Variant report

Variant	rs10841661
Chromosome Location	chr12:20984832-20984833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10743397	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10770742	0.85[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10770743	0.87[EUR][1000 genomes]
rs10770744	0.87[EUR][1000 genomes]
rs10770747	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770748	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10841662	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841664	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841666	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11045526	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11045527	0.84[EUR][1000 genomes]
rs11045532	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11045534	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11045538	0.81[ASN][1000 genomes]
rs11045542	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045543	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1115043	0.84[EUR][1000 genomes]
rs11513214	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11513396	0.85[EUR][1000 genomes]
rs11519058	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12314926	0.84[ASN][1000 genomes]
rs1581194	0.87[EUR][1000 genomes]
rs1850012	0.85[EUR][1000 genomes]
rs1850013	0.85[EUR][1000 genomes]
rs1850014	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2138334	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2196025	0.84[AMR][1000 genomes]
rs2196026	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2217695	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28811026	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4094277	0.85[EUR][1000 genomes]
rs4318024	0.82[EUR][1000 genomes]
rs4762674	0.85[EUR][1000 genomes]
rs4762675	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4762676	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs61921619	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7133030	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7962265	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971116	0.98[EUR][1000 genomes]
rs7977213	0.85[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs892289	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs9971929	0.87[EUR][1000 genomes]
rs9971933	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv17347	chr12:20892854-21029179	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1051454	chr12:20893994-20999635	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1040033	chr12:20914439-21078855	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv869995	chr12:20929531-21081863	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2758297	chr12:20942215-21117820	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2759882	chr12:20942215-21117820	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv427905	chr12:20942215-21117820	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv428275	chr12:20942215-21117820	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv898859	chr12:20950737-21082276	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv898860	chr12:20964557-21015760	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
14	nsv976583	chr12:20968620-21036807	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10841661	AEBP2	cis	cerebellum	SCAN
rs10841661	SLCO1B3	cis	Nerve Tibial	GTEx
rs10841661	SLCO1C1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20983400-20996400	Weak transcription	Hela-S3	cervix
2	chr12:20983600-20995600	Weak transcription	Liver	Liver
3	chr12:20984000-20985400	Weak transcription	A549	lung

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