Variant report

Variant	rs1948607
Chromosome Location	chr4:55706827-55706828
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	CTCF	chr4:55706760-55706910	BJ	skin:	n/a	chr4:55706810-55706828
2	RAD21	chr4:55706545-55707087	HCT-116	colon:	n/a	chr4:55706808-55706827
3	CTCF	chr4:55706740-55706890	RPTEC	kidney:	n/a	chr4:55706810-55706828
4	CTCF	chr4:55706779-55706882	LNCaP	prostate:	n/a	chr4:55706810-55706828
5	CTCF	chr4:55706820-55706970	AoAF	blood vessel:	n/a	n/a
6	RAD21	chr4:55706555-55707730	SK-N-SH	brain:	n/a	chr4:55707345-55707354 chr4:55707339-55707358 chr4:55706808-55706827
7	CTCF	chr4:55706700-55706850	AoAF	blood vessel:	n/a	chr4:55706810-55706828
8	CTCF	chr4:55706740-55706890	HFF	foreskin:	n/a	chr4:55706810-55706828
9	CTCF	chr4:55706780-55706930	AG04449	skin:	n/a	chr4:55706810-55706828
10	CTCF	chr4:55706783-55706857	Pancreas_OC	pancreas:	n/a	chr4:55706810-55706828
11	CTCF	chr4:55706648-55707518	GM12878	blood:	n/a	chr4:55706810-55706828 chr4:55707336-55707357
12	CTCF	chr4:55706720-55706870	HVMF	connective:	n/a	chr4:55706810-55706828
13	CTCF	chr4:55706720-55706870	AG09309	skin:	n/a	chr4:55706810-55706828
14	RAD21	chr4:55706645-55706981	MCF-7	breast:	n/a	chr4:55706808-55706827
15	RAD21	chr4:55706745-55706913	IMR90	lung:	n/a	chr4:55706808-55706827
16	ZNF143	chr4:55706739-55706886	GM12878	blood:	n/a	n/a
17	CTCF	chr4:55706723-55706925	K562	blood:	n/a	chr4:55706810-55706828
18	CTCF	chr4:55706720-55706870	HMF	breast:	n/a	chr4:55706810-55706828
19	CTCF	chr4:55706780-55706930	HPF	lung:	n/a	chr4:55706810-55706828
20	SMC3	chr4:55706597-55706966	GM12878	blood:	n/a	n/a
21	CTCF	chr4:55706752-55706889	GM12878	blood:	n/a	chr4:55706810-55706828
22	CTCF	chr4:55706800-55706950	AG10803	skin:	n/a	chr4:55706810-55706828
23	CTCF	chr4:55706800-55706950	GM12872	blood:	n/a	chr4:55706810-55706828
24	CTCF	chr4:55706794-55706881	LNCaP	prostate:	n/a	chr4:55706810-55706828
25	CTCF	chr4:55706737-55706871	Spleen_OC	spleen:	n/a	chr4:55706810-55706828
26	CTCF	chr4:55706820-55706970	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:55549430..55550445-chr4:55706754..55707711,7	MCF-7	breast:
2	chr4:55549261..55550394-chr4:55706621..55707808,6	MCF-7	breast:
3	chr4:55184800..55185406-chr4:55706810..55707325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251256	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1123272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1497476	0.87[CEU][hapmap]
rs1497477	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1497491	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1497492	0.91[ASN][1000 genomes]
rs17695485	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055222	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2132879	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132880	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173228	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2646314	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2646316	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2646317	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2646318	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2646319	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646320	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2646351	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2646355	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2646364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2646365	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2646368	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2646369	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2726610	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2726612	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2726613	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2726619	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726620	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726621	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2726623	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2726626	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726627	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2726628	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2726629	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2726630	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2726631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2726632	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28628137	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4280801	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345236	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs716919	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7668976	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7686543	0.82[ASN][1000 genomes]
rs7692346	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697169	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871693	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs871694	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1836939	chr4:55701134-55716601	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55704000-55708400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:55704200-55707400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:55704200-55708600	Weak transcription	Fetal Lung	lung
4	chr4:55704400-55708400	Weak transcription	Brain Germinal Matrix	brain
5	chr4:55704600-55712600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:55705600-55711400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:55706000-55708600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:55706600-55707400	Enhancers	Brain Hippocampus Middle	brain
9	chr4:55706600-55709000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr4:55706800-55707200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:55706800-55707200	Enhancers	Brain Substantia Nigra	brain
12	chr4:55706800-55709000	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:55706800-55709800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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