2	MCF-7	breast:
2	chr3:571404..573075-chr3:573790..576325,2	MCF-7	breast:
3	chr3:571404..573075-chr3:573790..576325,2	MCF-7	breast:
4	chr3:565796..568589-chr3:571178..572728,2	K562	blood:
5	chr3:554700..557337-chr3:557649..560284,2	K562	blood:
6	chr3:565796..568589-chr3:571178..572728,2	K562	blood:
7	chr3:554700..557337-chr3:557649..560284,2	K562	blood:
8	chr3:556350..557928-chr3:558208..559835,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHL1-3	chr3:577936-578010	ENSG00000224957
2	lnc-CHL1-6	chr3:552914-553010	ucscGeneNc_uc003boy_1
3	lnc-CHL1-3	chr3:577941-579275	NONHSAT087570

No data

Variant related genes	Relation type
ENSG00000224957	TF binding region
ENSG00000224957	CpG island
DCBLD2	miRNA target sites

Extended variants
information (count: 836 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:836 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184190128	chr3:533186-533187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs373405730	chr3:533216-533217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs114046359	chr3:533237-533238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs9311407	chr3:533258-533259	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs149450635	chr3:533261-533262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs114752118	chr3:533275-533276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs12491457	chr3:533279-533280	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs541960988	chr3:533281-533282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs116015716	chr3:533299-533300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs530633392	chr3:533330-533331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs552417701	chr3:533368-533369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs571288507	chr3:533371-533372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs565504681	chr3:533384-533385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs560002652	chr3:533387-533388	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs570789769	chr3:533388-533389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs77811453	chr3:533396-533397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs547606968	chr3:533417-533418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs375888526	chr3:533432-533433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs188932448	chr3:533458-533459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs143947735	chr3:533461-533462	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs181671086	chr3:533509-533510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs146393828	chr3:533521-533522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs77845863	chr3:533560-533561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs553870172	chr3:533576-533577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs537273438	chr3:533590-533591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs148974408	chr3:533600-533601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs77716281	chr3:533601-533602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs75410887	chr3:533602-533603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs572542428	chr3:533623-533624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs201859167	chr3:533638-533639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs200182220	chr3:533639-533640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs201202980	chr3:533644-533645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs558806591	chr3:533676-533677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs185395190	chr3:533679-533680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs60190041	chr3:533705-533706	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs139655919	chr3:533706-533707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs574750538	chr3:533745-533746	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs575148796	chr3:533746-533747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs576292628	chr3:533752-533753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs542273696	chr3:533780-533781	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs144415176	chr3:533838-533839	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs564888560	chr3:533851-533852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs569590907	chr3:533868-533869	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs375493235	chr3:533889-533890	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs537796835	chr3:533903-533904	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs530710493	chr3:533922-533923	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs546056418	chr3:533927-533928	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs9845876	chr3:533929-533930	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs151055374	chr3:533991-533992	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs546921917	chr3:533997-533998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:526800-533800	Weak transcription	Hela-S3	cervix
2	chr3:526800-543200	Weak transcription	Aorta	Aorta
3	chr3:528800-534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:528800-534200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:529000-534200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:533000-534200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:533800-534200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:533800-534200	Enhancers	Hela-S3	cervix
9	chr3:533800-535000	Enhancers	Fetal Intestine Large	intestine
10	chr3:534000-534200	Enhancers	GM12878-XiMat	blood
11	chr3:534000-534400	Enhancers	Liver	Liver
12	chr3:534000-534600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:534000-535000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:534000-535000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:534200-534600	Enhancers	Fetal Intestine Small	intestine
16	chr3:534200-534600	Active TSS	GM12878-XiMat	blood
17	chr3:534200-534800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:534200-534800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:534200-534800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:534200-535000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:534200-535000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:534200-535000	Flanking Active TSS	Hela-S3	cervix
23	chr3:534400-534800	Flanking Active TSS	Liver	Liver
24	chr3:534400-534800	Enhancers	Fetal Kidney	kidney
25	chr3:534400-535000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:534600-534800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:534600-534800	Enhancers	GM12878-XiMat	blood
28	chr3:534800-535000	Enhancers	Liver	Liver
29	chr3:534800-540600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:535000-535200	Enhancers	Hela-S3	cervix
31	chr3:540600-540800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:543600-543800	Enhancers	Aorta	Aorta
33	chr3:554600-556200	Enhancers	Hela-S3	cervix
34	chr3:554600-556400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:554800-556400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:555400-556400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:556000-556400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:560600-561200	Enhancers	Fetal Lung	lung
39	chr3:561200-562200	Weak transcription	Fetal Lung	lung
40	chr3:562600-562800	Enhancers	Fetal Lung	lung
41	chr3:563400-564600	Weak transcription	Aorta	Aorta
42	chr3:564200-564800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:564600-564800	Enhancers	Aorta	Aorta
44	chr3:577000-578800	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr3:577200-577600	Enhancers	Esophagus	oesophagus
46	chr3:577200-579000	Active TSS	Brain Hippocampus Middle	brain
47	chr3:577400-577600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr3:577400-577600	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr3:577400-577800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
50	chr3:577400-578000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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