Variant report

Variant	rs3959686
Chromosome Location	chr15:58430458-58430459
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	EBF1	chr15:58430389-58430585	GM12878	blood:	n/a	n/a
2	FOS	chr15:58430273-58430540	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr15:58430231-58430539	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr15:58430450-58430498	HepG2	liver:	n/a	n/a
5	CEBPB	chr15:58430360-58430546	A549	lung:	n/a	chr15:58430399-58430410
6	FOS	chr15:58430275-58430510	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr15:58430253-58430528	HepG2	liver:	n/a	chr15:58430399-58430410 chr15:58430353-58430366
8	STAT3	chr15:58430359-58430591	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
AQP9	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10518964	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12050800	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12437895	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440410	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12440784	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440934	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1554203	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16939816	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17571313	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1874156	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2642624	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2704203	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34034101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34246303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511467	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774289	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57139208	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60179196	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60401526	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60802802	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7180019	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73424166	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73426124	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8024969	1.00[YRI][hapmap]
rs8037263	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv904263	chr15:58340072-58437346	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv457172	chr15:58417895-58457507	Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv569597	chr15:58417895-58457507	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58427200-58431000	Enhancers	HMEC	breast
2	chr15:58427400-58430800	Enhancers	NHEK	skin
3	chr15:58427400-58431200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:58427600-58430800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:58428400-58430600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:58428800-58431600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:58428800-58433600	Weak transcription	K562	blood
8	chr15:58429200-58430600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr15:58429400-58430600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:58429600-58432000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr15:58429600-58436800	Active TSS	Primary hematopoietic stem cells	blood
12	chr15:58429800-58430600	Weak transcription	Adipose Nuclei	Adipose
13	chr15:58429800-58431600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:58430000-58436000	Active TSS	Primary B cells from cord blood	blood
15	chr15:58430200-58430800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr15:58430400-58430600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:58430400-58430800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr15:58430400-58430800	Enhancers	Fetal Lung	lung
19	chr15:58430400-58431000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr15:58430400-58431600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr15:58430400-58432400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr15:58430400-58433200	Active TSS	Liver	Liver

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