Variant report

Variant	esv2759156
Chromosome Location	chr3:68888730-68935796
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	chr3:68925289-68925627	HepG2	liver:	n/a	n/a
2	BACH1	chr3:68910069-68910337	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr3:68932592-68932613	GM12878	blood:	n/a	n/a
4	BRCA1	chr3:68915390-68915620	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:68900744-68900944	HepG2	liver:	n/a	chr3:68900823-68900836 chr3:68900823-68900836 chr3:68900825-68900834 chr3:68900823-68900834 chr3:68900825-68900836
6	CEBPB	chr3:68921692-68922073	HepG2	liver:	n/a	n/a
7	CTCF	chr3:68925360-68925510	NB4	blood:	n/a	chr3:68925447-68925468
8	CTCF	chr3:68925380-68925530	GM12865	blood:	n/a	chr3:68925447-68925468
9	CTCF	chr3:68927500-68927650	HAc	cerebellar:	n/a	n/a
10	CTCF	chr3:68925380-68925530	NHDF-neo	bronchial:	n/a	chr3:68925447-68925468
11	CTCF	chr3:68925380-68925530	HepG2	liver:	n/a	chr3:68925447-68925468
12	CTCF	chr3:68925360-68925510	HCPEpiC	choroid plexus:	n/a	chr3:68925447-68925468
13	CTCF	chr3:68925248-68925725	K562	blood:	n/a	chr3:68925447-68925468
14	CTCF	chr3:68927520-68927670	NHDF-neo	bronchial:	n/a	n/a
15	CTCF	chr3:68927620-68927770	GM12878	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
16	CTCF	chr3:68927405-68927858	MCF-7	breast:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
17	CTCF	chr3:68925205-68925724	MCF-7	breast:	n/a	chr3:68925447-68925468
18	CTCF	chr3:68927600-68927777	Pancreas_OC	pancreas:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
19	CTCF	chr3:68927600-68927750	HMF	breast:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
20	CTCF	chr3:68927462-68927780	H1-hESC	embryonic stem cell:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
21	CTCF	chr3:68927620-68927770	HMEC	breast:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
22	CTCF	chr3:68915380-68915530	BE2_C	brain:	n/a	n/a
23	CTCF	chr3:68927560-68927710	GM12871	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
24	CTCF	chr3:68927620-68927770	AG09319	gingival:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
25	CTCF	chr3:68927600-68927750	HBMEC	blood vessel:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
26	CTCF	chr3:68927600-68927750	GM12864	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
27	CTCF	chr3:68925360-68925510	BE2_C	brain:	n/a	chr3:68925447-68925468
28	CTCF	chr3:68925400-68925550	GM12865	blood:	n/a	chr3:68925447-68925468
29	CTCF	chr3:68925380-68925530	GM12868	blood:	n/a	chr3:68925447-68925468
30	CTCF	chr3:68927620-68927770	GM12865	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
31	CTCF	chr3:68925400-68925550	BE2_C	brain:	n/a	chr3:68925447-68925468
32	CTCF	chr3:68925360-68925510	HCM	heart:	n/a	chr3:68925447-68925468
33	CTCF	chr3:68927620-68927770	WI-38	lung:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
34	CTCF	chr3:68925324-68925610	GM12878	blood:	n/a	chr3:68925447-68925468
35	CTCF	chr3:68927473-68927867	HepG2	liver:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
36	CTCF	chr3:68925400-68925550	HBMEC	blood vessel:	n/a	chr3:68925447-68925468
37	CTCF	chr3:68927560-68927710	GM12865	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
38	CTCF	chr3:68927560-68927710	HMF	breast:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
39	CTCF	chr3:68933629-68933664	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr3:68927640-68927790	GM12872	blood:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
41	CTCF	chr3:68925360-68925510	HL-60	blood:	n/a	chr3:68925447-68925468
42	CTCF	chr3:68925340-68925490	GM12864	blood:	n/a	chr3:68925447-68925468
43	CTCF	chr3:68927600-68927750	HCPEpiC	choroid plexus:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
44	CTCF	chr3:68925400-68925550	SAEC	small airway:	n/a	chr3:68925447-68925468
45	CTCF	chr3:68927620-68927770	HepG2	liver:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
46	CTCF	chr3:68925400-68925550	GM12878	blood:	n/a	chr3:68925447-68925468
47	CTCF	chr3:68915440-68915590	HVMF	connective:	n/a	n/a
48	CTCF	chr3:68925380-68925530	GM12873	blood:	n/a	chr3:68925447-68925468
49	CTCF	chr3:68927600-68927750	HMEC	breast:	n/a	chr3:68927663-68927681 chr3:68927658-68927679
50	CTCF	chr3:68925234-68925600	A549	lung:	n/a	chr3:68925447-68925468

