Variant report

Variant	rs10878557
Chromosome Location	chr12:67490557-67490558
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	STAT3	chr12:67490138-67491480	MCF10A-Er-Src	breast:	n/a	chr12:67490805-67490816
2	POLR2A	chr12:67490109-67490570	U87	brain:	n/a	n/a
3	FOS	chr12:67490153-67491520	MCF10A-Er-Src	breast:	n/a	chr12:67490840-67490850 chr12:67490840-67490850 chr12:67490841-67490849 chr12:67490839-67490851 chr12:67490840-67490850
4	FOS	chr12:67490547-67491027	Hela-S3	cervix:	n/a	chr12:67490840-67490850 chr12:67490840-67490850 chr12:67490841-67490849 chr12:67490839-67490851 chr12:67490840-67490850
5	POLR2A	chr12:67490194-67491431	U87	brain:	n/a	n/a
6	FOS	chr12:67490430-67491395	MCF10A-Er-Src	breast:	n/a	chr12:67490840-67490850 chr12:67490840-67490850 chr12:67490841-67490849 chr12:67490839-67490851 chr12:67490840-67490850
7	MYC	chr12:67490394-67491246	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:67490120-67490573	U87	brain:	n/a	n/a
9	STAT3	chr12:67490421-67491150	MCF10A-Er-Src	breast:	n/a	chr12:67490805-67490816
10	STAT3	chr12:67490377-67491169	MCF10A-Er-Src	breast:	n/a	chr12:67490805-67490816
11	POLR2A	chr12:67490188-67491437	U87	brain:	n/a	n/a
12	FOS	chr12:67490329-67491209	MCF10A-Er-Src	breast:	n/a	chr12:67490840-67490850 chr12:67490840-67490850 chr12:67490841-67490849 chr12:67490839-67490851 chr12:67490840-67490850

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67461965..67464455-chr12:67489883..67491932,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257083	TF binding region
ENSG00000256248	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10784604	0.84[EUR][1000 genomes]
rs10878554	0.80[EUR][1000 genomes]
rs10878558	0.92[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11176559	0.82[EUR][1000 genomes]
rs11176566	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11176574	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1526834	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17781082	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1918144	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1949940	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2293420	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2870928	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4368011	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4913315	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4913316	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4913522	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4913524	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302646	1.00[CHB][hapmap]
rs7305168	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7962903	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7973341	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978633	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv899217	chr12:67472631-67501987	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67489400-67490800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:67489400-67491800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:67489800-67490600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:67489800-67491600	Enhancers	HMEC	breast
5	chr12:67489800-67491600	Enhancers	NHEK	skin
6	chr12:67490200-67491200	Enhancers	NHDF-Ad	bronchial
7	chr12:67490200-67491400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:67490200-67491600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:67490400-67490800	Enhancers	Right Ventricle	heart
10	chr12:67490400-67491000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:67490400-67491000	Enhancers	Right Atrium	heart
12	chr12:67490400-67491200	Enhancers	Placenta	Placenta

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