Variant report

Variant	esv1829356
Chromosome Location	chr3:20524946-20575986
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:283)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:20553373-20553610	HepG2	liver:	n/a	n/a
2	BACH1	chr3:20536253-20536368	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr3:20535546-20535645	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr3:20568523-20568549	K562	blood:	n/a	n/a
5	CEBPB	chr3:20551895-20552228	HepG2	liver:	n/a	n/a
6	CTCF	chr3:20529700-20529850	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr3:20553305-20553599	Lung_OC	lung:	n/a	n/a
8	CTCF	chr3:20553320-20553470	HL-60	blood:	n/a	n/a
9	CTCF	chr3:20553420-20553570	GM12867	blood:	n/a	n/a
10	CTCF	chr3:20553400-20553550	HRE	kidney:	n/a	n/a
11	CTCF	chr3:20553345-20553587	K562	blood:	n/a	n/a
12	CTCF	chr3:20553340-20553490	BE2_C	brain:	n/a	n/a
13	CTCF	chr3:20553400-20553550	GM12864	blood:	n/a	n/a
14	CTCF	chr3:20553396-20553533	GM19240	blood:	n/a	n/a
15	CTCF	chr3:20553380-20553530	SAEC	small airway:	n/a	n/a
16	CTCF	chr3:20553180-20553330	A549	lung:	n/a	n/a
17	CTCF	chr3:20553355-20553563	Fibrobl	skin:	n/a	n/a
18	CTCF	chr3:20553356-20553578	Spleen_OC	spleen:	n/a	n/a
19	CTCF	chr3:20553400-20553550	HMEC	breast:	n/a	n/a
20	CTCF	chr3:20553343-20553579	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr3:20553320-20553470	NHLF	lung:	n/a	n/a
22	CTCF	chr3:20553279-20553571	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr3:20553360-20553510	GM12872	blood:	n/a	n/a
24	CTCF	chr3:20553400-20553550	GM12878	blood:	n/a	n/a
25	CTCF	chr3:20553400-20553550	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:20553380-20553530	HCPEpiC	choroid plexus:	n/a	n/a
27	CTCF	chr3:20553380-20553530	HBMEC	blood vessel:	n/a	n/a
28	CTCF	chr3:20553332-20553561	GM20000	blood:	n/a	n/a
29	CTCF	chr3:20553420-20553570	GM12875	blood:	n/a	n/a
30	CTCF	chr3:20553341-20553574	HepG2	liver:	n/a	n/a
31	CTCF	chr3:20553342-20553583	ProgFib	skin:	n/a	n/a
32	CTCF	chr3:20553440-20553590	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:20553380-20553530	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr3:20553347-20553574	MCF-7	breast:	n/a	n/a
35	CTCF	chr3:20553354-20553584	Pancreas_OC	pancreas:	n/a	n/a
36	CTCF	chr3:20553400-20553550	AG04449	skin:	n/a	n/a
37	CTCF	chr3:20553738-20553767	GM19238	blood:	n/a	n/a
38	CTCF	chr3:20553380-20553530	AG09309	skin:	n/a	n/a
39	CTCF	chr3:20553280-20553566	A549	lung:	n/a	n/a
40	CTCF	chr3:20553380-20553530	GM12869	blood:	n/a	n/a
41	CTCF	chr3:20553344-20553570	HepG2	liver:	n/a	n/a
42	CTCF	chr3:20553420-20553570	HepG2	liver:	n/a	n/a
43	CTCF	chr3:20553360-20553510	GM12871	blood:	n/a	n/a
44	CTCF	chr3:20546240-20546390	WERI-Rb-1	eye:	n/a	n/a
45	CTCF	chr3:20529700-20529850	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr3:20553319-20553622	Gliobla	brain:	n/a	n/a
47	CTCF	chr3:20553379-20553547	GM19239	blood:	n/a	n/a
48	CTCF	chr3:20553331-20553588	LNCaP	prostate:	n/a	n/a
49	CTCF	chr3:20553346-20553629	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr3:20553380-20553530	GM12865	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20575513-20575563	SK-N-SH	brain:	n/a
2	chr3:20575513-20575563	AG04449	skin:	fetal
3	chr3:20575513-20575563	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:20575513-20575563	HepG2	liver:	n/a
5	chr3:20575513-20575563	ECC-1	luminal epithelium:	n/a
6	chr3:20575513-20575563	GM12878	blood:	n/a
7	chr3:20575513-20575563	U87	brain:	n/a
8	chr3:20575513-20575563	SK-N-SH_RA	brain:	n/a
9	chr3:20575513-20575563	NT2-D1	testis:	n/a
10	chr3:20575513-20575563	SK-N-MC	brain:	n/a
11	chr3:20575513-20575563	HEK293	kidney:	embryo
12	chr3:20575513-20575563	Hela-S3	cervix:	n/a
13	chr3:20575513-20575563	NHBE	bronchial:	n/a
14	chr3:20575513-20575563	PANC-1	pancreas:	n/a
15	chr3:20575513-20575563	H1-hESC	embryonic stem cell:	embryo
16	chr3:20575513-20575563	ProgFib	skin:	n/a
17	chr3:20575513-20575563	NH-A	brain:	n/a
18	chr3:20575513-20575563	GM12892	blood:	n/a
19	chr3:20575513-20575563	AG09309	skin:	n/a
20	chr3:20575513-20575563	Jurkat	blood:	n/a
21	chr3:20575513-20575563	GM06990	blood:	n/a
22	chr3:20575513-20575563	PrEC	prostate:	n/a
23	chr3:20575513-20575563	BE2_C	brain:	n/a
24	chr3:20575513-20575563	HAEpiC	amniotic membrane:	n/a
25	chr3:20575513-20575563	HL-60	blood:	n/a
26	chr3:20575513-20575563	LNCaP	prostate:	n/a
27	chr3:20575513-20575563	GM19239	blood:	n/a