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:68925535-68925585	SK-N-SH	brain:	n/a
2	chr3:68925535-68925585	RPTEC	kidney:	n/a
3	chr3:68925535-68925585	PANC-1	pancreas:	n/a
4	chr3:68925535-68925585	LNCaP	prostate:	n/a
5	chr3:68925535-68925585	HEK293	kidney:	embryo
6	chr3:68925535-68925585	HRCEpiC	kidney:	n/a
7	chr3:68925535-68925585	ovcar-3	ovarian:	n/a
8	chr3:68925535-68925585	H1-hESC	embryonic stem cell:	embryo
9	chr3:68925535-68925585	HRE	kidney:	n/a
10	chr3:68925535-68925585	ProgFib	skin:	n/a
11	chr3:68925535-68925585	HEEpiC	esophagus:	n/a
12	chr3:68925535-68925585	MCF-7	breast:	n/a
13	chr3:68925535-68925585	NHDF-neo	bronchial:	n/a
14	chr3:68925535-68925585	GM12891	blood:	n/a
15	chr3:68925535-68925585	Jurkat	blood:	n/a
16	chr3:68925535-68925585	AG04449	skin:	fetal
17	chr3:68925535-68925585	AG09309	skin:	n/a
18	chr3:68925535-68925585	NHBE	bronchial:	n/a
19	chr3:68925535-68925585	SK-N-MC	brain:	n/a
20	chr3:68925535-68925585	Caco-2	colon:	n/a
21	chr3:68925535-68925585	ECC-1	luminal epithelium:	n/a
22	chr3:68925535-68925585	A549	lung:	n/a
23	chr3:68925535-68925585	HCT-116	colon:	n/a
24	chr3:68925535-68925585	GM06990	blood:	n/a
25	chr3:68925535-68925585	SAEC	small airway:	n/a
26	chr3:68925535-68925585	GM12892	blood:	n/a
27	chr3:68925535-68925585	MCF10A-Er-Src	breast:	n/a
28	chr3:68925535-68925585	SKMC	muscle:	n/a
29	chr3:68925535-68925585	PrEC	prostate:	n/a
30	chr3:68925535-68925585	GM12878	blood:	n/a
31	chr3:68925535-68925585	HPAEpiC	pulmonary alveolar:	n/a
32	chr3:68925535-68925585	AG10803	skin:	n/a
33	chr3:68925535-68925585	AG04450	lung:	fetal
34	chr3:68925535-68925585	NH-A	brain:	n/a
35	chr3:68925535-68925585	HepG2	liver:	n/a
36	chr3:68925535-68925585	NT2-D1	testis:	n/a
37	chr3:68925535-68925585	IMR90	lung:	fetal
38	chr3:68925535-68925585	HIPEpiC	eye:	n/a
39	chr3:68925535-68925585	HMEC	breast:	n/a
40	chr3:68925535-68925585	HNPCEpiC	eye:	n/a
41	chr3:68925535-68925585	HL-60	blood:	n/a
42	chr3:68925535-68925585	PFSK-1	brain:	n/a
43	chr3:68925535-68925585	Hepatocyte	liver:	n/a
44	chr3:68925535-68925585	Hela-S3	cervix:	n/a
45	chr3:68925535-68925585	NB4	blood:	n/a
46	chr3:68925535-68925585	BJ	skin:	n/a
47	chr3:68925535-68925585	AG09319	gingival:	n/a
48	chr3:68925535-68925585	T-47D	breast:	n/a
49	chr3:68925535-68925585	K562	blood:	n/a
50	chr3:68925535-68925585	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:67952201..67952773-chr3:68925063..68925992,2	MCF-7	breast:
2	chr3:66988494..66989399-chr3:68925421..68925952,2	K562	blood:
3	chr3:67869561..67870138-chr3:68927224..68928400,3	MCF-7	breast:
4	chr3:68927346..68928063-chr4:97807302..97808145,2	MCF-7	breast:
5	chr3:67022337..67023183-chr3:68925421..68925921,2	K562	blood:
6	chr3:68927239..68928502-chr3:69021583..69022148,4	MCF-7	breast:
7	chr3:66988749..66989610-chr3:68927193..68927742,2	K562	blood:
8	chr3:67159823..67160870-chr3:68924556..68925868,3	MCF-7	breast:
9	chr3:67159850..67160749-chr3:68927123..68927995,3	MCF-7	breast:

