Variant report

Variant	esv3346517
Chromosome Location	chr5:28595244-28630628
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr5:28629799-28629979	K562	blood:	n/a	n/a
2	CEBPB	chr5:28623857-28624057	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr5:28619860-28620010	GM06990	blood:	n/a	n/a
4	CTCF	chr5:28596006-28596051	Kidney_OC	kidney:	n/a	n/a
5	CTCF	chr5:28621679-28621875	K562	blood:	n/a	n/a
6	CTCF	chr5:28598637-28598672	GM10248	blood:	n/a	n/a
7	CTCF	chr5:28596180-28596235	LNCaP	prostate:	n/a	n/a
8	CTCF	chr5:28610315-28610383	Kidney_OC	kidney:	n/a	n/a
9	CTCF	chr5:28621320-28621470	GM12869	blood:	n/a	n/a
10	CTCF	chr5:28595980-28596004	GM10248	blood:	n/a	n/a
11	E2F4	chr5:28620222-28620422	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr5:28618054-28618577	MCF10A-Er-Src	breast:	n/a	n/a
13	E2F4	chr5:28607779-28607979	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr5:28604084-28604270	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXA2	chr5:28621639-28621913	A549	lung:	n/a	n/a
16	GATA1	chr5:28617326-28618514	PBDE	blood:	n/a	chr5:28618319-28618332 chr5:28617418-28617428
17	HCFC1	chr5:28629524-28629588	K562	blood:	n/a	n/a
18	JUN	chr5:28607616-28607623	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAFK	chr5:28602610-28602810	HepG2	liver:	n/a	n/a
20	MAFK	chr5:28602550-28602782	HepG2	liver:	n/a	n/a
21	MAFK	chr5:28602506-28602732	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAFK	chr5:28602616-28602776	K562	blood:	n/a	n/a
23	NFYA	chr5:28605057-28605089	Hela-S3	cervix:	n/a	n/a
24	NFYA	chr5:28615534-28615588	Hela-S3	cervix:	n/a	n/a
25	NFYB	chr5:28615419-28615619	Hela-S3	cervix:	n/a	n/a
26	NR2F2	chr5:28596356-28596745	K562	blood:	n/a	n/a
27	POLR2A	chr5:28606286-28606327	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr5:28626235-28626567	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr5:28612708-28612926	A549	lung:	n/a	n/a
30	POLR2A	chr5:28612557-28612903	MCF-7	breast:	n/a	n/a
31	POLR2A	chr5:28607996-28608196	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr5:28599730-28599778	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr5:28612748-28612760	Gliobla	brain:	n/a	n/a
34	POLR2A	chr5:28604774-28604917	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr5:28612765-28612866	Gliobla	brain:	n/a	n/a
36	POLR2A	chr5:28612929-28612951	Gliobla	brain:	n/a	n/a
37	RAD21	chr5:28601191-28601222	A549	lung:	n/a	n/a
38	STAT3	chr5:28615344-28615419	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr5:28608574-28608608	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF7L2	chr5:28615617-28615849	HepG2	liver:	n/a	n/a
41	ZNF274	chr5:28615560-28616332	K562	blood:	n/a	n/a
42	ZNF274	chr5:28618123-28618423	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:28596874-28596924	GM12891	blood:	n/a
2	chr5:28596874-28596924	PANC-1	pancreas:	n/a
3	chr5:28596874-28596924	HEEpiC	esophagus:	n/a
4	chr5:28596874-28596924	HL-60	blood:	n/a
5	chr5:28596874-28596924	HMEC	breast:	n/a
6	chr5:28596874-28596924	AG04450	lung:	fetal
7	chr5:28596874-28596924	SK-N-SH_RA	brain:	n/a
8	chr5:28596874-28596924	HEK293	kidney:	embryo
9	chr5:28596874-28596924	HIPEpiC	eye:	n/a
10	chr5:28596874-28596924	GM12878	blood:	n/a
11	chr5:28596874-28596924	Hepatocyte	liver:	n/a
12	chr5:28596874-28596924	HCF	heart:	n/a
13	chr5:28596874-28596924	LNCaP	prostate:	n/a
14	chr5:28596874-28596924	HRPEpiC	eye:	n/a
15	chr5:28596874-28596924	RPTEC	kidney:	n/a
16	chr5:28596874-28596924	HNPCEpiC	eye:	n/a
17	chr5:28596874-28596924	HPAEpiC	pulmonary alveolar:	n/a
18	chr5:28596874-28596924	U87	brain:	n/a
19	chr5:28596874-28596924	ECC-1	luminal epithelium:	n/a
20	chr5:28596874-28596924	ProgFib	skin:	n/a
21	chr5:28596874-28596924	K562	blood:	n/a
22	chr5:28596874-28596924	SK-N-SH	brain:	n/a
23	chr5:28596874-28596924	AG10803	skin:	n/a
24	chr5:28596874-28596924	IMR90	lung:	fetal
25	chr5:28596874-28596924	PrEC	prostate:	n/a
26	chr5:28596874-28596924	ovcar-3	ovarian:	n/a
27	chr5:28596874-28596924	T-47D	breast:	n/a
28	chr5:28596874-28596924	H1-hESC	embryonic stem cell:	embryo
29	chr5:28596874-28596924	HAEpiC	amniotic membrane:	n/a
30	chr5:28596874-28596924	NHDF-neo	bronchial:	n/a
31	chr5:28596874-28596924	HCT-116	colon:	n/a
32	chr5:28596874-28596924	AG09309	skin:	n/a
33	chr5:28596874-28596924	Caco-2	colon:	n/a
34	chr5:28596874-28596924	A549	lung:	n/a
35	chr5:28596874-28596924	AG09319	gingival:	n/a
36	chr5:28596874-28596924	MCF-7	breast:	n/a
37	chr5:28596874-28596924	NH-A	brain:	n/a
38	chr5:28596874-28596924	GM06990	blood:	n/a
39	chr5:28596874-28596924	SK-N-MC	brain:	n/a
40	chr5:28596874-28596924	BE2_C	brain:	n/a
41	chr5:28596874-28596924	MCF10A-Er-Src	breast:	n/a
42	chr5:28596874-28596924	Jurkat	blood:	n/a
43	chr5:28596874-28596924	HRE	kidney:	n/a
44	chr5:28596874-28596924	Hela-S3	cervix:	n/a
45	chr5:28596874-28596924	HCPEpiC	choroid plexus:	n/a
46	chr5:28596874-28596924	HRCEpiC	kidney:	n/a
47	chr5:28596874-28596924	NB4	blood:	n/a
48	chr5:28596874-28596924	CMK	blood:	n/a
49	chr5:28596874-28596924	SAEC	small airway:	n/a
50	chr5:28596874-28596924	BJ	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:28607591..28610399-chr5:28611364..28613106,2	K562	blood:
2	chr5:28607591..28610399-chr5:28611364..28613106,2	K562	blood:
3	chr5:28622865..28624500-chr5:28625376..28628306,2	MCF-7	breast:
4	chr5:28622865..28624500-chr5:28625376..28628306,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDH9-11	chr5:28625400-28625629	NONHSAT100819
2	lnc-CDH9-11	chr5:28629932-28630057	NONHSAT100819
3	lnc-CDH6-18	chr5:28602704-28602803	NONHSAT100815
4	lnc-CDH6-17	chr5:28603723-28604954	NONHSAT100817
5	lnc-CDH6-18	chr5:28602704-28602704	FPKM1_group_25126_transcript_1

