Variant report

Variant	rs56169451
Chromosome Location	chr12:86268941-86268942
allele	G/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	chr12:86267796-86270056	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
NTS	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1800832	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55644633	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55694421	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55736533	0.92[EUR][1000 genomes]
rs55746689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55754162	0.83[EUR][1000 genomes]
rs55811116	0.91[EUR][1000 genomes]
rs55811700	0.90[EUR][1000 genomes]
rs55853578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55856700	0.92[EUR][1000 genomes]
rs55899243	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55900789	0.90[EUR][1000 genomes]
rs55926212	0.92[EUR][1000 genomes]
rs55966514	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56055322	0.83[EUR][1000 genomes]
rs56208754	0.83[EUR][1000 genomes]
rs56298026	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323012	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928894	0.90[EUR][1000 genomes]
rs61928895	0.90[EUR][1000 genomes]
rs61928896	0.90[EUR][1000 genomes]
rs61928898	0.90[EUR][1000 genomes]
rs61928900	0.90[EUR][1000 genomes]
rs61928903	0.90[EUR][1000 genomes]
rs61928904	0.88[EUR][1000 genomes]
rs61928908	0.90[EUR][1000 genomes]
rs61928913	0.91[EUR][1000 genomes]
rs61928917	0.91[EUR][1000 genomes]
rs61928918	0.84[EUR][1000 genomes]
rs61928956	0.91[EUR][1000 genomes]
rs61928957	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928958	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928959	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930060	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930061	0.83[EUR][1000 genomes]
rs61930062	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930069	0.91[EUR][1000 genomes]
rs61930070	0.83[EUR][1000 genomes]
rs61930071	0.84[AMR][1000 genomes]
rs61930073	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930075	0.83[EUR][1000 genomes]
rs61930079	0.83[EUR][1000 genomes]
rs61930080	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930082	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930122	0.84[EUR][1000 genomes]
rs61930124	0.92[EUR][1000 genomes]
rs61930128	0.92[EUR][1000 genomes]
rs61930130	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61930131	0.84[EUR][1000 genomes]
rs61930135	0.92[EUR][1000 genomes]
rs61930136	0.84[EUR][1000 genomes]
rs61930642	0.90[EUR][1000 genomes]
rs61930643	0.90[EUR][1000 genomes]
rs61930649	0.81[EUR][1000 genomes]
rs61930651	0.90[EUR][1000 genomes]
rs61930652	0.81[EUR][1000 genomes]
rs61930653	0.90[EUR][1000 genomes]
rs61930863	0.92[EUR][1000 genomes]
rs61930876	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61930878	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61930880	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61930881	0.94[EUR][1000 genomes]
rs61930882	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61930895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7132746	0.81[EUR][1000 genomes]
rs7962310	0.92[EUR][1000 genomes]
rs7973110	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1049443	chr12:86185887-86272493	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	esv1797806	chr12:86198935-86425608	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1036914	chr12:86201703-86272493	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86267600-86269200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr12:86267600-86270000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:86267800-86269000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:86267800-86269000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:86267800-86271200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:86268600-86269200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:86268600-86269800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:86268800-86270800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:86268800-86271200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:86268800-86271200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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