Variant report

Variant	esv1002835
Chromosome Location	chr6:87792224-87800627
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	ATF2	chr6:87797762-87798194	GM12878	blood:	n/a	n/a
2	ATF2	chr6:87797755-87798253	GM12878	blood:	n/a	n/a
3	BATF	chr6:87797746-87798075	GM12878	blood:	n/a	n/a
4	BATF	chr6:87797786-87798113	GM12878	blood:	n/a	n/a
5	BATF	chr6:87791902-87792351	GM12878	blood:	n/a	n/a
6	BCL11A	chr6:87797775-87798107	GM12878	blood:	n/a	n/a
7	BCL3	chr6:87797793-87798126	GM12878	blood:	n/a	n/a
8	BCLAF1	chr6:87797660-87798172	GM12878	blood:	n/a	n/a
9	ELF1	chr6:87796618-87796833	K562	blood:	n/a	n/a
10	EP300	chr6:87797881-87798107	GM12878	blood:	n/a	chr6:87797947-87797961
11	EP300	chr6:87800089-87800128	K562	blood:	n/a	n/a
12	EP300	chr6:87797744-87798091	GM12878	blood:	n/a	chr6:87797947-87797961
13	FOXM1	chr6:87797757-87798235	GM12878	blood:	n/a	n/a
14	IKZF1	chr6:87792007-87792329	GM12878	blood:	n/a	n/a
15	IRF4	chr6:87797729-87798105	GM12878	blood:	n/a	n/a
16	MEF2A	chr6:87797754-87798298	GM12878	blood:	n/a	chr6:87798015-87798031
17	MEF2A	chr6:87797726-87798245	GM12878	blood:	n/a	chr6:87798015-87798031
18	MEF2C	chr6:87797793-87798066	GM12878	blood:	n/a	chr6:87798015-87798031
19	MEF2C	chr6:87797722-87798144	GM12878	blood:	n/a	chr6:87798015-87798031
20	MTA3	chr6:87797720-87798213	GM12878	blood:	n/a	n/a
21	NFATC1	chr6:87797769-87798129	GM12878	blood:	n/a	n/a
22	NFATC1	chr6:87797755-87798120	GM12878	blood:	n/a	n/a
23	NFIC	chr6:87791951-87792313	GM12878	blood:	n/a	n/a
24	NFIC	chr6:87797682-87798285	GM12878	blood:	n/a	n/a
25	NFIC	chr6:87797682-87798262	GM12878	blood:	n/a	n/a
26	NRF1	chr6:87792715-87792777	GM12878	blood:	n/a	n/a
27	PAX5	chr6:87797521-87798077	GM12878	blood:	n/a	n/a
28	PAX5	chr6:87797565-87798038	GM12892	blood:	n/a	n/a
29	PAX5	chr6:87797684-87797963	GM12878	blood:	n/a	n/a
30	PAX5	chr6:87797680-87798052	GM12891	blood:	n/a	n/a
31	PAX5	chr6:87797642-87797979	GM12878	blood:	n/a	n/a
32	PAX5	chr6:87797652-87798034	GM12878	blood:	n/a	n/a
33	PML	chr6:87797668-87798180	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:87792220-87796423	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr6:87794266-87794420	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:87798506-87799187	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:87793902-87793945	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr6:87792821-87792860	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr6:87793961-87794048	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr6:87796073-87796089	Gliobla	brain:	n/a	n/a
41	POLR2A	chr6:87797124-87797258	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:87792874-87793107	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr6:87796131-87796157	Gliobla	brain:	n/a	n/a
44	POLR2A	chr6:87793982-87794103	MCF10A-Er-Src	breast:	n/a	n/a
45	RUNX3	chr6:87797644-87798140	GM12878	blood:	n/a	n/a
46	RUNX3	chr6:87797618-87798176	GM12878	blood:	n/a	n/a
47	SPI1	chr6:87793706-87794019	GM12891	blood:	n/a	chr6:87793881-87793894
48	STAT3	chr6:87797041-87797147	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT5A	chr6:87797778-87798085	GM12878	blood:	n/a	n/a
50	STAT5A	chr6:87797735-87798202	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:87793956..87798150-chr6:87800009..87803465,4	K562	blood:
2	chr6:87793956..87798150-chr6:87800009..87803465,4	K562	blood:
3	chr6:87789226..87790732-chr6:87794986..87797378,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HTR1E-2	chr6:87792951-87793254	NONHSAT113894

