Variant report

Variant	rs7661952
Chromosome Location	chr4:6994811-6994812
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	POLR2A	chr4:6994762-6994828	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr4:6994747-6994954	MCF10A-Er-Src	breast:	n/a	chr4:6994826-6994837
3	STAT3	chr4:6994535-6994993	MCF10A-Er-Src	breast:	n/a	chr4:6994826-6994837
4	POLR2A	chr4:6992742-6995081	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr4:6994492-6994996	MCF10A-Er-Src	breast:	n/a	chr4:6994826-6994837

No.	Distal block	Cell Line	Cell type
1	chr4:6993091..6995373-chr4:7043423..7046431,3	MCF-7	breast:
2	chr4:6992471..6995105-chr4:7038359..7040025,2	MCF-7	breast:
3	chr4:6910242..6912678-chr4:6994521..6998393,5	MCF-7	breast:

Variant related genes	Relation type
TBC1D14	TF binding region
ENSG00000187904	TF binding region
ENSG00000265550	TF binding region
RN7SKP292	TF binding region
ENSG00000173013	Chromatin interaction
ENSG00000132405	Chromatin interaction
ENSG00000173011	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10012590	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10025310	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10516181	0.81[ASN][1000 genomes]
rs10937774	1.00[CHB][hapmap]
rs10937776	0.81[ASN][1000 genomes]
rs11732898	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11938701	1.00[ASN][1000 genomes]
rs11944897	1.00[ASN][1000 genomes]
rs12502513	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12503027	1.00[ASN][1000 genomes]
rs12510715	0.81[ASN][1000 genomes]
rs12511796	0.89[AFR][1000 genomes]
rs12512484	0.84[EUR][1000 genomes]
rs13107989	1.00[ASN][1000 genomes]
rs13108082	0.86[ASN][1000 genomes]
rs13111887	0.86[ASN][1000 genomes]
rs13122119	1.00[CHB][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs13148395	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149411	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13149923	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2301818	0.94[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301819	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2359194	0.81[ASN][1000 genomes]
rs3188939	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34219101	0.86[ASN][1000 genomes]
rs34221933	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34335938	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34379427	0.84[EUR][1000 genomes]
rs34463709	0.93[ASN][1000 genomes]
rs34481892	0.93[ASN][1000 genomes]
rs34953654	0.81[ASN][1000 genomes]
rs34959511	0.93[ASN][1000 genomes]
rs34990775	0.87[EUR][1000 genomes]
rs35170004	0.93[ASN][1000 genomes]
rs35680216	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3857171	0.81[ASN][1000 genomes]
rs3892490	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3894945	1.00[ASN][1000 genomes]
rs4234788	0.86[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4234793	1.00[ASN][1000 genomes]
rs4327487	0.92[YRI][hapmap]
rs4376137	0.93[YRI][hapmap]
rs4544710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689056	0.87[EUR][1000 genomes]
rs4689058	0.86[YRI][hapmap]
rs4689560	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4689563	0.93[ASN][1000 genomes]
rs4689564	0.93[ASN][1000 genomes]
rs4689565	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4689566	0.81[ASN][1000 genomes]
rs4689567	0.81[ASN][1000 genomes]
rs4689568	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4689573	0.81[ASN][1000 genomes]
rs4689575	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4689577	0.81[ASN][1000 genomes]
rs4689579	0.93[ASN][1000 genomes]
rs55822670	0.86[ASN][1000 genomes]
rs62289166	1.00[ASN][1000 genomes]
rs6446554	0.86[YRI][hapmap]
rs6446559	0.86[ASN][1000 genomes]
rs66530709	0.93[ASN][1000 genomes]
rs66640699	0.93[ASN][1000 genomes]
rs66841627	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66931928	0.93[ASN][1000 genomes]
rs66992702	0.93[ASN][1000 genomes]
rs6811496	1.00[ASN][1000 genomes]
rs6816660	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6816882	0.86[ASN][1000 genomes]
rs6818744	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6831129	0.86[ASN][1000 genomes]
rs6834102	1.00[ASN][1000 genomes]
rs6840780	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854776	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7655563	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7655773	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658198	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7661462	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7673901	1.00[ASN][1000 genomes]
rs7675524	1.00[CHB][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7685667	1.00[ASN][1000 genomes]
rs7689324	0.93[YRI][hapmap]
rs7693321	0.81[ASN][1000 genomes]
rs9291126	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 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	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:6990200-6995200	Enhancers	Brain Substantia Nigra	brain
4	chr4:6990200-6995800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:6990600-6995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:6991200-6995200	Weak transcription	Placenta	Placenta
9	chr4:6991200-6995400	Enhancers	Brain Hippocampus Middle	brain
10	chr4:6991200-6995800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr4:6991200-6996000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:6991400-6995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:6991400-6996000	Weak transcription	Fetal Lung	lung
14	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
15	chr4:6991600-7000000	Weak transcription	Hela-S3	cervix
16	chr4:6991800-6995200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:6991800-6995800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:6991800-6995800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:6992200-6995400	Genic enhancers	Fetal Thymus	thymus
20	chr4:6992200-6995600	Enhancers	Primary B cells from cord blood	blood
21	chr4:6992400-6995000	Genic enhancers	K562	blood
22	chr4:6992400-6995400	Enhancers	Stomach Mucosa	stomach
23	chr4:6992400-6995600	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:6992600-6995400	Enhancers	Brain Angular Gyrus	brain
25	chr4:6992600-6995600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:6992800-6995400	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:6993000-6995600	Enhancers	Liver	Liver
28	chr4:6993200-6995200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr4:6993200-6995600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr4:6993200-6999000	Strong transcription	Dnd41	blood
31	chr4:6993200-7006800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:6993400-6995200	Enhancers	Esophagus	oesophagus
33	chr4:6993400-6995200	Genic enhancers	Fetal Intestine Small	intestine
34	chr4:6993600-6995400	Enhancers	HSMMtube	muscle
35	chr4:6993600-6995600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:6993600-6995600	Enhancers	HMEC	breast
37	chr4:6993600-6995800	Weak transcription	A549	lung
38	chr4:6993800-6995000	Enhancers	Brain Anterior Caudate	brain
39	chr4:6993800-6995000	Strong transcription	HepG2	liver
40	chr4:6993800-6995400	Enhancers	NH-A	brain
41	chr4:6993800-6998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:6993800-7008400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:6994000-6995000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:6994000-6995200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr4:6994000-6995400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:6994000-6995400	Enhancers	Brain Germinal Matrix	brain
47	chr4:6994000-6995800	Weak transcription	Fetal Brain Male	brain
48	chr4:6994000-6996600	Weak transcription	Left Ventricle	heart
49	chr4:6994000-6996600	Weak transcription	NHDF-Ad	bronchial
50	chr4:6994000-6998000	Weak transcription	Aorta	Aorta

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