Variant report

Variant	nsv964826
Chromosome Location	chr5:28926717-28929071
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	CTCF	chr5:28928592-28928769	A549	lung:	n/a	n/a
2	CTCF	chr5:28928660-28928705	MCF-7	breast:	n/a	n/a
3	CTCF	chr5:28928560-28928710	A549	lung:	n/a	n/a
4	CTCF	chr5:28928662-28928724	H1-hESC	embryonic stem cell:	n/a	n/a
5	EBF1	chr5:28928088-28928281	GM12878	blood:	n/a	chr5:28928184-28928193 chr5:28928183-28928193
6	EBF1	chr5:28928375-28928544	GM12878	blood:	n/a	n/a
7	EBF1	chr5:28927876-28928367	GM12878	blood:	n/a	chr5:28928184-28928193 chr5:28928183-28928193
8	HA-E2F1	chr5:28927497-28928103	MCF-7	breast:	n/a	chr5:28927880-28927894 chr5:28927877-28927891 chr5:28927761-28927771
9	HEY1	chr5:28927895-28928152	K562	blood:	n/a	chr5:28927956-28927971
10	HEY1	chr5:28927602-28927767	K562	blood:	n/a	n/a
11	HEY1	chr5:28928153-28928454	K562	blood:	n/a	chr5:28928272-28928287 chr5:28928308-28928323 chr5:28928320-28928335
12	HEY1	chr5:28927884-28928355	K562	blood:	n/a	chr5:28928272-28928287 chr5:28927956-28927971 chr5:28928308-28928323 chr5:28928320-28928335
13	HEY1	chr5:28928211-28928329	HepG2	liver:	n/a	chr5:28928272-28928287 chr5:28928308-28928323
14	HEY1	chr5:28927875-28928461	HepG2	liver:	n/a	chr5:28928272-28928287 chr5:28927956-28927971 chr5:28928308-28928323 chr5:28928320-28928335
15	HEY1	chr5:28927911-28928039	HepG2	liver:	n/a	chr5:28927956-28927971
16	JUND	chr5:28928215-28928343	HepG2	liver:	n/a	n/a
17	MYC	chr5:28928846-28928959	MCF-7	breast:	n/a	n/a
18	POLR2A	chr5:28927736-28927927	A549	lung:	n/a	n/a
19	POLR2A	chr5:28927600-28928739	A549	lung:	n/a	n/a
20	POLR2A	chr5:28928399-28928545	A549	lung:	n/a	n/a
21	POLR2A	chr5:28928808-28928817	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:28927827-28928077	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:28927931-28928397	A549	lung:	n/a	n/a
24	POLR2A	chr5:28927834-28927918	ProgFib	skin:	n/a	n/a
25	POLR2A	chr5:28927801-28928021	K562	blood:	n/a	n/a
26	POLR2A	chr5:28927900-28928105	GM12891	blood:	n/a	n/a
27	POLR2A	chr5:28927653-28928056	A549	lung:	n/a	n/a
28	POLR2A	chr5:28927926-28928062	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:28927602-28927790	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr5:28927935-28928018	ProgFib	skin:	n/a	n/a
31	POLR2A	chr5:28927913-28928366	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:28927857-28928267	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:28927657-28928537	A549	lung:	n/a	n/a
34	POLR2A	chr5:28927514-28928461	GM12892	blood:	n/a	n/a
35	POLR2A	chr5:28927887-28928397	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:28928219-28928733	A549	lung:	n/a	n/a
37	POLR2A	chr5:28927607-28928684	A549	lung:	n/a	n/a
38	POLR2A	chr5:28927870-28928152	GM12891	blood:	n/a	n/a
39	POLR2A	chr5:28928221-28928358	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:28927784-28928317	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:28928155-28928200	A549	lung:	n/a	n/a
42	POLR2A	chr5:28928819-28928988	MCF-7	breast:	n/a	n/a
43	POLR2A	chr5:28928034-28928128	Gliobla	brain:	n/a	n/a
44	POLR2A	chr5:28927986-28928018	Gliobla	brain:	n/a	n/a
45	RXRA	chr5:28927915-28928298	HepG2	liver:	n/a	n/a
46	TCF12	chr5:28927907-28928330	GM12878	blood:	n/a	n/a
47	TCF3	chr5:28927876-28928365	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:28928346-28928396	GM12891	blood:	n/a
2	chr5:28926868-28926918	HCM	heart:	n/a
3	chr5:28928735-28928785	HAEpiC	amniotic membrane:	n/a
4	chr5:28927606-28927656	SAEC	small airway:	n/a
5	chr5:28926682-28926732	SK-N-SH_RA	brain:	n/a
6	chr5:28926868-28926918	AoSMC	blood vessel:	n/a
7	chr5:28926837-28926887	GM12891	blood:	n/a
8	chr5:28928735-28928785	HRCEpiC	kidney:	n/a
9	chr5:28926868-28926918	HPAEpiC	pulmonary alveolar:	n/a
10	chr5:28926682-28926732	HepG2	liver:	n/a
11	chr5:28928158-28928208	HRCEpiC	kidney:	n/a
12	chr5:28926682-28926732	PrEC	prostate:	n/a
13	chr5:28926682-28926732	Hepatocyte	liver:	n/a
14	chr5:28928346-28928396	SAEC	small airway:	n/a
15	chr5:28928735-28928785	HRPEpiC	eye:	n/a
16	chr5:28927606-28927656	NT2-D1	testis:	n/a
17	chr5:28926682-28926732	RPTEC	kidney:	n/a
18	chr5:28926837-28926887	BJ	skin:	n/a
19	chr5:28926837-28926887	NH-A	brain:	n/a
20	chr5:28926682-28926732	SKMC	muscle:	n/a
21	chr5:28928735-28928785	HCT-116	colon:	n/a
22	chr5:28926868-28926918	SKMC	muscle:	n/a
23	chr5:28928735-28928785	ovcar-3	ovarian:	n/a
24	chr5:28927606-28927656	HCT-116	colon:	n/a
25	chr5:28926682-28926732	HIPEpiC	eye:	n/a
26	chr5:28928735-28928785	SK-N-MC	brain:	n/a
27	chr5:28926837-28926887	AG09319	gingival:	n/a
28	chr5:28926868-28926918	SK-N-SH	brain:	n/a
29	chr5:28926682-28926732	Caco-2	colon:	n/a
30	chr5:28926837-28926887	HL-60	blood:	n/a
31	chr5:28928158-28928208	K562	blood:	n/a
32	chr5:28928735-28928785	PANC-1	pancreas:	n/a
33	chr5:28928346-28928396	SK-N-MC	brain:	n/a
34	chr5:28928735-28928785	RPTEC	kidney:	n/a
35	chr5:28926682-28926732	H1-hESC	embryonic stem cell:	embryo
36	chr5:28926868-28926918	SK-N-SH_RA	brain:	n/a
37	chr5:28928346-28928396	GM12878	blood:	n/a
38	chr5:28928158-28928208	NB4	blood:	n/a
39	chr5:28926868-28926918	MCF10A-Er-Src	breast:	n/a
40	chr5:28928158-28928208	HCT-116	colon:	n/a
41	chr5:28928346-28928396	MCF-7	breast:	n/a
42	chr5:28926868-28926918	HEK293	kidney:	embryo
43	chr5:28927606-28927656	GM12878	blood:	n/a
44	chr5:28926682-28926732	AG10803	skin:	n/a
45	chr5:28926682-28926732	HPAEpiC	pulmonary alveolar:	n/a
46	chr5:28928735-28928785	PFSK-1	brain:	n/a
47	chr5:28926682-28926732	NT2-D1	testis:	n/a
48	chr5:28928158-28928208	ProgFib	skin:	n/a
49	chr5:28926868-28926918	PrEC	prostate:	n/a
50	chr5:28928158-28928208	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
LSP1P3	TF binding region
ENSG00000226400	TF binding region
LSP1P3	CpG island
ENSG00000226400	CpG island

