Variant report

Variant	esv3515549
Chromosome Location	chr6:79520383-79529881
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:79520364-79520709	MCF-7	breast:	n/a	n/a
2	CEBPB	chr6:79520350-79520744	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr6:79520313-79520791	MCF-7	breast:	n/a	n/a
4	CEBPB	chr6:79528045-79528073	IMR90	lung:	n/a	n/a
5	CEBPB	chr6:79520489-79520812	IMR90	lung:	n/a	n/a
6	CEBPD	chr6:79529447-79529729	K562	blood:	n/a	n/a
7	CTCF	chr6:79519680-79520482	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr6:79519786-79520385	MCF-7	breast:	n/a	n/a
9	CTCF	chr6:79520560-79520710	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr6:79520320-79520470	AG04450	lung:	n/a	n/a
11	CTCF	chr6:79520640-79520790	SAEC	small airway:	n/a	n/a
12	CTCF	chr6:79519833-79520443	A549	lung:	n/a	n/a
13	CTCF	chr6:79526849-79526879	LNCaP	prostate:	n/a	n/a
14	CTCF	chr6:79520300-79520450	SAEC	small airway:	n/a	n/a
15	E2F4	chr6:79522269-79522469	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr6:79520381-79520855	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr6:79520383-79520826	T-47D	breast:	n/a	n/a
18	EP300	chr6:79520238-79520945	T-47D	breast:	n/a	n/a
19	ESR1	chr6:79520356-79520673	T-47D	breast:	n/a	n/a
20	FOS	chr6:79519928-79521010	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr6:79520399-79520933	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr6:79520002-79521016	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr6:79520302-79520965	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXA1	chr6:79520343-79520788	T-47D	breast:	n/a	n/a
25	FOXA1	chr6:79520385-79520766	T-47D	breast:	n/a	n/a
26	GATA2	chr6:79522643-79523186	HUVEC	blood vessel:	n/a	n/a
27	GATA3	chr6:79519678-79520821	T-47D	breast:	n/a	n/a
28	GATA3	chr6:79529418-79529768	MCF-7	breast:	n/a	n/a
29	GATA3	chr6:79520238-79520814	T-47D	breast:	n/a	n/a
30	MAFK	chr6:79521110-79521345	IMR90	lung:	n/a	n/a
31	MYC	chr6:79519850-79521225	MCF10A-Er-Src	breast:	n/a	n/a
32	MYC	chr6:79519863-79520913	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr6:79521525-79521562	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:79526013-79526030	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:79519682-79521018	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr6:79520611-79520926	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr6:79524028-79524173	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr6:79519691-79520509	SK-N-SH	brain:	n/a	n/a
39	RAD21	chr6:79519756-79520436	MCF-7	breast:	n/a	n/a
40	SMC3	chr6:79519693-79520445	SK-N-SH	brain:	n/a	n/a
41	STAT3	chr6:79519971-79520896	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr6:79520293-79520915	MCF10A-Er-Src	breast:	n/a	n/a
43	STAT3	chr6:79525384-79525549	MCF10A-Er-Src	breast:	n/a	n/a
44	STAT3	chr6:79520441-79520857	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr6:79524978-79525070	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr6:79520329-79520863	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:36762385..36763233-chr6:79519693..79520512,2	MCF-7	breast:
2	chr6:79522220..79524770-chr6:79527033..79529117,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHIP-1	chr6:79522839-79523020	XLOC_005771
2	lnc-PHIP-1	chr6:79519432-79521881	XLOC_005771

No data

Variant related genes	Relation type
ENSG00000229495	TF binding region
ENSG00000229495	chromatin interactions

