Variant report

Variant	rs6765840
Chromosome Location	chr3:99217455-99217456
allele	C/T
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	chr3:99217437-99217656	IMR90	lung:	n/a	n/a
2	CTCF	chr3:99217113-99218871	SK-N-SH	brain:	n/a	chr3:99218227-99218248 chr3:99218228-99218241 chr3:99218230-99218240 chr3:99218225-99218243 chr3:99218228-99218237
3	CTCF	chr3:99217420-99217570	AG09309	skin:	n/a	n/a
4	SMC3	chr3:99217286-99218889	SK-N-SH	brain:	n/a	chr3:99218227-99218241 chr3:99217999-99218013
5	CTCF	chr3:99217420-99217570	HRPEpiC	eye:	n/a	n/a
6	CTCF	chr3:99217420-99217570	HPAF	blood vessel:	n/a	n/a
7	CTCF	chr3:99217420-99217570	AG10803	skin:	n/a	n/a
8	CTCF	chr3:99217440-99217590	HA-sp	spinal cord:	n/a	n/a
9	CTCF	chr3:99217420-99217570	HVMF	connective:	n/a	n/a
10	RAD21	chr3:99217316-99218656	SK-N-SH	brain:	n/a	chr3:99218230-99218239 chr3:99218229-99218242 chr3:99218226-99218245 chr3:99218231-99218241
11	CTCF	chr3:99217400-99217550	HMEC	breast:	n/a	n/a
12	CTCF	chr3:99217440-99217590	NHEK	skin:	n/a	n/a
13	CTCF	chr3:99217420-99217570	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99217180..99218833-chr3:99471535..99472845,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243296	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10511174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12636295	0.87[AFR][1000 genomes]
rs13063175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13064696	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13065138	0.91[EUR][1000 genomes]
rs13070584	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13075415	0.87[AFR][1000 genomes]
rs13084282	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13086098	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13098261	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13101237	0.95[ASN][1000 genomes]
rs16841321	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16841339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2342465	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34060873	0.91[EUR][1000 genomes]
rs34162135	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34201317	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34468147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34580839	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34686662	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34964323	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35217023	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35479623	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35722344	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35787037	0.91[EUR][1000 genomes]
rs35892771	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35981855	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36015505	0.83[EUR][1000 genomes]
rs4928134	0.88[EUR][1000 genomes]
rs4928201	0.92[EUR][1000 genomes]
rs4928208	0.83[JPT][hapmap]
rs71313539	0.87[AFR][1000 genomes]
rs71313550	1.00[ASN][1000 genomes]
rs71313551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71313553	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71313554	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71313556	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628820	0.87[AFR][1000 genomes]
rs7629812	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630545	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv3916	chr3:99186008-99232052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1831522	chr3:99207253-99219235	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3422853	chr3:99208019-99342748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99217000-99219400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:99217200-99218000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:99217200-99218000	Enhancers	Lung	lung
4	chr3:99217200-99218800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:99217200-99218800	Enhancers	NHEK	skin
6	chr3:99217200-99219000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:99217200-99219400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:99217200-99219600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:99217200-99219800	Enhancers	NHDF-Ad	bronchial
10	chr3:99217200-99220200	Enhancers	Osteobl	bone
11	chr3:99217400-99217800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:99217400-99219400	Weak transcription	Aorta	Aorta

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