Variant report

Variant	rs3733306
Chromosome Location	chr4:57843295-57843296
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr4:57842986-57845530	K562	blood:	n/a	n/a
2	POLR2A	chr4:57843148-57844199	MCF10A-Er-Src	breast:	n/a	n/a
3	CREB1	chr4:57842552-57844155	HepG2	liver:	n/a	n/a
4	TAF1	chr4:57842946-57844201	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr4:57843240-57843390	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr4:57843220-57843370	HCFaa	heart:	n/a	n/a
7	CHD2	chr4:57842839-57844138	HepG2	liver:	n/a	n/a
8	PML	chr4:57843213-57844137	K562	blood:	n/a	n/a
9	SMC3	chr4:57843140-57843304	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr4:57843025-57845454	GM19193	blood:	n/a	n/a
11	POLR2A	chr4:57842995-57844138	HepG2	liver:	n/a	n/a
12	MAZ	chr4:57842757-57844079	K562	blood:	n/a	n/a
13	MXI1	chr4:57843030-57844166	GM12878	blood:	n/a	n/a
14	CTCF	chr4:57843052-57844048	K562	blood:	n/a	n/a
15	TCF3	chr4:57843063-57843446	GM12878	blood:	n/a	n/a
16	MAX	chr4:57842636-57844048	K562	blood:	n/a	n/a
17	POLR2A	chr4:57843038-57843329	A549	lung:	n/a	n/a
18	CTCF	chr4:57843280-57843430	AG10803	skin:	n/a	n/a
19	ZEB1	chr4:57842826-57843560	GM12878	blood:	n/a	chr4:57843160-57843169
20	POLR2A	chr4:57842336-57844381	HepG2	liver:	n/a	n/a
21	BACH1	chr4:57842701-57844036	H1-hESC	embryonic stem cell:	n/a	n/a
22	RCOR1	chr4:57842559-57844013	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr4:57843260-57843410	GM12869	blood:	n/a	n/a
24	CTCF	chr4:57843200-57843350	HPAF	blood vessel:	n/a	n/a
25	MXI1	chr4:57842644-57844103	HepG2	liver:	n/a	n/a
26	SIN3A	chr4:57842653-57844100	H1-hESC	embryonic stem cell:	n/a	n/a
27	YY1	chr4:57843086-57843395	GM12892	blood:	n/a	n/a
28	POLR2A	chr4:57843085-57844234	MCF-7	breast:	n/a	n/a
29	POLR2A	chr4:57843031-57845484	NB4	blood:	n/a	n/a
30	TAF1	chr4:57843068-57844121	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr4:57842981-57843312	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr4:57843218-57844165	A549	lung:	n/a	n/a
33	YY1	chr4:57842518-57843952	HepG2	liver:	n/a	n/a
34	PAX5	chr4:57842952-57843411	GM12892	blood:	n/a	n/a
35	POLR2A	chr4:57843225-57844184	PBDE	blood:	n/a	n/a
36	POLR2A	chr4:57842975-57844144	H1-neurons	neurons:	n/a	n/a
37	HA-E2F1	chr4:57842459-57844083	MCF-7	breast:	n/a	chr4:57843786-57843795
38	CHD2	chr4:57842923-57844178	GM12878	blood:	n/a	n/a
39	MAX	chr4:57843068-57844090	NB4	blood:	n/a	n/a
40	POLR2A	chr4:57843293-57844308	SK-N-MC	brain:	n/a	n/a
41	MAX	chr4:57843158-57844104	GM12878	blood:	n/a	n/a
42	MAX	chr4:57842627-57844165	HepG2	liver:	n/a	n/a
43	CTCF	chr4:57843260-57843410	GM12864	blood:	n/a	n/a
44	HDAC2	chr4:57842881-57844157	MCF-7	breast:	n/a	chr4:57843785-57843794
45	MYC	chr4:57843013-57843330	MCF-7	breast:	n/a	n/a
46	CTCF	chr4:57843240-57843390	AG10803	skin:	n/a	n/a
47	STAT5A	chr4:57843236-57844148	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:57843005-57845508	GM18505	blood:	n/a	n/a
49	CTCF	chr4:57843260-57843345	GM10266	blood:	n/a	n/a
50	POLR2A	chr4:57843236-57844136	HL-60	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57843255..57844990-chr4:57888825..57890332,2	K562	blood:
2	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
3	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
4	chr4:57843255..57845274-chr4:57888366..57890332,2	K562	blood:
5	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
6	chr4:57826815..57829812-chr4:57841300..57844628,3	MCF-7	breast:
7	chr4:57333087..57335313-chr4:57842375..57845002,3	K562	blood:
8	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
9	chr4:56211110..56213027-chr4:57841438..57843848,2	K562	blood:
10	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:

