Variant report

Variant	rs12646486
Chromosome Location	chr4:120594077-120594078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10007021	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012609	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10013319	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015250	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024373	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10034636	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11929853	1.00[EUR][1000 genomes]
rs11944683	1.00[EUR][1000 genomes]
rs11947667	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12642764	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643785	0.81[ASN][1000 genomes]
rs12648324	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648560	1.00[EUR][1000 genomes]
rs12711079	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13106925	0.82[JPT][hapmap]
rs13108160	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120581	1.00[CHB][hapmap]
rs13121100	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13132106	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137327	0.84[ASN][1000 genomes]
rs17005622	1.00[EUR][1000 genomes]
rs17005818	1.00[EUR][1000 genomes]
rs17005819	1.00[EUR][1000 genomes]
rs17051362	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17051363	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17292047	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs17358524	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs17839126	1.00[EUR][1000 genomes]
rs2252946	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2253534	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389868	1.00[JPT][hapmap]
rs2389870	1.00[CHD][hapmap]
rs2389893	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2389894	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389895	1.00[EUR][1000 genomes]
rs2389896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583607	1.00[EUR][1000 genomes]
rs2583613	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2583614	1.00[EUR][1000 genomes]
rs2714974	1.00[EUR][1000 genomes]
rs2714982	1.00[EUR][1000 genomes]
rs2714983	1.00[EUR][1000 genomes]
rs2714986	1.00[EUR][1000 genomes]
rs2715017	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2715024	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2715025	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2892872	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35581370	0.81[ASN][1000 genomes]
rs36100748	1.00[EUR][1000 genomes]
rs3756155	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs3775846	0.82[JPT][hapmap]
rs3775856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4146267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450908	1.00[EUR][1000 genomes]
rs4834790	0.85[JPT][hapmap]
rs4834796	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58797432	1.00[EUR][1000 genomes]
rs59755197	1.00[EUR][1000 genomes]
rs6817975	0.82[JPT][hapmap]
rs6820878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6821083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6843112	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6843408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6844603	1.00[AMR][1000 genomes]
rs6844952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7441168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676589	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120577600-120605000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:120589400-120599800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120589600-120599800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:120592200-120594600	Enhancers	Rectal Smooth Muscle	rectum
5	chr4:120592600-120594400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:120592800-120595400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:120593400-120594600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:120593400-120594800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:120593400-120594800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:120593600-120594800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:120593800-120594800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr4:120593800-120594800	Enhancers	HUES64 Cell Line	embryonic stem cell

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