Variant report

Variant	rs7658198
Chromosome Location	chr4:6994489-6994490
allele	C/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	CHD1	chr4:6994463-6994496	GM12878	blood:	n/a	n/a
2	USF2	chr4:6994318-6994718	GM12878	blood:	n/a	n/a
3	WRNIP1	chr4:6994311-6994507	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:6992742-6995081	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF143	chr4:6994298-6994560	GM12878	blood:	n/a	n/a

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

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

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10012590	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10025310	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1048009	0.89[YRI][hapmap]
rs10516181	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10937772	0.88[ASN][1000 genomes]
rs10937774	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs10937776	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732898	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11938701	0.86[ASN][1000 genomes]
rs11944897	0.86[ASN][1000 genomes]
rs12502513	1.00[CHB][hapmap]
rs12503027	0.86[ASN][1000 genomes]
rs12642852	0.85[EUR][1000 genomes]
rs13107989	0.86[ASN][1000 genomes]
rs13122119	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs13135912	0.89[EUR][1000 genomes]
rs13148395	0.86[ASN][1000 genomes]
rs13149411	0.80[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2301818	0.80[ASN][1000 genomes]
rs2301819	0.80[ASN][1000 genomes]
rs2359194	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3188939	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs34219101	1.00[ASN][1000 genomes]
rs34221933	0.86[ASN][1000 genomes]
rs34335938	0.80[ASN][1000 genomes]
rs34463709	0.80[ASN][1000 genomes]
rs34481892	0.80[ASN][1000 genomes]
rs34959511	0.80[ASN][1000 genomes]
rs35170004	0.80[ASN][1000 genomes]
rs3857171	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3892490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894945	0.86[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4234793	0.86[ASN][1000 genomes]
rs4296677	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4428285	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4458452	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4544710	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4645214	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4689059	0.95[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689060	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4689560	1.00[CHB][hapmap]
rs4689563	0.80[ASN][1000 genomes]
rs4689564	0.80[ASN][1000 genomes]
rs4689565	0.80[ASN][1000 genomes]
rs4689568	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689573	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689575	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4689579	0.80[ASN][1000 genomes]
rs55822670	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289166	0.86[ASN][1000 genomes]
rs66530709	0.80[ASN][1000 genomes]
rs66640699	0.80[ASN][1000 genomes]
rs66931928	0.80[ASN][1000 genomes]
rs66992702	0.80[ASN][1000 genomes]
rs6811496	0.86[ASN][1000 genomes]
rs6816882	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818744	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6831129	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6834102	0.86[ASN][1000 genomes]
rs6840780	0.86[ASN][1000 genomes]
rs6854776	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs73202120	0.81[AFR][1000 genomes]
rs7655563	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655773	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7661462	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7661952	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7673901	0.86[ASN][1000 genomes]
rs7675524	1.00[CHB][hapmap]
rs7685667	0.86[ASN][1000 genomes]
rs7693321	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8180337	0.95[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	chr4:6990400-6994600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:6990600-6995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:6991200-6995200	Weak transcription	Placenta	Placenta
10	chr4:6991200-6995400	Enhancers	Brain Hippocampus Middle	brain
11	chr4:6991200-6995800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:6991200-6996000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr4:6991400-6995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:6991400-6996000	Weak transcription	Fetal Lung	lung
15	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
16	chr4:6991600-7000000	Weak transcription	Hela-S3	cervix
17	chr4:6991800-6995200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:6991800-6995800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:6991800-6995800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:6992200-6994600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:6992200-6994800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:6992200-6995400	Genic enhancers	Fetal Thymus	thymus
23	chr4:6992200-6995600	Enhancers	Primary B cells from cord blood	blood
24	chr4:6992400-6994600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:6992400-6994600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:6992400-6994600	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:6992400-6995000	Genic enhancers	K562	blood
28	chr4:6992400-6995400	Enhancers	Stomach Mucosa	stomach
29	chr4:6992400-6995600	Enhancers	Brain Cingulate Gyrus	brain
30	chr4:6992600-6994600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:6992600-6994600	Genic enhancers	Spleen	Spleen
32	chr4:6992600-6994800	Genic enhancers	Thymus	Thymus
33	chr4:6992600-6995400	Enhancers	Brain Angular Gyrus	brain
34	chr4:6992600-6995600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:6992800-6995400	Enhancers	Primary B cells from peripheral blood	blood
36	chr4:6993000-6994600	Enhancers	Gastric	stomach
37	chr4:6993000-6995600	Enhancers	Liver	Liver
38	chr4:6993200-6994600	Enhancers	NHLF	lung
39	chr4:6993200-6995200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr4:6993200-6995600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr4:6993200-6999000	Strong transcription	Dnd41	blood
42	chr4:6993200-7006800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:6993400-6995200	Enhancers	Esophagus	oesophagus
44	chr4:6993400-6995200	Genic enhancers	Fetal Intestine Small	intestine
45	chr4:6993600-6994800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:6993600-6995400	Enhancers	HSMMtube	muscle
47	chr4:6993600-6995600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:6993600-6995600	Enhancers	HMEC	breast
49	chr4:6993600-6995800	Weak transcription	A549	lung
50	chr4:6993800-6994600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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