Variant report

Variant	rs56394279
Chromosome Location	chr3:160171092-160171093
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	chr3:160167088..160169183-chr3:160170999..160172775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10212236	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047210	0.81[AMR][1000 genomes]
rs10513551	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706810	0.82[AMR][1000 genomes]
rs11718121	0.81[AMR][1000 genomes]
rs11918749	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13403	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451761	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1451762	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1451764	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1551190	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1584688	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17236473	0.83[AMR][1000 genomes]
rs17570467	0.84[ASN][1000 genomes]
rs17826221	0.82[AMR][1000 genomes]
rs1882126	0.85[ASN][1000 genomes]
rs1882127	0.81[EUR][1000 genomes]
rs1953506	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2152425	0.83[EUR][1000 genomes]
rs2279457	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305407	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28705750	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3732707	0.85[ASN][1000 genomes]
rs3773372	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3851365	0.83[AMR][1000 genomes]
rs3851366	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4091703	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272947	0.84[EUR][1000 genomes]
rs4292273	0.85[ASN][1000 genomes]
rs4292274	0.85[ASN][1000 genomes]
rs4679655	0.85[ASN][1000 genomes]
rs4679881	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4679885	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4679888	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679889	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4679890	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679891	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4679900	0.85[ASN][1000 genomes]
rs4680576	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4680579	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680580	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680585	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680587	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680588	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55687857	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55731730	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56197102	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58322641	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58665246	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60009222	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60460891	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62272186	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62272791	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272792	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62272794	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272800	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272810	0.85[ASN][1000 genomes]
rs6441313	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441314	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441319	0.87[EUR][1000 genomes]
rs6441320	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6785881	0.81[AMR][1000 genomes]
rs6791261	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6792612	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6793560	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6798668	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803828	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6806505	0.85[ASN][1000 genomes]
rs6808083	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721023	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154592	0.89[EUR][1000 genomes]
rs7356111	0.83[EUR][1000 genomes]
rs7611130	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7618974	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7621724	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7624902	0.81[AMR][1000 genomes]
rs7627749	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7627756	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7629	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7629202	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7631792	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7634108	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7634826	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640072	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643779	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7644453	0.85[ASN][1000 genomes]
rs7645832	0.83[EUR][1000 genomes]
rs7647873	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs869468	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9798898	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9799314	0.85[EUR][1000 genomes]
rs9968151	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56394279	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160168400-160172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:160168400-160172600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:160168400-160172800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:160170200-160171400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:160170200-160175600	Weak transcription	K562	blood
6	chr3:160171000-160171600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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