Variant report

Variant	rs4856241
Chromosome Location	chr3:84094818-84094819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CADM2-3	chr3:84094756-84095040	XLOC_002722
2	lnc-CADM2-3	chr3:84094756-84095040	XLOC_002722
3	lnc-CADM2-3	chr3:84094756-84095040	XLOC_002722
4	lnc-CADM2-3	chr3:84094756-84095040	XLOC_002722
5	lnc-CADM2-3	chr3:84094756-84096044	XLOC_002722
6	lnc-CADM2-3	chr3:84094756-84096044	XLOC_002722

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10511091	0.93[ASN][1000 genomes]
rs1528055	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609243	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1918776	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141293	0.94[ASN][1000 genomes]
rs2204663	0.98[ASN][1000 genomes]
rs2204664	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325770	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34843962	0.95[ASN][1000 genomes]
rs34867519	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4053477	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4856481	0.98[ASN][1000 genomes]
rs4856485	0.95[ASN][1000 genomes]
rs4856486	1.00[ASN][1000 genomes]
rs59556403	0.98[ASN][1000 genomes]
rs6548931	0.97[ASN][1000 genomes]
rs6548934	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796519	0.98[ASN][1000 genomes]
rs6798585	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809274	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7631290	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633979	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9863455	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9870140	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006081	chr3:83421626-84262106	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1012918	chr3:83784488-84191829	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv536610	chr3:83784488-84191829	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv877075	chr3:83952144-84199075	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv877076	chr3:83970787-84094818	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv877077	chr3:83976987-84094818	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv834751	chr3:83987488-84133470	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv877078	chr3:83991464-84199075	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv877080	chr3:84056075-84106241	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1007008	chr3:84069044-84653896	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv536612	chr3:84069044-84653896	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv508225	chr3:84084088-84123022	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv877081	chr3:84094818-84199075	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv460743	chr3:84094818-84644186	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv590814	chr3:84094818-84644186	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84094800-84095000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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