Variant report

Variant	rs7309684
Chromosome Location	chr12:9397430-9397431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:9397417-9397798	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr12:9396996-9397883	MCF10A-Er-Src	breast:	n/a	n/a
3	BATF	chr12:9397419-9397933	GM12878	blood:	n/a	n/a
4	FOS	chr12:9396995-9397976	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:9397065-9397793	MCF10A-Er-Src	breast:	n/a	n/a
6	SMC3	chr12:9397388-9397690	HepG2	liver:	n/a	n/a
7	ARID3A	chr12:9396541-9397803	HepG2	liver:	n/a	chr12:9397251-9397267
8	STAT3	chr12:9396876-9397945	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr12:9396585-9397538	HepG2	liver:	n/a	chr12:9397349-9397360
10	FOS	chr12:9396851-9397913	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr12:9396963-9397929	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr12:9397129-9397600	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr12:9397264-9397955	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000256427	TF binding region
PTMAP4	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10771440	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771443	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771445	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843242	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843243	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843244	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11049800	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11049844	0.92[ASN][1000 genomes]
rs11611191	0.81[CEU][hapmap]
rs12579180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581534	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12815281	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12816390	0.83[EUR][1000 genomes]
rs187536	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs194037	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059760	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059761	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288363	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs252019	0.85[ASN][1000 genomes]
rs252027	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252028	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252030	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252032	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252033	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34333	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34334	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34371	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs34372	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs34856550	0.85[EUR][1000 genomes]
rs4883225	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883226	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913537	0.85[EUR][1000 genomes]
rs56288591	0.83[EUR][1000 genomes]
rs61916190	0.88[ASN][1000 genomes]
rs717179	0.91[ASN][1000 genomes]
rs717181	0.91[ASN][1000 genomes]
rs7299846	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958291	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967738	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974378	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7976100	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980226	0.91[ASN][1000 genomes]
rs7980256	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs877169	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs968786	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1048917	chr12:9393282-9436132	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7309684	RP11-22B23.1	cis	Artery Tibial	GTEx
rs7309684	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs7309684	DDX12P	cis	Muscle Skeletal	GTEx
rs7309684	A2MP1	cis	Adipose Subcutaneous	GTEx
rs7309684	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7309684	DDX12P	cis	Artery Tibial	GTEx
rs7309684	DDX12P	cis	Nerve Tibial	GTEx
rs7309684	RP11-22B23.1	cis	lung	GTEx
rs7309684	DDX12P	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9393400-9398200	Enhancers	HepG2	liver
2	chr12:9393600-9408200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:9393600-9411400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:9394200-9397800	Enhancers	Brain Hippocampus Middle	brain
5	chr12:9395200-9407800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:9395800-9398000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:9396000-9398000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:9396400-9398200	Enhancers	Liver	Liver
9	chr12:9396800-9397800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:9396800-9397800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:9396800-9399000	Enhancers	Fetal Lung	lung
12	chr12:9397200-9397600	Active TSS	Brain Substantia Nigra	brain
13	chr12:9397400-9397600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:9397400-9397800	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr12:9397400-9397800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr12:9397400-9397800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr12:9397400-9397800	Enhancers	Esophagus	oesophagus
18	chr12:9397400-9397800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:9397400-9397800	Enhancers	Fetal Muscle Leg	muscle
20	chr12:9397400-9397800	Enhancers	Pancreas	Pancrea
21	chr12:9397400-9397800	Enhancers	Right Ventricle	heart
22	chr12:9397400-9398000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:9397400-9398000	Enhancers	HMEC	breast
24	chr12:9397400-9398200	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links