Variant report

Variant	nsv880732
Chromosome Location	chr5:29397044-29461973
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	ATF1	chr5:29431656-29431817	K562	blood:	n/a	n/a
2	ATF1	chr5:29425063-29425178	K562	blood:	n/a	n/a
3	ATF1	chr5:29425986-29425989	K562	blood:	n/a	n/a
4	BACH1	chr5:29433080-29433172	K562	blood:	n/a	n/a
5	CEBPB	chr5:29459773-29459805	K562	blood:	n/a	n/a
6	CEBPB	chr5:29433473-29433683	K562	blood:	n/a	chr5:29433543-29433554 chr5:29433541-29433552
7	CEBPB	chr5:29433374-29433733	IMR90	lung:	n/a	chr5:29433543-29433554 chr5:29433541-29433552
8	CEBPB	chr5:29413274-29413380	A549	lung:	n/a	chr5:29413367-29413380 chr5:29413367-29413378
9	CEBPB	chr5:29425611-29425821	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr5:29424882-29425230	A549	lung:	n/a	chr5:29425044-29425055
11	CEBPB	chr5:29414090-29414343	K562	blood:	n/a	n/a
12	CEBPB	chr5:29424874-29425236	HepG2	liver:	n/a	chr5:29425044-29425055
13	CEBPB	chr5:29433358-29433700	HepG2	liver:	n/a	chr5:29433543-29433554 chr5:29433541-29433552
14	CHD2	chr5:29432942-29433044	K562	blood:	n/a	n/a
15	CTCF	chr5:29409126-29409166	Spleen_OC	spleen:	n/a	n/a
16	CTCF	chr5:29444410-29444477	GM10248	blood:	n/a	n/a
17	CTCF	chr5:29433060-29433210	AG10803	skin:	n/a	n/a
18	CTCF	chr5:29436124-29436217	Kidney_OC	kidney:	n/a	n/a
19	CTCF	chr5:29418998-29419090	GM13976	blood:	n/a	n/a
20	CTCF	chr5:29436800-29436950	GM06990	blood:	n/a	n/a
21	CTCF	chr5:29397806-29397832	GM20000	blood:	n/a	n/a
22	CTCF	chr5:29430620-29430770	AG10803	skin:	n/a	n/a
23	CTCF	chr5:29449131-29449185	GM13976	blood:	n/a	n/a
24	CTCF	chr5:29449645-29449703	ProgFib	skin:	n/a	n/a
25	CTCF	chr5:29422074-29422156	GM13976	blood:	n/a	n/a
26	CTCF	chr5:29432240-29432390	NHDF-neo	bronchial:	n/a	n/a
27	CTCF	chr5:29430100-29430250	AG10803	skin:	n/a	n/a
28	CUX1	chr5:29433555-29433729	K562	blood:	n/a	n/a
29	CUX1	chr5:29426609-29426621	GM12878	blood:	n/a	n/a
30	E2F4	chr5:29418923-29419123	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr5:29429967-29430903	MCF10A-Er-Src	breast:	n/a	n/a
32	EBF1	chr5:29405141-29405158	GM12878	blood:	n/a	n/a
33	EP300	chr5:29457823-29457902	GM12878	blood:	n/a	n/a
34	EP300	chr5:29425549-29425778	GM12878	blood:	n/a	chr5:29425712-29425719
35	FAM48A	chr5:29460747-29460813	GM12878	blood:	n/a	n/a
36	FOSL2	chr5:29438689-29439069	HepG2	liver:	n/a	n/a
37	FOSL2	chr5:29438680-29439108	HepG2	liver:	n/a	n/a
38	FOSL2	chr5:29437606-29437807	HepG2	liver:	n/a	n/a
39	FOXA1	chr5:29435995-29436288	HepG2	liver:	n/a	n/a
40	GATA3	chr5:29408144-29408514	MCF-7	breast:	n/a	n/a
41	GATA3	chr5:29427733-29428172	SH-SY5Y	brain:	n/a	n/a
42	IKZF1	chr5:29433704-29433874	GM12878	blood:	n/a	n/a
43	IRF3	chr5:29410293-29410368	GM12878	blood:	n/a	n/a
44	JUND	chr5:29438790-29438988	HepG2	liver:	n/a	chr5:29438943-29438954
45	JUND	chr5:29438844-29438997	HepG2	liver:	n/a	chr5:29438943-29438954
46	JUND	chr5:29438775-29439000	HepG2	liver:	n/a	chr5:29438943-29438954
47	KAP1	chr5:29415207-29415300	K562	blood:	n/a	n/a
48	KAP1	chr5:29398679-29399057	K562	blood:	n/a	n/a
49	MAFF	chr5:29433064-29433121	K562	blood:	n/a	n/a
50	MAFF	chr5:29402428-29402706	HepG2	liver:	n/a	chr5:29402572-29402590