No data

Variant related genes	Relation type
RNU6-909P	TF binding region
RNU6-909P	CpG island

Extended variants
information (count: 188 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:188 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564479257	chr5:28602704-28602705	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs537716347	chr5:28602715-28602716	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs546617015	chr5:28602745-28602746	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs187312499	chr5:28602751-28602752	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs529383789	chr5:28602785-28602786	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs368603539	chr5:28602795-28602796	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs566736246	chr5:28603734-28603735	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs534099982	chr5:28603774-28603775	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs10472137	chr5:28603791-28603792	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs567162470	chr5:28603794-28603795	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs548293004	chr5:28603819-28603820	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs568436949	chr5:28603845-28603846	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs557457042	chr5:28603853-28603854	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs191428760	chr5:28603854-28603855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs200860455	chr5:28603856-28603857	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs577696350	chr5:28603857-28603858	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs539631261	chr5:28603933-28603934	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs557945991	chr5:28603938-28603939	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs143673327	chr5:28604022-28604023	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs573172030	chr5:28604074-28604075	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs540534179	chr5:28604112-28604113	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs562444500	chr5:28604151-28604152	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs12655653	chr5:28604170-28604171	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs138289268	chr5:28604181-28604182	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs562824432	chr5:28604228-28604229	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs533478835	chr5:28604246-28604247	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs112296652	chr5:28604263-28604264	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs551571028	chr5:28604324-28604325	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs560388828	chr5:28604328-28604329	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs116460599	chr5:28604349-28604350	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs570818023	chr5:28604351-28604352	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs185571577	chr5:28604367-28604368	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs188835881	chr5:28604387-28604388	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs146884847	chr5:28604398-28604399	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs537422862	chr5:28604533-28604534	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs549783393	chr5:28604555-28604556	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs571220825	chr5:28604576-28604577	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs117727483	chr5:28604602-28604603	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs557890272	chr5:28604641-28604642	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs372442183	chr5:28604653-28604654	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs566712958	chr5:28604664-28604665	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs193076238	chr5:28604800-28604801	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs185274887	chr5:28604830-28604831	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs549229797	chr5:28604878-28604879	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs77178243	chr5:28604885-28604886	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs574308645	chr5:28604953-28604954	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs62359328	chr5:28612612-28612613	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs144646577	chr5:28612613-28612614	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs4449545	chr5:28612667-28612668	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs564604509	chr5:28612686-28612687	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Salivary gland tumor	18059337	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Kartagener syndrome	16639409	CNVD
Medulloblastoma	21979893	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Non-small cell lung cancer	20864512	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Multiple myeloma	17550852	CNVD
prenatal diagnosis	22389664	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Cancer	16751803	CNVD
Breast cancer	16608533	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Intellectual disability	22102821	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18194544	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Non-small cell lung cancer	19010865	CNVD
Glioblastoma multiforme	22286061	CNVD
Compulsive disorder	18923513	CNVD
Epilepsy	18923513	CNVD
Prader-willi syndrome	18923513	CNVD
small cell lung cancer	20016488	CNVD
Ovarian cancer	21720365	CNVD
Lung cancer	18438408	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21364760	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28612600-28613000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:28624600-28626600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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