Variant related genes	Relation type
RN7SKP209	TF binding region

Extended variants
information (count: 306 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:306 , 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	rs560517223	chr6:87792229-87792230	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs151189794	chr6:87792236-87792237	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs554744445	chr6:87792323-87792324	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs191594027	chr6:87792331-87792332	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs547635412	chr6:87792364-87792365	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs549444465	chr6:87792391-87792392	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs5878014	chr6:87792438-87792439	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs397885381	chr6:87792439-87792440	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs571302168	chr6:87792441-87792442	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs538818841	chr6:87792467-87792468	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs547227755	chr6:87792487-87792488	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs182133236	chr6:87792497-87792498	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs187190813	chr6:87792502-87792503	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs554936898	chr6:87792525-87792526	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs192620662	chr6:87792529-87792530	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs140306924	chr6:87792537-87792538	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs535315892	chr6:87792555-87792556	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs555532080	chr6:87792588-87792589	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs35562563	chr6:87792641-87792642	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs573092248	chr6:87792675-87792676	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs150028454	chr6:87792683-87792684	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs545489304	chr6:87792690-87792691	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs560454675	chr6:87792717-87792718	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs572323649	chr6:87792724-87792725	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs144037573	chr6:87792811-87792812	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs114360202	chr6:87792815-87792816	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs116439831	chr6:87792817-87792818	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs549407798	chr6:87792899-87792900	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs564899113	chr6:87792903-87792904	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs9294365	chr6:87792908-87792909	Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs185338698	chr6:87793000-87793001	Active TSS Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs565721040	chr6:87793026-87793027	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs111414171	chr6:87793034-87793035	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs190118644	chr6:87793084-87793085	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs570004456	chr6:87793108-87793109	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs34811728	chr6:87793195-87793196	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs193060354	chr6:87793233-87793234	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs556239737	chr6:87793264-87793265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs577989354	chr6:87793316-87793317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs9362387	chr6:87793401-87793402	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs554278642	chr6:87793436-87793437	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs146438359	chr6:87793527-87793528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs368761260	chr6:87793532-87793533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs10542137	chr6:87793552-87793553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs71014984	chr6:87793572-87793573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs200714450	chr6:87793573-87793574	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs554834112	chr6:87793625-87793626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs185730968	chr6:87793629-87793630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs544114542	chr6:87793634-87793635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs578084956	chr6:87793659-87793660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:104)

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
Endometrioid adenocarcinoma	16974079	CNVD
Autism	22495311	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
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
Follicular lymphoma	17699855	CNVD
Breast cancer	17133270	CNVD
Leukemia	18688285	CNVD
Prostate cancer	19242612	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
Lung adenocarcinoma	21935476	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
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Acute lymphoblastic leukemia	17640729	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	17603634	CNVD
Chondromyxoid Fibroma	20696777	CNVD
Cancer	21183584	CNVD
abnormal development	18461090	CNVD
Myelodysplastic syndrome	18508791	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	21364760	CNVD
Developmental delay	19490664	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87790600-87793200	Enhancers	GM12878-XiMat	blood
2	chr6:87791600-87793200	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:87792200-87794000	Weak transcription	Placenta	Placenta
4	chr6:87792800-87793000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:87793000-87798200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:87793200-87797600	Weak transcription	GM12878-XiMat	blood
7	chr6:87794000-87799800	Strong transcription	Placenta	Placenta
8	chr6:87797600-87798200	Enhancers	GM12878-XiMat	blood
9	chr6:87799800-87801400	Weak transcription	Placenta	Placenta

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