Extended variants
information (count: 387 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:387 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529081146	chr6:79520397-79520398	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
2	rs140769036	chr6:79520407-79520408	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
3	rs186345889	chr6:79520425-79520426	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
4	rs190652410	chr6:79520454-79520455	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
5	rs549002442	chr6:79520484-79520485	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
6	rs144729453	chr6:79520560-79520561	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
7	rs115709699	chr6:79520567-79520568	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
8	rs116095096	chr6:79520568-79520569	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
9	rs534278800	chr6:79520570-79520571	Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
10	rs906319	chr6:79520689-79520690	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs570982015	chr6:79520715-79520716	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs542811089	chr6:79520734-79520735	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs553486451	chr6:79520761-79520762	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs200803515	chr6:79520790-79520791	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs376431111	chr6:79520797-79520798	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs115364775	chr6:79520805-79520806	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs542775095	chr6:79520815-79520816	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs532935549	chr6:79520816-79520817	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs538361301	chr6:79520835-79520836	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs543774812	chr6:79520870-79520871	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs148669528	chr6:79520871-79520872	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs529146531	chr6:79520879-79520880	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs369480397	chr6:79520885-79520886	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs113273336	chr6:79520908-79520909	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs528601420	chr6:79520925-79520926	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs551833823	chr6:79520935-79520936	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs78145536	chr6:79520972-79520973	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs537038486	chr6:79520979-79520980	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs550910396	chr6:79520994-79520995	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs570717108	chr6:79521035-79521036	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs567623422	chr6:79521099-79521100	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs556671925	chr6:79521139-79521140	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs186487897	chr6:79521158-79521159	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs553305507	chr6:79521163-79521164	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs573356757	chr6:79521187-79521188	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs190947093	chr6:79521211-79521212	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs562795134	chr6:79521242-79521243	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs41269337	chr6:79521269-79521270	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs183030751	chr6:79521281-79521282	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs543438688	chr6:79521284-79521285	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs187563363	chr6:79521293-79521294	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs573991967	chr6:79521361-79521362	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs542881133	chr6:79521371-79521372	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs559313042	chr6:79521374-79521375	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs537698462	chr6:79521403-79521404	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs190868410	chr6:79521435-79521436	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs183005078	chr6:79521440-79521441	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs565038547	chr6:79521485-79521486	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs151217944	chr6:79521494-79521495	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs140448290	chr6:79521518-79521519	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Systemic lupus erythematosus	17503323	CNVD
Melanoma	18172304	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Cancer	21637783	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
T-cell lymphomas	19863542	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Ependymoma	16718352	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16272173	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Urothelial carcinoma	18382360	CNVD
Ovarian neoplasms	16753589	CNVD
Hepatocellular carcinoma	16750200	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Follicular lymphoma	17699855	CNVD
Breast cancer	17133270	CNVD
Leukemia	18688285	CNVD
Prostate cancer	19242612	CNVD
Developmental delay	21147756	CNVD
Glioma	21046410	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Zellweger syndrome	21572526	CNVD
Follicular lymphoma	20505157	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Malignant melanoma	18718029	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Lung adenocarcinoma	21935476	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Salivary gland tumor	18059337	CNVD
Lung cancer	16773561	CNVD
Glioblastoma multiforme	22286061	CNVD
Urothelial cell carcinoma	18451213	CNVD
Prostate cancer	16461572	CNVD
Mental retardation	21045960	CNVD
Obesity	21045960	CNVD
learning difficulties	21045960	CNVD
Prostate cancer	17245344	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Cancer	20164920	CNVD
Burkitt''s lymphoma	20823134	CNVD
Ductal carcinoma	22052326	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	18458336	CNVD

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79519000-79521800	Enhancers	HMEC	breast
2	chr6:79519200-79521400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:79519200-79521800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:79519200-79521800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:79519600-79521400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:79519800-79521200	Enhancers	Liver	Liver
7	chr6:79519800-79521600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:79520200-79520600	Flanking Active TSS	NHEK	skin
9	chr6:79520200-79520800	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:79520200-79521000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:79520200-79521200	Enhancers	Osteobl	bone
12	chr6:79520400-79520800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:79520400-79520800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:79520400-79521200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:79520600-79521600	Enhancers	NHEK	skin
16	chr6:79521400-79522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:79521800-79522800	Weak transcription	HMEC	breast
18	chr6:79521800-79527000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:79522800-79523000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:79522800-79523000	Enhancers	HMEC	breast

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