Variant related genes	Relation type
RNA5SP135	TF binding region
RNA5SP135	CpG island

Extended variants
information (count: 454 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:454 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76104233	chr3:68889048-68889049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs371774240	chr3:68889085-68889086	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs139569773	chr3:68889129-68889130	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs578243391	chr3:68889230-68889231	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs537658031	chr3:68889232-68889233	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs575556885	chr3:68889238-68889239	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs574130535	chr3:68889325-68889326	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs542754642	chr3:68889334-68889335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs145082957	chr3:68889338-68889339	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs572514990	chr3:68889350-68889351	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs544555533	chr3:68889364-68889365	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs376723665	chr3:68889370-68889371	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs115980209	chr3:68889382-68889383	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs563152177	chr3:68904669-68904670	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs529008475	chr3:68904675-68904676	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs147925182	chr3:68904678-68904679	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs573799639	chr3:68904683-68904684	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs548299370	chr3:68904698-68904699	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs542670157	chr3:68904722-68904723	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs3943100	chr3:68904737-68904738	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs527771652	chr3:68904762-68904763	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6797048	chr3:68904763-68904764	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs570824443	chr3:68904765-68904766	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs78281648	chr3:68904779-68904780	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs556852940	chr3:68904794-68904795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs545051271	chr3:68904825-68904826	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs550903723	chr3:68904827-68904828	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs189624756	chr3:68904843-68904844	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs148835442	chr3:68904912-68904913	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs555453055	chr3:68904921-68904922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143452020	chr3:68904999-68905000	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs565604178	chr3:68905004-68905005	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs541098658	chr3:68905047-68905048	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs569406164	chr3:68905057-68905058	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs181951944	chr3:68905065-68905066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs543315834	chr3:68905072-68905073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs563214802	chr3:68905077-68905078	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs2171871	chr3:68905094-68905095	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs185908781	chr3:68905142-68905143	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs559479609	chr3:68905148-68905149	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs2171870	chr3:68905151-68905152	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs368645713	chr3:68905152-68905153	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs561281653	chr3:68905185-68905186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs367637060	chr3:68905191-68905192	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs150919824	chr3:68905212-68905213	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs13078150	chr3:68905216-68905217	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs142286652	chr3:68905228-68905229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs77310400	chr3:68905274-68905275	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs116033162	chr3:68905287-68905288	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs562943503	chr3:68905302-68905303	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	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
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Breast cancer	21509527	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Autism	22102821	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Prostate cancer	17217626	CNVD
Urothelial cell carcinoma	18451213	CNVD
Alzheimer''s disease	22166940	CNVD
Mental retardation	20848658	CNVD
Breast cancer	17142309	CNVD
Breast cancer	21364760	CNVD
lymphocytic leukemia	21291569	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68889000-68889400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:68904600-68905400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:68904600-68905400	Enhancers	HMEC	breast
4	chr3:68904800-68905200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:68910200-68912000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:68910800-68911200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:68924000-68924200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:68925200-68925400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:68925200-68925400	Enhancers	Fetal Kidney	kidney
10	chr3:68925400-68933600	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:68926800-68930200	Active TSS	Stomach Smooth Muscle	stomach
12	chr3:68927600-68928200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:68928000-68928400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:68928200-68928400	Enhancers	Fetal Stomach	stomach
15	chr3:68928200-68929200	Enhancers	Fetal Intestine Large	intestine
16	chr3:68928600-68928800	Bivalent Enhancer	Fetal Heart	heart
17	chr3:68928600-68928800	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:68928600-68929600	Weak transcription	Fetal Stomach	stomach
19	chr3:68928600-68929800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:68928800-68929400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:68929200-68929800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:68929400-68930600	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:68929600-68930000	Enhancers	Fetal Stomach	stomach
24	chr3:68929800-68930000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:68929800-68930000	Enhancers	Fetal Intestine Large	intestine
26	chr3:68930000-68931000	Weak transcription	Fetal Stomach	stomach
27	chr3:68930800-68931200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:68931000-68931200	Enhancers	Fetal Stomach	stomach
29	chr3:68931000-68933400	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:68931200-68931600	Enhancers	Brain Germinal Matrix	brain
31	chr3:68933400-68933800	Enhancers	Adipose Nuclei	Adipose
32	chr3:68933600-68934000	Enhancers	Colon Smooth Muscle	Colon
33	chr3:68933800-68934000	Enhancers	Rectal Smooth Muscle	rectum

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