Variant report

Variant	rs3806745
Chromosome Location	chr4:57773388-57773389
allele	A/G
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	SP1	chr4:57773313-57773965	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952
2	CTBP2	chr4:57773280-57774131	H1-hESC	embryonic stem cell:	n/a	n/a
3	ELK1	chr4:57773360-57773554	K562	blood:	n/a	n/a
4	MXI1	chr4:57773345-57776166	IMR90	lung:	n/a	n/a
5	TBP	chr4:57773376-57774951	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr4:57773105-57774259	H1-hESC	embryonic stem cell:	n/a	chr4:57774088-57774097
7	NANOG	chr4:57773256-57774100	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF143	chr4:57773032-57773971	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr4:57773123-57773433	H1-hESC	embryonic stem cell:	n/a	chr4:57773249-57773260
10	SP1	chr4:57773236-57774607	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952 chr4:57774283-57774297
11	MYC	chr4:57773385-57773442	MCF-7	breast:	n/a	n/a
12	JUND	chr4:57773247-57773956	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr4:57773045-57776084	H1-hESC	embryonic stem cell:	n/a	chr4:57774969-57774978 chr4:57774574-57774587 chr4:57774972-57774985 chr4:57774938-57774951 chr4:57774480-57774493 chr4:57774388-57774401 chr4:57774851-57774862
14	POLR2A	chr4:57773375-57773408	MCF-7	breast:	n/a	n/a
15	USF2	chr4:57773328-57773516	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr4:57773202-57773912	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAZ	chr4:57773290-57775623	K562	blood:	n/a	n/a
18	MAX	chr4:57773120-57773576	H1-hESC	embryonic stem cell:	n/a	chr4:57773249-57773260
19	TCF7L2	chr4:57773240-57773511	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57772988..57775343-chr4:57776220..57778579,3	MCF-7	breast:
2	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
3	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
4	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10008356	0.83[ASN][1000 genomes]
rs10030913	0.88[ASN][1000 genomes]
rs10866440	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10866441	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1105434	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1107675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11729152	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11730321	0.88[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs11730476	0.80[ASN][1000 genomes]
rs11730525	0.90[ASN][1000 genomes]
rs11734953	0.86[ASN][1000 genomes]
rs11736192	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736808	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11736869	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs11932673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11933908	0.90[ASN][1000 genomes]
rs12500454	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12501990	0.80[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap]
rs13108245	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13113802	0.87[ASN][1000 genomes]
rs13116564	0.87[ASN][1000 genomes]
rs13146960	0.87[ASN][1000 genomes]
rs13149162	0.89[ASN][1000 genomes]
rs13353552	0.86[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap]
rs17081937	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17087307	0.81[ASN][1000 genomes]
rs17087317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17087411	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs17087414	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1718839	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1877669	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1976780	0.81[ASN][1000 genomes]
rs2002153	0.84[ASN][1000 genomes]
rs2090962	0.87[ASN][1000 genomes]
rs2228991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3000	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34659774	0.81[ASN][1000 genomes]
rs3733306	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs3796528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4276341	0.87[ASN][1000 genomes]
rs4864606	0.90[ASN][1000 genomes]
rs4864607	0.89[ASN][1000 genomes]
rs4864608	0.80[ASN][1000 genomes]
rs4865156	0.80[ASN][1000 genomes]
rs4865157	0.83[ASN][1000 genomes]
rs4865158	0.82[ASN][1000 genomes]
rs4865159	0.84[ASN][1000 genomes]
rs4865160	0.84[ASN][1000 genomes]
rs55822707	0.88[ASN][1000 genomes]
rs56122758	0.81[ASN][1000 genomes]
rs62308110	0.80[ASN][1000 genomes]
rs62308111	0.80[ASN][1000 genomes]
rs62308135	0.90[ASN][1000 genomes]
rs62308136	0.90[ASN][1000 genomes]
rs62308137	0.89[ASN][1000 genomes]
rs6554393	0.83[ASN][1000 genomes]
rs6554394	0.83[ASN][1000 genomes]
rs6554397	0.90[ASN][1000 genomes]
rs6554398	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6554399	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6816950	0.80[ASN][1000 genomes]
rs6838948	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6839845	0.82[ASN][1000 genomes]
rs6840805	0.80[ASN][1000 genomes]
rs6847086	0.82[JPT][hapmap]
rs6852110	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6854420	0.90[ASN][1000 genomes]
rs6855212	0.87[ASN][1000 genomes]
rs6858216	0.80[ASN][1000 genomes]
rs729844	0.87[ASN][1000 genomes]
rs73242609	0.90[ASN][1000 genomes]
rs73242616	0.89[ASN][1000 genomes]
rs73818661	0.94[AFR][1000 genomes]
rs7661194	1.00[JPT][hapmap]
rs7666804	0.87[ASN][1000 genomes]
rs7667302	0.87[ASN][1000 genomes]
rs7680734	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7685576	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7695970	0.90[ASN][1000 genomes]
rs781666	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs781668	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs899632	0.87[ASN][1000 genomes]
rs9684742	0.87[ASN][1000 genomes]
rs9942208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv12676	chr4:57772270-57775584	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3374947	chr4:57773220-57776168	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3389347	chr4:57773345-57775893	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57772000-57773400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:57772600-57773400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
3	chr4:57772600-57773600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
4	chr4:57772800-57773400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr4:57772800-57773400	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:57772800-57773400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr4:57772800-57773600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
8	chr4:57772800-57773800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:57772800-57773800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr4:57772800-57776200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:57773000-57773400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr4:57773000-57773400	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr4:57773000-57773400	Enhancers	Brain Cingulate Gyrus	brain
14	chr4:57773000-57773400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr4:57773000-57773400	Enhancers	Esophagus	oesophagus
16	chr4:57773000-57773400	Enhancers	Fetal Intestine Small	intestine
17	chr4:57773000-57773400	Enhancers	Fetal Muscle Leg	muscle
18	chr4:57773000-57773400	Enhancers	Fetal Stomach	stomach
19	chr4:57773000-57773400	Enhancers	Left Ventricle	heart
20	chr4:57773000-57773400	Enhancers	Right Atrium	heart
21	chr4:57773000-57773400	Flanking Bivalent TSS/Enh	HepG2	liver
22	chr4:57773000-57773400	Bivalent Enhancer	NHLF	lung
23	chr4:57773000-57773400	Bivalent/Poised TSS	Osteobl	bone
24	chr4:57773000-57773600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:57773000-57773600	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr4:57773000-57773600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:57773000-57773600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr4:57773000-57773600	Flanking Active TSS	Fetal Lung	lung
29	chr4:57773000-57773600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr4:57773000-57773600	Flanking Active TSS	Thymus	Thymus
31	chr4:57773000-57773800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr4:57773000-57773800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr4:57773000-57773800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr4:57773000-57773800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr4:57773000-57773800	Enhancers	Lung	lung
36	chr4:57773000-57773800	Enhancers	Spleen	Spleen
37	chr4:57773000-57774000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr4:57773000-57774800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr4:57773000-57776000	Active TSS	Rectal Smooth Muscle	rectum
40	chr4:57773200-57773400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:57773200-57773400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:57773200-57773400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr4:57773200-57773400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:57773200-57773400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:57773200-57773400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr4:57773200-57773400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:57773200-57773400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:57773200-57773400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:57773200-57773400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr4:57773200-57773400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links