Variant report

Variant	rs10743685
Chromosome Location	chr12:9528951-9528952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9526563..9529363-chr12:9530052..9533405,3	MCF-7	breast:
2	chr12:9516871..9518767-chr12:9528942..9530878,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10743683	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1076524	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10771610	0.93[ASN][1000 genomes]
rs10771613	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771614	0.95[ASN][1000 genomes]
rs10771615	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771616	0.86[ASN][1000 genomes]
rs10843575	0.95[ASN][1000 genomes]
rs11050535	0.88[ASN][1000 genomes]
rs11050600	0.95[ASN][1000 genomes]
rs11050615	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12320763	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1549432	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1549433	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1549434	0.94[ASN][1000 genomes]
rs17732137	0.92[ASN][1000 genomes]
rs2003608	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2113905	0.94[ASN][1000 genomes]
rs28545519	0.81[CEU][hapmap]
rs4882995	0.87[ASN][1000 genomes]
rs4883248	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6487874	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487875	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487876	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68104378	0.91[ASN][1000 genomes]
rs7138857	0.83[ASN][1000 genomes]
rs7139275	0.84[ASN][1000 genomes]
rs7297302	0.93[ASN][1000 genomes]
rs7300552	0.86[ASN][1000 genomes]
rs7301079	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310818	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7398952	0.83[ASN][1000 genomes]
rs7485128	0.89[ASN][1000 genomes]
rs7486071	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7486289	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7487757	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7487829	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7487953	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7488426	0.88[ASN][1000 genomes]
rs7488627	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488926	0.89[ASN][1000 genomes]
rs7955383	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958583	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7968901	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs880369	0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9634110	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv898744	chr12:9518222-9668380	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1049903	chr12:9521487-9546454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10743685	LOH12CR1	cis	cerebellum	SCAN
rs10743685	LOC653113	cis	parietal	SCAN
rs10743685	LOC728715///OVOS2	Cis_chr	lymphoblastoid	RTeQTL
rs10743685	VWF	cis	cerebellum	SCAN
rs10743685	DCAL1	cis	multi-tissue	Pritchard
rs10743685	CLEC6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9526600-9530200	Strong transcription	Fetal Lung	lung
2	chr12:9528000-9531400	Weak transcription	HepG2	liver
3	chr12:9528600-9529000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:9528600-9533400	Weak transcription	Gastric	stomach

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