Variant report

Variant	esv3470440
Chromosome Location	chr5:37254506-37257876
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	chr5:37257505-37257605	GM13976	blood:	n/a	n/a
2	FOXA1	chr5:37254773-37255113	T-47D	breast:	n/a	n/a
3	FOXA1	chr5:37256145-37256412	HepG2	liver:	n/a	n/a
4	GATA3	chr5:37254677-37255160	T-47D	breast:	n/a	chr5:37254978-37254986
5	GATA3	chr5:37254641-37255333	MCF-7	breast:	n/a	chr5:37254978-37254986
6	GATA3	chr5:37254748-37255206	MCF-7	breast:	n/a	chr5:37254978-37254986
7	GATA3	chr5:37254785-37255197	MCF-7	breast:	n/a	chr5:37254978-37254986
8	GATA3	chr5:37254674-37255174	T-47D	breast:	n/a	chr5:37254978-37254986
9	JUN	chr5:37256337-37256347	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr5:37256350-37256439	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr5:37254907-37255111	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37248443..37250196-chr5:37254645..37256658,2	MCF-7	breast:
2	chr5:37248340..37251803-chr5:37254807..37257992,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR70-5	chr5:37254685-37254730	NONHSAT101057

Variant related genes	Relation type
C5orf42	TF binding region
ENSG00000197603	chromatin interactions

Extended variants
information (count: 123 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:123 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs60031919	chr5:37254522-37254523	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs369040410	chr5:37254588-37254589	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs564563250	chr5:37254609-37254610	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs140882344	chr5:37254625-37254626	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs377106642	chr5:37254694-37254695	Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs28609469	chr5:37254744-37254745	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs529792695	chr5:37254747-37254748	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs186669119	chr5:37254895-37254896	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs540483764	chr5:37254964-37254965	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs150177242	chr5:37254980-37254981	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs534094304	chr5:37255042-37255043	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs558863039	chr5:37255050-37255051	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs570737082	chr5:37255112-37255113	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs576885068	chr5:37255130-37255131	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs144418338	chr5:37255145-37255146	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs537885961	chr5:37255149-37255150	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs376636661	chr5:37255199-37255200	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs34303545	chr5:37255225-37255226	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs556509210	chr5:37255274-37255275	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs369582524	chr5:37255290-37255291	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs371375786	chr5:37255303-37255304	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs12516313	chr5:37255309-37255310	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs542261160	chr5:37255312-37255313	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs373251680	chr5:37255313-37255314	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs10043784	chr5:37255322-37255323	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs141281554	chr5:37255332-37255333	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs572280006	chr5:37255333-37255334	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs112535794	chr5:37255350-37255351	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs192633706	chr5:37255360-37255361	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs564477301	chr5:37255363-37255364	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs532024738	chr5:37255401-37255402	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs543918781	chr5:37255415-37255416	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs371156757	chr5:37255425-37255426	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs377636059	chr5:37255430-37255431	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs137976774	chr5:37255432-37255433	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs548272262	chr5:37255450-37255451	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs184523605	chr5:37255462-37255463	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs566692912	chr5:37255489-37255490	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs527509937	chr5:37255491-37255492	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs371365038	chr5:37255503-37255504	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs190636737	chr5:37255507-37255508	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs193102300	chr5:37255508-37255509	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs149492771	chr5:37255534-37255535	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs559387518	chr5:37255571-37255572	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs115389385	chr5:37255630-37255631	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs375523518	chr5:37255693-37255694	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs568400009	chr5:37255710-37255711	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs535600044	chr5:37255715-37255716	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs528220698	chr5:37255757-37255758	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs143015058	chr5:37255797-37255798	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:98)

Disease	PMID	Source
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
Medulloblastoma	21979893	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
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	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
Non-small cell lung cancer	19010865	CNVD
Glioblastoma multiforme	22286061	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
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
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Acute lymphoblastic leukemia	17640729	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Lung cancer	19153074	CNVD
Cornelia de Lange syndrome	21085971	CNVD
Autism	21701786	CNVD
Cervical cancer	16585170	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37250200-37257200	Weak transcription	Psoas Muscle	Psoas
2	chr5:37250200-37260000	Weak transcription	Brain Anterior Caudate	brain
3	chr5:37250400-37256600	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:37250400-37257400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:37250400-37264200	Weak transcription	Brain Substantia Nigra	brain
6	chr5:37254200-37254800	ZNF genes & repeats	Hela-S3	cervix
7	chr5:37254200-37255000	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr5:37254800-37263400	Weak transcription	Hela-S3	cervix
9	chr5:37255000-37260000	Weak transcription	Left Ventricle	heart
10	chr5:37255000-37261800	Weak transcription	Fetal Intestine Small	intestine
11	chr5:37256000-37256400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links