Variant report

Variant	rs6858086
Chromosome Location	chr4:74737471-74737472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74736057..74738818-chr4:74920006..74922107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248848	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10007826	0.94[ASN][1000 genomes]
rs1366946	0.94[ASN][1000 genomes]
rs1366949	0.94[ASN][1000 genomes]
rs16850137	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2115691	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs2145615	0.87[ASN][1000 genomes]
rs2367291	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2367293	0.94[ASN][1000 genomes]
rs24772	0.87[ASN][1000 genomes]
rs2886927	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2968710	0.94[ASN][1000 genomes]
rs3097409	0.94[ASN][1000 genomes]
rs3097411	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs3097412	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs3111694	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs3111697	0.94[ASN][1000 genomes]
rs3111698	0.99[ASN][1000 genomes]
rs3117597	0.85[JPT][hapmap]
rs3117598	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs3117600	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs3117604	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs4074	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482239	0.87[ASN][1000 genomes]
rs492155	0.87[ASN][1000 genomes]
rs493091	0.88[ASN][1000 genomes]
rs508977	0.87[ASN][1000 genomes]
rs512606	0.87[ASN][1000 genomes]
rs516224	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[ASN][1000 genomes]
rs518632	0.87[ASN][1000 genomes]
rs519565	0.87[ASN][1000 genomes]
rs537373	0.87[ASN][1000 genomes]
rs541923	0.87[ASN][1000 genomes]
rs548068	0.87[ASN][1000 genomes]
rs551744	0.87[ASN][1000 genomes]
rs569390	0.87[ASN][1000 genomes]
rs573878	0.87[ASN][1000 genomes]
rs593641	0.87[ASN][1000 genomes]
rs596352	0.87[ASN][1000 genomes]
rs623659	0.87[ASN][1000 genomes]
rs638767	0.87[ASN][1000 genomes]
rs654871	0.87[ASN][1000 genomes]
rs655328	0.87[ASN][1000 genomes]
rs680044	0.88[ASN][1000 genomes]
rs680452	0.88[ASN][1000 genomes]
rs683671	0.87[ASN][1000 genomes]
rs684080	0.86[ASN][1000 genomes]
rs9991272	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6858086	SEPT11	cis	parietal	SCAN
rs6858086	PF4V1	cis	multi-tissue	Pritchard
rs6858086	NPFFR2	cis	parietal	SCAN
rs6858086	SLC17A7	trans	parietal	SCAN
rs6858086	CXCL6	cis	parietal	SCAN
rs6858086	G3BP2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74733600-74738800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:74735400-74738000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr4:74736000-74738000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
4	chr4:74736000-74741600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:74736200-74737800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:74736400-74738200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr4:74736400-74738400	Weak transcription	Adipose Nuclei	Adipose
8	chr4:74736400-74739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:74736600-74738000	Active TSS	HMEC	breast
10	chr4:74736800-74740600	Weak transcription	NHDF-Ad	bronchial
11	chr4:74736800-74749000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:74737000-74739200	Enhancers	HUVEC	blood vessel
13	chr4:74737000-74740600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:74737000-74740800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:74737000-74741600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:74737200-74739600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:74737400-74739800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links