No data

Variant related genes	Relation type
POLR2B	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000269949	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10866440	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs10866441	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1105434	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1107675	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs11727683	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11729152	0.84[ASN][1000 genomes]
rs11730321	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11736192	0.80[ASN][1000 genomes]
rs11736808	0.80[ASN][1000 genomes]
rs11736869	0.89[CHB][hapmap]
rs11932673	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12500454	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1277271	0.88[ASN][1000 genomes]
rs1277287	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1277288	0.85[ASN][1000 genomes]
rs13108245	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs13121176	0.91[ASN][1000 genomes]
rs1315005	0.85[ASN][1000 genomes]
rs1625691	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs17081937	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17087307	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17087317	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17087411	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs17087414	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs1718839	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1877669	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1976780	0.93[ASN][1000 genomes]
rs2228991	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3000	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs34576794	0.86[ASN][1000 genomes]
rs34659774	0.93[ASN][1000 genomes]
rs3796528	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3806745	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs41552420	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41556916	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56182208	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56285301	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57469512	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554398	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs6554399	0.84[ASN][1000 genomes]
rs6816457	0.88[ASN][1000 genomes]
rs6838948	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs6852110	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs73242616	0.84[ASN][1000 genomes]
rs73242631	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7661194	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs7680734	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs7685576	0.84[ASN][1000 genomes]
rs781665	0.87[ASN][1000 genomes]
rs781666	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs781668	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9942208	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57840800-57843600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr4:57840800-57846800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:57841400-57846200	Active TSS	HMEC	breast
4	chr4:57841400-57846200	Active TSS	NHEK	skin
5	chr4:57841400-57846400	Active TSS	GM12878-XiMat	blood
6	chr4:57841400-57846600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:57841400-57846600	Active TSS	Hela-S3	cervix
8	chr4:57841600-57846600	Active TSS	NHLF	lung
9	chr4:57841800-57843400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:57841800-57843400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr4:57841800-57846400	Active TSS	Fetal Intestine Large	intestine
12	chr4:57842000-57843400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:57842000-57846000	Active TSS	Gastric	stomach
14	chr4:57842000-57846200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:57842000-57846200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:57842000-57846200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:57842000-57846200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr4:57842000-57846200	Active TSS	Fetal Kidney	kidney
19	chr4:57842000-57846200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr4:57842000-57846200	Active TSS	Ovary	ovary
21	chr4:57842000-57846400	Active TSS	Fetal Intestine Small	intestine
22	chr4:57842000-57846600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:57842000-57846600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:57842000-57846600	Active TSS	HSMM	muscle
25	chr4:57842000-57846600	Active TSS	K562	blood
26	chr4:57842000-57846800	Active TSS	HSMMtube	muscle
27	chr4:57842000-57847000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr4:57842000-57847000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:57842000-57847000	Active TSS	A549	lung
30	chr4:57842200-57843800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr4:57842200-57844000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:57842200-57846000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:57842200-57846000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:57842200-57846000	Active TSS	Lung	lung
35	chr4:57842200-57846000	Active TSS	Small Intestine	intestine
36	chr4:57842200-57846000	Active TSS	Stomach Mucosa	stomach
37	chr4:57842200-57846600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:57842400-57843400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:57842400-57843800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:57842400-57843800	Active TSS	Fetal Heart	heart
41	chr4:57842400-57843800	Bivalent/Poised TSS	HepG2	liver
42	chr4:57842400-57846000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:57842400-57846200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:57842600-57845800	Active TSS	Colon Smooth Muscle	Colon
45	chr4:57842600-57846000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:57842600-57846000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:57842600-57846000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:57842600-57846000	Active TSS	Aorta	Aorta
49	chr4:57842600-57846000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr4:57842600-57846000	Active TSS	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links