Variant report

Variant	rs12493620
Chromosome Location	chr3:140422914-140422915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10804678	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714676	0.80[EUR][1000 genomes]
rs11716099	0.81[EUR][1000 genomes]
rs11719022	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11927105	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13434128	0.80[EUR][1000 genomes]
rs1604044	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047563	0.84[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs28594654	0.84[EUR][1000 genomes]
rs3856754	0.82[EUR][1000 genomes]
rs3913019	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683376	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683377	0.84[EUR][1000 genomes]
rs4683516	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4683517	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs58602051	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6762605	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6765617	0.89[EUR][1000 genomes]
rs6807820	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651388	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs961554	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9810295	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9815853	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9816082	0.83[EUR][1000 genomes]
rs9845821	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851873	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852037	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876490	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs9878690	0.91[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	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv877546	chr3:140299603-140468370	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv997694	chr3:140324012-140464786	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1008123	chr3:140328825-140464786	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv460869	chr3:140330108-140450655	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv591864	chr3:140330108-140450655	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv818170	chr3:140330108-140454836	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1008838	chr3:140355975-140588726	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv877547	chr3:140366948-140575287	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv829743	chr3:140384246-140559778	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140402000-140424400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:140421200-140423000	Weak transcription	HepG2	liver
3	chr3:140422200-140423200	Enhancers	Placenta	Placenta
4	chr3:140422200-140424400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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