Variant report

Variant	rs61930652
Chromosome Location	chr12:86179005-86179006
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	POLR2A	chr12:86178978-86179130	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000258206	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs17345327	0.85[EUR][1000 genomes]
rs1800832	0.85[EUR][1000 genomes]
rs55694421	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55736533	0.88[EUR][1000 genomes]
rs55754162	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55758854	0.86[EUR][1000 genomes]
rs55795518	0.86[EUR][1000 genomes]
rs55811116	0.89[EUR][1000 genomes]
rs55811700	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55853578	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55856700	0.88[EUR][1000 genomes]
rs55899243	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55900789	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55926212	0.88[EUR][1000 genomes]
rs55966514	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56020312	0.86[EUR][1000 genomes]
rs56055322	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56169451	0.81[EUR][1000 genomes]
rs56208754	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56298026	0.81[EUR][1000 genomes]
rs61928894	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928895	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928896	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928898	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928900	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928903	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928904	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61928908	0.91[EUR][1000 genomes]
rs61928913	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61928917	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61928918	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61928956	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61928957	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61928958	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61928959	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930060	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930061	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930062	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930069	0.89[EUR][1000 genomes]
rs61930070	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930071	0.84[AMR][1000 genomes]
rs61930073	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930075	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930079	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930080	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930082	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61930122	0.97[EUR][1000 genomes]
rs61930124	0.88[EUR][1000 genomes]
rs61930128	0.88[EUR][1000 genomes]
rs61930130	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930131	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930135	0.88[EUR][1000 genomes]
rs61930136	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930584	0.83[EUR][1000 genomes]
rs61930595	0.87[EUR][1000 genomes]
rs61930642	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930643	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930651	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930653	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930863	0.88[EUR][1000 genomes]
rs61930876	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930878	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61930880	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61930881	0.87[EUR][1000 genomes]
rs61930882	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61930895	0.81[EUR][1000 genomes]
rs7962310	0.88[EUR][1000 genomes]
rs7973110	0.88[EUR][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	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86170200-86179200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:86176600-86179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:86176800-86179200	Weak transcription	Esophagus	oesophagus
4	chr12:86179000-86180000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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