Variant report

Variant	rs4682288
Chromosome Location	chr3:111297296-111297297
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111295970..111297364-chr3:111335015..111336070,12	MCF-7	breast:
2	chr3:111295710..111298170-chr3:111384643..111386877,2	MCF-7	breast:
3	chr3:111296456..111297303-chr3:111434475..111435453,4	MCF-7	breast:
4	chr3:111296348..111297359-chr3:111409950..111410781,3	MCF-7	breast:
5	chr3:111296559..111298306-chr3:111299158..111301794,2	MCF-7	breast:
6	chr3:111296389..111297299-chr3:111340223..111341030,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11919740	0.95[ASN][1000 genomes]
rs12497656	0.92[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs1282090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391361	1.00[JPT][hapmap]
rs17202775	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17202782	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34111129	0.85[ASN][1000 genomes]
rs4682051	0.95[ASN][1000 genomes]
rs4682289	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55900677	0.85[ASN][1000 genomes]
rs7612391	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4682288	CD200	cis	parietal	SCAN
rs4682288	VASH2	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111291800-111298000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:111292000-111297600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:111294200-111302000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr3:111295400-111298800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:111295600-111301600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:111295800-111301400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:111295800-111311400	Strong transcription	Fetal Thymus	thymus
8	chr3:111296000-111314400	Strong transcription	Primary T cells from cord blood	blood
9	chr3:111296200-111297800	Weak transcription	Thymus	Thymus
10	chr3:111296400-111314600	Strong transcription	Dnd41	blood
11	chr3:111296600-111301800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:111296800-111299200	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr3:111296800-111299200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:111296800-111299200	Enhancers	HMEC	breast
15	chr3:111296800-111299600	Enhancers	NHEK	skin
16	chr3:111296800-111299800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:111297000-111297400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:111297000-111297400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:111297000-111297600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:111297000-111297800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:111297000-111299200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:111297000-111299400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:111297000-111301200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:111297000-111302000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:111297200-111297600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:111297200-111297600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:111297200-111298000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:111297200-111299600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:111297200-111300000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:111297200-111300200	Weak transcription	Osteobl	bone
31	chr3:111297200-111300800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:111297200-111300800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:111297200-111307200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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