Variant report

Variant	rs71322854
Chromosome Location	chr3:89164468-89164469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88268096..88268898-chr3:89163502..89164670,4	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1040015	0.96[ASN][1000 genomes]
rs11914760	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916891	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11928901	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487141	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490373	0.91[EUR][1000 genomes]
rs12490659	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491480	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493524	0.92[EUR][1000 genomes]
rs12493527	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494615	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12495783	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496609	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496791	0.96[ASN][1000 genomes]
rs13058761	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13058886	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13060198	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13071923	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13074291	0.92[EUR][1000 genomes]
rs13084503	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089469	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095092	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13097212	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13097548	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13098003	0.92[ASN][1000 genomes]
rs34493897	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34638812	0.91[EUR][1000 genomes]
rs34855223	0.96[ASN][1000 genomes]
rs34893903	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34992749	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35053334	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35156943	0.96[ASN][1000 genomes]
rs35445148	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35971332	0.96[ASN][1000 genomes]
rs56408441	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56938121	0.92[ASN][1000 genomes]
rs59668913	0.92[ASN][1000 genomes]
rs71322851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322855	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322856	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322857	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322858	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7430987	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7638207	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642606	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89163800-89164600	Flanking Active TSS	Brain Germinal Matrix	brain
2	chr3:89164200-89164600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr3:89164200-89164600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr3:89164200-89164600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
5	chr3:89164200-89165000	Flanking Active TSS	Fetal Brain Female	brain
6	chr3:89164200-89165200	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:89164200-89166000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:89164200-89168800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:89164400-89164600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:89164400-89164600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:89164400-89164600	Weak transcription	Fetal Brain Male	brain
12	chr3:89164400-89164800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr3:89164400-89166400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:89164400-89169000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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