Variant report

Variant	rs1389326
Chromosome Location	chr12:66877250-66877251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10506484	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878437	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176196	0.86[AMR][1000 genomes]
rs11176204	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11176205	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11176206	0.89[ASN][1000 genomes]
rs11608268	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11613371	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12229196	0.82[CEU][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12229755	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423909	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12426780	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426787	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12426810	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581104	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12581129	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581152	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12581225	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582720	0.81[EUR][1000 genomes]
rs1289	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1290	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1493485	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1565730	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17245879	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17245893	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17245914	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17245927	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17245958	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17826399	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17826610	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36193666	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751276	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3891951	0.81[JPT][hapmap]
rs3920021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4628763	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4644699	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4913301	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4913306	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4913309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4913434	0.85[EUR][1000 genomes]
rs4913435	0.85[EUR][1000 genomes]
rs4913501	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4913503	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4913510	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4913511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55650393	0.84[EUR][1000 genomes]
rs56219012	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57923140	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58459118	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58720434	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59747012	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60282479	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61690286	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66656315	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66718779	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67093681	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67312362	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67385685	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67590485	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132569	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7135845	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7135945	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72648170	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7304369	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304443	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304485	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7307402	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7307540	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7311930	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7313348	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7316727	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7316747	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7961635	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7976314	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9989032	0.81[JPT][hapmap]

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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv469459	chr12:66854354-66950289	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv559206	chr12:66854354-66950289	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1389326	HELB	cis	parietal	SCAN
rs1389326	AVPR1A	cis	cerebellum	SCAN
rs1389326	TC2N	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66876000-66877400	Enhancers	Brain Germinal Matrix	brain
2	chr12:66876400-66893600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:66876600-66877400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:66876600-66877400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:66876800-66877600	Enhancers	Fetal Heart	heart

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