Variant report

Variant	rs4680312
Chromosome Location	chr3:156605929-156605930
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	chr3:156603770..156606924-chr3:156607944..156610272,5	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10212230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10936040	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10936043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707914	0.80[ASN][1000 genomes]
rs11709901	0.94[ASN][1000 genomes]
rs11712111	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629380	0.97[ASN][1000 genomes]
rs12634915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12638253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068223	0.84[JPT][hapmap]
rs13070271	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs13088978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1320011	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs13322318	0.83[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1384538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1574980	0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs17382070	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.91[ASN][1000 genomes]
rs2321290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2321292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2874488	0.84[JPT][hapmap]
rs2874494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs344073	0.84[JPT][hapmap]
rs344079	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344080	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs344082	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs344084	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs344087	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs34667021	0.95[ASN][1000 genomes]
rs3910072	0.89[ASN][1000 genomes]
rs4315647	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs453219	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4589888	0.89[ASN][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4680314	0.80[ASN][1000 genomes]
rs4680317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62275765	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762708	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6765353	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6780427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7622309	0.80[ASN][1000 genomes]
rs7637701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs7638625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9812895	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9818684	0.88[CEU][hapmap];0.80[JPT][hapmap]
rs9820830	0.85[CEU][hapmap]
rs9837038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9847187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9858158	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9863643	0.83[ASN][1000 genomes]
rs9865905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866373	0.96[ASN][1000 genomes]
rs9867621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9871817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875585	0.86[ASN][1000 genomes]
rs9875688	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9876010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9876148	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs987724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9878585	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680312	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs4680312	LINC00886	cis	Adipose Subcutaneous	GTEx
rs4680312	LINC00886	cis	Stomach	GTEx
rs4680312	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156598200-156609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156605200-156606600	Enhancers	Brain Substantia Nigra	brain
3	chr3:156605800-156607600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:156605800-156607800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:156605800-156607800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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