Variant report

Variant	rs28425774
Chromosome Location	chr8:49221390-49221391
allele	C/T
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	FOS	chr8:49221096-49221439	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr8:49221123-49221472	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr8:49221079-49221417	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr8:49221094-49221488	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr8:49221118-49221462	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr8:49221060-49221411	IMR90	lung:	n/a	n/a
7	STAT3	chr8:49221083-49221444	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr8:49221086-49221432	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr8:49221273-49221482	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
RNU6-295P	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10089957	0.98[EUR][1000 genomes]
rs10090055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094488	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10103603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10429331	1.00[ASN][1000 genomes]
rs10441555	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779066	0.84[EUR][1000 genomes]
rs11780976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781996	1.00[ASN][1000 genomes]
rs11783234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12334641	0.84[EUR][1000 genomes]
rs13261537	1.00[ASN][1000 genomes]
rs16935766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873278	0.88[EUR][1000 genomes]
rs4873279	0.88[EUR][1000 genomes]
rs56379242	1.00[ASN][1000 genomes]
rs58478977	1.00[ASN][1000 genomes]
rs59662112	1.00[ASN][1000 genomes]
rs7017698	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72635679	1.00[ASN][1000 genomes]
rs72635680	1.00[ASN][1000 genomes]
rs72635681	1.00[ASN][1000 genomes]
rs72635683	1.00[ASN][1000 genomes]
rs72635685	1.00[ASN][1000 genomes]
rs72635687	1.00[ASN][1000 genomes]
rs72635692	1.00[ASN][1000 genomes]
rs7833910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834216	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831310	chr8:49080177-49256440	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831311	chr8:49106160-49290209	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1018242	chr8:49190915-49243694	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv539600	chr8:49190915-49243694	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49217400-49222400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:49218000-49222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:49218200-49228600	Weak transcription	Esophagus	oesophagus
4	chr8:49219200-49222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:49219200-49227400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:49219200-49228000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:49220200-49221800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:49220200-49222000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:49220400-49221400	Weak transcription	Fetal Stomach	stomach
10	chr8:49221200-49221400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:49221200-49221800	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links