28	chr3:20575513-20575563	HRE	kidney:	n/a
29	chr3:20575513-20575563	AoSMC	blood vessel:	n/a
30	chr3:20575513-20575563	Hepatocyte	liver:	n/a
31	chr3:20575513-20575563	HEEpiC	esophagus:	n/a
32	chr3:20575513-20575563	HCF	heart:	n/a
33	chr3:20575513-20575563	SAEC	small airway:	n/a
34	chr3:20575513-20575563	AG10803	skin:	n/a
35	chr3:20575513-20575563	HMEC	breast:	n/a
36	chr3:20575513-20575563	CMK	blood:	n/a
37	chr3:20575513-20575563	NHDF-neo	bronchial:	n/a
38	chr3:20575513-20575563	HUVEC	blood vessel:	n/a
39	chr3:20575513-20575563	HRCEpiC	kidney:	n/a
40	chr3:20575513-20575563	A549	lung:	n/a
41	chr3:20575513-20575563	IMR90	lung:	fetal
42	chr3:20575513-20575563	BJ	skin:	n/a
43	chr3:20575513-20575563	SKMC	muscle:	n/a
44	chr3:20575513-20575563	HCT-116	colon:	n/a
45	chr3:20575513-20575563	AG04450	lung:	fetal
46	chr3:20575513-20575563	GM12891	blood:	n/a
47	chr3:20575513-20575563	MCF-7	breast:	n/a
48	chr3:20575513-20575563	Caco-2	colon:	n/a
49	chr3:20575513-20575563	HCM	heart:	n/a
50	chr3:20575513-20575563	HNPCEpiC	eye:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:20553254..20553852-chr3:21257816..21258713,2	MCF-7	breast:
2	chr3:20558136..20559640-chr3:20560230..20563085,2	K562	blood:
3	chr3:20545213..20547317-chr3:20547570..20549760,2	K562	blood:
4	chr3:20558136..20559640-chr3:20560230..20563085,2	K562	blood:
5	chr3:20553366..20553898-chr3:21257700..21258348,2	MCF-7	breast:
6	chr3:20553071..20554107-chr3:20781207..20782086,3	MCF-7	breast:
7	chr3:20552973..20553911-chr3:20970672..20972125,8	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-815P	TF binding region
RNU6-815P	CpG island
ENSG00000206807	chromatin interactions

Extended variants
information (count: 1054 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:1054 , 50 per page) page: 1 2 3 4 5 6 7 ... 22

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9968234	chr3:20524946-20524947	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs552194885	chr3:20525000-20525001	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs186227151	chr3:20525008-20525009	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs116514779	chr3:20525009-20525010	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs546591404	chr3:20525057-20525058	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs115957985	chr3:20525125-20525126	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs9968243	chr3:20525177-20525178	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs556696655	chr3:20525235-20525236	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs569049422	chr3:20525255-20525256	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs544308642	chr3:20525258-20525259	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs539526250	chr3:20525267-20525268	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs546048008	chr3:20525274-20525275	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs150213969	chr3:20525275-20525276	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs191427313	chr3:20525292-20525293	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs573172369	chr3:20525302-20525303	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs181494892	chr3:20525336-20525337	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs138741768	chr3:20525345-20525346	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs114435737	chr3:20525346-20525347	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs371118405	chr3:20525361-20525362	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs562842598	chr3:20528881-20528882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs541464333	chr3:20528918-20528919	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs115762590	chr3:20528922-20528923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs530363342	chr3:20528939-20528940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs548489570	chr3:20529014-20529015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs563609342	chr3:20529050-20529051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs531010471	chr3:20529062-20529063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs189204065	chr3:20529105-20529106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs571357442	chr3:20529153-20529154	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs139767499	