Variant report

Variant	rs2059759
Chromosome Location	chr12:9396938-9396939
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	NFIC	chr12:9396502-9397225	HepG2	liver:	n/a	n/a
2	JUN	chr12:9396553-9397238	HepG2	liver:	n/a	chr12:9396575-9396584
3	MAFK	chr12:9396632-9397192	HepG2	liver:	n/a	n/a
4	SP1	chr12:9396532-9396971	HepG2	liver:	n/a	n/a
5	CUX1	chr12:9396615-9396986	GM12878	blood:	n/a	n/a
6	ZNF384	chr12:9396786-9397024	GM12878	blood:	n/a	n/a
7	FOXA1	chr12:9396574-9397088	HepG2	liver:	n/a	n/a
8	FOXA1	chr12:9396655-9396946	HepG2	liver:	n/a	n/a
9	JUND	chr12:9396580-9397055	HepG2	liver:	n/a	n/a
10	MYBL2	chr12:9396529-9397056	HepG2	liver:	n/a	n/a
11	ARID3A	chr12:9396541-9397803	HepG2	liver:	n/a	chr12:9397251-9397267
12	STAT3	chr12:9396876-9397945	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr12:9396585-9397538	HepG2	liver:	n/a	chr12:9397349-9397360
14	FOS	chr12:9396851-9397913	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXA2	chr12:9396537-9397212	HepG2	liver:	n/a	n/a
16	FOXA1	chr12:9396564-9397064	HepG2	liver:	n/a	n/a
17	EP300	chr12:9396764-9396938	GM12878	blood:	n/a	chr12:9396856-9396870

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

Extended variants
information (count: 24 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10843222	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10843223	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs11049326	0.85[CHB][hapmap]
rs11049781	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11049845	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs11049846	0.83[ASN][1000 genomes]
rs12303039	0.83[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs12369816	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12423745	0.85[CHB][hapmap]
rs1863841	0.88[YRI][hapmap]
rs2195208	0.85[CHB][hapmap]
rs3741847	0.91[ASN][1000 genomes]
rs3741848	0.91[ASN][1000 genomes]
rs7954451	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2059759	OLR1	cis	parietal	SCAN
rs2059759	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2059759	LOC374443	cis	lymphoblastoid	seeQTL
rs2059759	RP11-22B23.1	cis	Artery Aorta	GTEx
rs2059759	RP11-22B23.1	cis	Whole Blood	GTEx
rs2059759	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs2059759	CREBL2	cis	cerebellum	SCAN
rs2059759	RP11-22B23.1	cis	Artery Tibial	GTEx
rs2059759	RP11-22B23.1	cis	lung	GTEx
rs2059759	DDX12P	cis	Muscle Skeletal	GTEx
rs2059759	DDX12	cis	multi-tissue	Pritchard
rs2059759	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs2059759	RP11-22B23.1	cis	Esophagus Muscularis	GTEx
rs2059759	RP11-22B23.1	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9393200-9397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:9393200-9397400	Weak transcription	Pancreas	Pancrea
3	chr12:9393200-9397400	Weak transcription	Right Ventricle	heart
4	chr12:9393400-9397400	Weak transcription	HMEC	breast
5	chr12:9393400-9398200	Enhancers	HepG2	liver
6	chr12:9393600-9408200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:9393600-9411400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:9394200-9397200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:9394200-9397800	Enhancers	Brain Hippocampus Middle	brain
10	chr12:9395000-9397400	Weak transcription	Brain Angular Gyrus	brain
11	chr12:9395200-9407800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:9395800-9398000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:9396000-9398000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:9396400-9397400	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:9396400-9398200	Enhancers	Liver	Liver
16	chr12:9396600-9397400	Enhancers	GM12878-XiMat	blood
17	chr12:9396800-9397000	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr12:9396800-9397000	Enhancers	Hela-S3	cervix
19	chr12:9396800-9397400	Enhancers	Brain Anterior Caudate	brain
20	chr12:9396800-9397800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:9396800-9397800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:9396800-9399000	Enhancers	Fetal Lung	lung

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