Variant report

Variant	rs12054457
Chromosome Location	chr3:179691094-179691095
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	POLR2A	chr3:179691076-179691311	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:179690933-179691302	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:179690845-179691251	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PEX5L	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10804882	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715337	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2031044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056597	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383017	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67420747	0.93[ASN][1000 genomes]
rs6764609	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67667466	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9817201	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9822440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9841654	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871887	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9875854	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv33044	chr3:179688785-179691941	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region lncRNA	1 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	chr3:179686000-179691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:179686400-179691800	Weak transcription	Osteobl	bone
3	chr3:179686800-179692000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:179686800-179692200	Active TSS	Brain Substantia Nigra	brain
5	chr3:179687400-179692200	Active TSS	Brain Anterior Caudate	brain
6	chr3:179688400-179692200	Active TSS	Brain Hippocampus Middle	brain
7	chr3:179688800-179691400	Weak transcription	Fetal Thymus	thymus
8	chr3:179688800-179691600	Weak transcription	Thymus	Thymus
9	chr3:179688800-179692000	Active TSS	Brain Angular Gyrus	brain
10	chr3:179689400-179691200	Flanking Active TSS	Dnd41	blood
11	chr3:179689400-179710200	Weak transcription	Fetal Brain Male	brain
12	chr3:179690200-179691800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:179690200-179692200	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:179690400-179692200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:179690600-179691600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:179690800-179691800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:179690800-179691800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr3:179690800-179692200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:179690800-179692400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:179690800-179692600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:179691000-179691200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:179691000-179692000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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