chr3:20529180-20529181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs547396046	chr3:20529204-20529205	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs565663354	chr3:20529224-20529225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs536219778	chr3:20529374-20529375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs181649556	chr3:20529439-20529440	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs569925480	chr3:20529450-20529451	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs77515953	chr3:20529461-20529462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs568638067	chr3:20529479-20529480	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs545215458	chr3:20529497-20529498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs558471139	chr3:20529510-20529511	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs564916354	chr3:20529515-20529516	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs1506051	chr3:20529538-20529539	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs541152482	chr3:20529544-20529545	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs9680942	chr3:20529624-20529625	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs1506052	chr3:20529661-20529662	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs76590858	chr3:20529662-20529663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs563646007	chr3:20529673-20529674	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs531100169	chr3:20529678-20529679	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs546422321	chr3:20529694-20529695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs564500386	chr3:20529713-20529714	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs150054764	chr3:20529716-20529717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs547190598	chr3:20529721-20529722	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20524200-20525400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:20528800-20536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:20529200-20529800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:20529800-20531000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:20531000-20532600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:20531400-20532600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:20531600-20533200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:20532400-20533000	Enhancers	HUVEC	blood vessel
9	chr3:20532600-20533000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:20533000-20533600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:20543600-20544000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:20551800-20553800	Enhancers	Liver	Liver
13	chr3:20552200-20552600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:20552200-20552800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:20552600-20553200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:20553600-20554000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:20553600-20554000	Enhancers	Left Ventricle	heart
18	chr3:20553600-20554000	Enhancers	Right Atrium	heart
19	chr3:20553600-20554000	Enhancers	NHDF-Ad	bronchial
20	chr3:20553600-20554400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:20553800-20554000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:20553800-20554000	Enhancers	Gastric	stomach
23	chr3:20553800-20557200	Weak transcription	Liver	Liver
24	chr3:20557200-20558200	Enhancers	Liver	Liver
25	chr3:20557400-20558000	Enhancers	Adipose Nuclei	Adipose
26	chr3:20559400-20569400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:20565000-20565400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:20565000-20565400	ZNF genes & repeats	Pancreas	Pancrea
29	chr3:20569000-20569800	Enhancers	Fetal Stomach	stomach
30	chr3:20569000-20571200	Enhancers	Fetal Intestine Small	intestine
31	chr3:20569200-20571200	Enhancers	Fetal Intestine Large	intestine
32	chr3:20569400-20569600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:20569600-20570000	Enhancers	Fetal Lung	lung
34	chr3:20569800-20570200	Weak transcription	Fetal Stomach	stomach
35	chr3:20570000-20570400	Weak transcription	Fetal Lung	lung
36	chr3:20570200-20571000	Enhancers	Fetal Stomach	stomach
37	chr3:20570400-20571000	Enhancers	Fetal Lung	lung
38	chr3:20575800-20578600	Weak transcription	NHDF-Ad	bronchial

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