Variant report

Variant	nsv520875
Chromosome Location	chr3:139648326-139649663
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:139648920-139649315	T-47D	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139649460-139649510	GM06990	blood:	n/a
2	chr3:139649460-139649510	GM12891	blood:	n/a
3	chr3:139649460-139649510	HNPCEpiC	eye:	n/a
4	chr3:139649460-139649510	AG09319	gingival:	n/a
5	chr3:139649460-139649510	SK-N-SH_RA	brain:	n/a
6	chr3:139649460-139649510	PrEC	prostate:	n/a
7	chr3:139649460-139649510	HEK293	kidney:	embryo
8	chr3:139649460-139649510	RPTEC	kidney:	n/a
9	chr3:139649460-139649510	LNCaP	prostate:	n/a
10	chr3:139649460-139649510	Hela-S3	cervix:	n/a
11	chr3:139649460-139649510	T-47D	breast:	n/a
12	chr3:139649460-139649510	NHBE	bronchial:	n/a
13	chr3:139649460-139649510	Hepatocyte	liver:	n/a
14	chr3:139649460-139649510	HPAEpiC	pulmonary alveolar:	n/a
15	chr3:139649460-139649510	K562	blood:	n/a
16	chr3:139649460-139649510	SKMC	muscle:	n/a
17	chr3:139649460-139649510	HCM	heart:	n/a
18	chr3:139649460-139649510	HRCEpiC	kidney:	n/a
19	chr3:139649460-139649510	NHDF-neo	bronchial:	n/a
20	chr3:139649460-139649510	NT2-D1	testis:	n/a
21	chr3:139649460-139649510	AG09309	skin:	n/a
22	chr3:139649460-139649510	A549	lung:	n/a
23	chr3:139649460-139649510	U87	brain:	n/a
24	chr3:139649460-139649510	ProgFib	skin:	n/a
25	chr3:139649460-139649510	HMEC	breast:	n/a
26	chr3:139649460-139649510	ECC-1	luminal epithelium:	n/a
27	chr3:139649460-139649510	SK-N-MC	brain:	n/a
28	chr3:139649460-139649510	BE2_C	brain:	n/a
29	chr3:139649460-139649510	CMK	blood:	n/a
30	chr3:139649460-139649510	NB4	blood:	n/a
31	chr3:139649460-139649510	SK-N-SH	brain:	n/a
32	chr3:139649460-139649510	AG10803	skin:	n/a
33	chr3:139649460-139649510	PANC-1	pancreas:	n/a
34	chr3:139649460-139649510	HCF	heart:	n/a
35	chr3:139649460-139649510	MCF10A-Er-Src	breast:	n/a
36	chr3:139649460-139649510	HRE	kidney:	n/a
37	chr3:139649460-139649510	H1-hESC	embryonic stem cell:	embryo
38	chr3:139649460-139649510	MCF-7	breast:	n/a
39	chr3:139649460-139649510	PFSK-1	brain:	n/a
40	chr3:139649460-139649510	AG04450	lung:	fetal
41	chr3:139649460-139649510	AG04449	skin:	fetal
42	chr3:139649460-139649510	IMR90	lung:	fetal
43	chr3:139649460-139649510	GM12892	blood:	n/a
44	chr3:139649460-139649510	ovcar-3	ovarian:	n/a
45	chr3:139649460-139649510	AoSMC	blood vessel:	n/a
46	chr3:139649460-139649510	HCPEpiC	choroid plexus:	n/a
47	chr3:139649460-139649510	GM19239	blood:	n/a
48	chr3:139649460-139649510	BJ	skin:	n/a
49	chr3:139649460-139649510	Jurkat	blood:	n/a
50	chr3:139649460-139649510	SAEC	small airway:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139641405..139642937-chr3:139647406..139649250,2	K562	blood:
2	chr3:139645968..139647481-chr3:139648116..139649820,2	MCF-7	breast:
3	chr3:139646808..139649286-chr3:139653164..139655013,2	MCF-7	breast:

No data

Variant related genes	Relation type
CLSTN2	TF binding region
CLSTN2	CpG island
ENSG00000158258	chromatin interactions

Extended variants
information (count: 67 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:67 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs727763	chr3:139648326-139648327	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs535033985	chr3:139648357-139648358	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs555240127	chr3:139648383-139648384	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs144318473	chr3:139648409-139648410	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs76609731	chr3:139648452-139648453	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs183208709	chr3:139648458-139648459	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs188562836	chr3:139648469-139648470	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs116953478	chr3:139648490-139648491	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs192966589	chr3:139648525-139648526	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs559523681	chr3:139648562-139648563	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs115607065	chr3:139648565-139648566	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs733775	chr3:139648588-139648589	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs78499040	chr3:139648621-139648622	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs530775767	chr3:139648625-139648626	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs74963861	chr3:139648630-139648631	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs192499901	chr3:139648698-139648699	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs533094186	chr3:139648707-139648708	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs733774	chr3:139648716-139648717	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs140824868	chr3:139648732-139648733	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs538101713	chr3:139648764-139648765	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs555024548	chr3:139648825-139648826	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs147468938	chr3:139648865-139648866	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs9869519	chr3:139648874-139648875	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs557150527	chr3:139648875-139648876	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs9850110	chr3:139648953-139648954	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs56370145	chr3:139648965-139648966	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs553431345	chr3:139648981-139648982	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs78588480	chr3:139648996-139648997	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs542209030	chr3:139649011-139649012	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs9850149	chr3:139649029-139649030	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs530839816	chr3:139649038-139649039	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs544501700	chr3:139649051-139649052	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs183484216	chr3:139649067-139649068	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs533146984	chr3:139649090-139649091	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs546417819	chr3:139649096-139649097	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs189365354	chr3:139649101-139649102	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs531344143	chr3:139649127-139649128	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs181221681	chr3:139649138-139649139	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs544845821	chr3:139649167-139649168	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs530592018	chr3:139649196-139649197	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs568480114	chr3:139649206-139649207	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs116373441	chr3:139649221-139649222	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs550843025	chr3:139649236-139649237	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs570759083	chr3:139649240-139649241	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs533564325	chr3:139649242-139649243	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs540031759	chr3:139649253-139649254	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs553242423	chr3:139649257-139649258	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs573305775	chr3:139649258-139649259	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs13085522	chr3:139649297-139649298	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs58306556	chr3:139649326-139649327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139642800-139651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:139647600-139649200	Enhancers	Ovary	ovary
3	chr3:139647800-139648800	Weak transcription	HMEC	breast
4	chr3:139648000-139649600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:139648800-139649600	Enhancers	HMEC	breast
6	chr3:139649600-139653400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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