Extended variants
information (count: 139 )
Associated
traits (count: 96 )

Variant overlapped rSNPs/rCNVs (count:139 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs568938665	chr5:28926732-28926733	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
2	rs561777862	chr5:28926840-28926841	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
3	rs529333654	chr5:28926848-28926849	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
4	rs544342155	chr5:28926855-28926856	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
5	rs562702193	chr5:28926858-28926859	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
6	rs532938581	chr5:28926860-28926861	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
7	rs551562337	chr5:28926876-28926877	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
8	rs566627170	chr5:28926877-28926878	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
9	rs527612433	chr5:28926882-28926883	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
10	rs577262486	chr5:28926895-28926896	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
11	rs111410623	chr5:28926909-28926910	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
12	rs555937230	chr5:28927005-28927006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs76013254	chr5:28927028-28927029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571326536	chr5:28927029-28927030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs434405	chr5:28927036-28927037	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs558356151	chr5:28927082-28927083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs573181860	chr5:28927100-28927101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs411622	chr5:28927134-28927135	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs555333845	chr5:28927141-28927142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs375555523	chr5:28927142-28927143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs544598984	chr5:28927158-28927159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs562801905	chr5:28927160-28927161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs486473	chr5:28927163-28927164	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs545566597	chr5:28927164-28927165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs373645962	chr5:28927194-28927195	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs646799	chr5:28927195-28927196	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs655444	chr5:28927209-28927210	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs527573336	chr5:28927215-28927216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs73747105	chr5:28927224-28927225	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs561168760	chr5:28927225-28927226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs531289750	chr5:28927242-28927243	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs549762973	chr5:28927279-28927280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs369781330	chr5:28927318-28927319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs193273060	chr5:28927323-28927324	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs654985	chr5:28927327-28927328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs654983	chr5:28927329-28927330	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs139708340	chr5:28927350-28927351	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs534220706	chr5:28927377-28927378	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs573961	chr5:28927390-28927391	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs78020817	chr5:28927405-28927406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs537818046	chr5:28927414-28927415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556543728	chr5:28927450-28927451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs548992447	chr5:28927480-28927481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545524088	chr5:28927513-28927514	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs560384541	chr5:28927523-28927524	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs536485248	chr5:28927559-28927560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs115572812	chr5:28927579-28927580	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs537638515	chr5:28927583-28927584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs413031	chr5:28927598-28927599	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs542851454	chr5:28927619-28927620	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:96)

Disease	PMID	Source
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
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
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

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28927000-28929200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:28927600-28928400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:28927600-28928400	Active TSS	Fetal Brain Female	brain
4	chr5:28927600-28928600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:28927600-28928600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr5:28927600-28928600	Active TSS	NH-A	brain
7	chr5:28927600-28928800	Active TSS	A549	lung
8	chr5:28927800-28928400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
9	chr5:28927800-28928800	Active TSS	Primary hematopoietic stem cells	blood

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