Variant report

Variant	esv3474616
Chromosome Location	chr6:79521733-79530731
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	chr6:79528045-79528073	IMR90	lung:	n/a	n/a
2	CEBPD	chr6:79529447-79529729	K562	blood:	n/a	n/a
3	CTCF	chr6:79526849-79526879	LNCaP	prostate:	n/a	n/a
4	E2F4	chr6:79522269-79522469	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA2	chr6:79522643-79523186	HUVEC	blood vessel:	n/a	n/a
6	GATA3	chr6:79529418-79529768	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:79526013-79526030	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr6:79524028-79524173	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr6:79525384-79525549	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr6:79524978-79525070	MCF10A-Er-Src	breast:	n/a	n/a

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

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

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

Extended variants
information (count: 329 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:329 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557614797	chr6:79521745-79521746	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs577814898	chr6:79521757-79521758	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs541391926	chr6:79521774-79521775	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs564868955	chr6:79521775-79521776	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs537101685	chr6:79521781-79521782	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs184290068	chr6:79521797-79521798	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs578120266	chr6:79521806-79521807	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs573658395	chr6:79521825-79521826	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs377757531	chr6:79521826-79521827	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs542591328	chr6:79521831-79521832	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs559589028	chr6:79521862-79521863	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs573004088	chr6:79521865-79521866	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs545194846	chr6:79521871-79521872	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs564699147	chr6:79521889-79521890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs530929492	chr6:79521929-79521930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs187876155	chr6:79521954-79521955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560972342	chr6:79521975-79521976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs140870377	chr6:79521998-79521999	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs547016598	chr6:79522004-79522005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs563851004	chr6:79522054-79522055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs370921158	chr6:79522065-79522066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs375340819	chr6:79522090-79522091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs530605699	chr6:79522100-79522101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs532649309	chr6:79522102-79522103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs552813406	chr6:79522128-79522129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs569437630	chr6:79522130-79522131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs537173171	chr6:79522144-79522145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs6454086	chr6:79522163-79522164	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs192488458	chr6:79522169-79522170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs540142830	chr6:79522181-79522182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs184651011	chr6:79522182-79522183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs372011981	chr6:79522197-79522198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs189212961	chr6:79522208-79522209	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs544942263	chr6:79522225-79522226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs558354611	chr6:79522241-79522242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs111782885	chr6:79522246-79522247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs79254459	chr6:79522264-79522265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs544331974	chr6:79522298-79522299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs561033736	chr6:79522319-79522320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs530083707	chr6:79522329-79522330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs374000541	chr6:79522354-79522355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs150120184	chr6:79522381-79522382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs138539893	chr6:79522405-79522406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs552883219	chr6:79522410-79522411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs149399717	chr6:79522469-79522470	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs531933849	chr6:79522513-79522514	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs550742036	chr6:79522516-79522517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs113889413	chr6:79522520-79522521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs567360716	chr6:79522538-79522539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs56176829	chr6:79522654-79522655	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79519000-79521800	Enhancers	HMEC	breast
2	chr6:79519200-79521800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:79519200-79521800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:79521400-79522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:79521800-79522800	Weak transcription	HMEC	breast
6	chr6:79521800-79527000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:79522800-79523000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:79522800-79523000	Enhancers	HMEC	breast

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