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:29394432..29396496-chr5:29400311..29402057,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DROSHA-12	chr5:29425675-29425803	l_2897_chr5:29390052-29431912_testes
2	lnc-DROSHA-12	chr5:29431718-29431912	l_2897_chr5:29390052-29431912_testes
3	lnc-DROSHA-12	chr5:29399178-29399246	l_2897_chr5:29390052-29431912_testes
4	lnc-DROSHA-12	chr5:29415951-29416189	l_2897_chr5:29390052-29431912_testes
5	lnc-DROSHA-12	chr5:29417717-29417826	l_2897_chr5:29390052-29431912_testes
6	lnc-DROSHA-12	chr5:29420161-29420256	l_2897_chr5:29390052-29431912_testes

Variant related genes	Relation type
ENSG00000248391	TF binding region
ENSG00000248391	chromatin interactions

Extended variants
information (count: 565 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:565 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547847246	chr5:29397242-29397243	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs569635155	chr5:29397246-29397247	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs538113292	chr5:29397248-29397249	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs189839023	chr5:29397295-29397296	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs537085164	chr5:29397319-29397320	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs181540638	chr5:29397391-29397392	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs79925868	chr5:29397395-29397396	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs12653215	chr5:29397409-29397410	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs201956294	chr5:29397437-29397438	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs111716786	chr5:29397456-29397457	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs576305689	chr5:29397471-29397472	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs553982348	chr5:29397481-29397482	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs572175388	chr5:29397527-29397528	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs2877057	chr5:29397534-29397535	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs554622843	chr5:29397563-29397564	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs143300255	chr5:29397575-29397576	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs144821045	chr5:29397596-29397597	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs529766509	chr5:29397807-29397808	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs78490648	chr5:29398750-29398751	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs553298177	chr5:29398807-29398808	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs548359653	chr5:29398888-29398889	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs541988701	chr5:29398937-29398938	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs57660613	chr5:29398975-29398976	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs563350878	chr5:29398978-29398979	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs568243843	chr5:29399004-29399005	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs545586156	chr5:29399186-29399187	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs192355790	chr5:29399188-29399189	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs550738520	chr5:29399234-29399235	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs528069751	chr5:29399238-29399239	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs572334331	chr5:29399547-29399548	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs561545708	chr5:29399902-29399903	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs530371858	chr5:29399905-29399906	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs569370373	chr5:29399916-29399917	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs543516457	chr5:29400053-29400054	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs556968061	chr5:29400344-29400345	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs569182292	chr5:29400386-29400387	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs207465855	chr5:29400474-29400475	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs74738296	chr5:29400527-29400528	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs187305573	chr5:29400546-29400547	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs572570210	chr5:29400561-29400562	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs146434556	chr5:29400616-29400617	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs139051449	chr5:29400636-29400637	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs555301835	chr5:29400663-29400664	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs141399085	chr5:29400672-29400673	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs150484093	chr5:29400697-29400698	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs138305497	chr5:29400720-29400721	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs531264212	chr5:29400747-29400748	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs546382508	chr5:29400755-29400756	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs564689156	chr5:29400816-29400817	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs371123645	chr5:29400825-29400826	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
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
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
Chronic lymphocytic leukemia	21546498	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
Breast cancer	20409316	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	19553991	CNVD
Lung cancer	19553991	CNVD
Melanoma	19553991	CNVD
Ovarian cancer	19553991	CNVD
Prostate cancer	19553991	CNVD
Non-small cell lung cancer	17156491	CNVD
Breast cancer	17133270	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29408200-29408400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:29408400-29410800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:29410800-29411200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:29417600-29418000	Enhancers	Fetal Brain Male	brain
5	chr5:29417600-29418000	Enhancers	Psoas Muscle	Psoas
6	chr5:29429200-29429400	ZNF genes & repeats	Pancreas	Pancrea
7	chr5:29433000-29433200	Enhancers	Aorta	Aorta
8	chr5:29450400-29450800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:29456800-29461400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:29461200-29461600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:29461200-29461600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr5:29461400-29461800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:29461600-29462800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:29461800-29467000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links