Variant report

Variant	rs6486847
Chromosome Location	chr12:8309235-8309236
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	chr12:8309005-8310061	MCF10A-Er-Src	breast:	n/a	chr12:8309988-8309999 chr12:8309713-8309720 chr12:8309662-8309685
2	STAT3	chr12:8309093-8309239	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:8309025-8310321	MCF10A-Er-Src	breast:	n/a	chr12:8309427-8309439 chr12:8309700-8309711 chr12:8309425-8309436 chr12:8310054-8310063 chr12:8309810-8309822
4	FOS	chr12:8309039-8309943	MCF10A-Er-Src	breast:	n/a	chr12:8309427-8309439 chr12:8309700-8309711 chr12:8309425-8309436 chr12:8309810-8309822
5	FOS	chr12:8309050-8310069	HUVEC	blood vessel:	n/a	chr12:8309427-8309439 chr12:8309700-8309711 chr12:8309425-8309436 chr12:8310054-8310063 chr12:8309810-8309822
6	FOS	chr12:8309039-8309877	MCF10A-Er-Src	breast:	n/a	chr12:8309427-8309439 chr12:8309700-8309711 chr12:8309425-8309436 chr12:8309810-8309822
7	STAT3	chr12:8309080-8309897	MCF10A-Er-Src	breast:	n/a	chr12:8309713-8309720 chr12:8309662-8309685

Variant related genes	Relation type
ZNF705A	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10840780	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10840818	0.89[EUR][1000 genomes]
rs10840833	0.89[EUR][1000 genomes]
rs10840834	0.89[EUR][1000 genomes]
rs10840849	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs10840850	0.89[EUR][1000 genomes]
rs10840851	0.88[EUR][1000 genomes]
rs10840853	0.89[EUR][1000 genomes]
rs11043583	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11043584	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11043596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11043622	0.89[EUR][1000 genomes]
rs11519179	0.82[EUR][1000 genomes]
rs11561182	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12821184	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12821378	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4293193	0.96[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs4297540	0.96[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs4589367	0.89[EUR][1000 genomes]
rs4604965	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294887	0.89[EUR][1000 genomes]
rs7296152	0.89[EUR][1000 genomes]
rs7296176	0.89[EUR][1000 genomes]
rs7963107	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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 target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
9	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv430460	chr12:8225225-8388656	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	esv1796538	chr12:8276546-8508693	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv427902	chr12:8276546-8623987	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	esv2757488	chr12:8280755-8580804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1800691	chr12:8295128-8379865	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	esv1799331	chr12:8308073-8568222	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	esv1808210	chr12:8309095-8530951	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6486847	PRH2	cis	parietal	SCAN
rs6486847	LOC283314	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8306400-8311000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:8306600-8311000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:8307800-8309400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:8308000-8309400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:8308600-8309400	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:8308600-8309400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:8308600-8309400	Enhancers	HUVEC	blood vessel
8	chr12:8308600-8310800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:8308600-8310800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:8308800-8309400	Weak transcription	Primary T cells from cord blood	blood
11	chr12:8308800-8309600	Enhancers	A549	lung
12	chr12:8308800-8310600	Enhancers	HMEC	breast
13	chr12:8309000-8309600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:8309000-8310400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:8309000-8310600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:8309200-8309800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:8309200-8309800	Enhancers	HSMM	muscle
18	chr12:8309200-8310000	Enhancers	NHEK	skin
19	chr12:8309200-8310200	Enhancers	K562	blood
20	chr12:8309200-8310200	Enhancers	Osteobl	bone
21	chr12:8309200-8310600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:8309200-8310600	Enhancers	NH-A	brain
23	chr12:8309200-8311000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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