Variant report

Variant	rs59339937
Chromosome Location	chr12:48559528-48559529
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	CTCF	chr12:48558763-48559625	A549	lung:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
2	RAD21	chr12:48558777-48559582	SK-N-SH	brain:	n/a	chr12:48558865-48558875
3	CTCF	chr12:48559400-48559550	NHLF	lung:	n/a	n/a
4	CTCF	chr12:48559517-48559610	Spleen_OC	spleen:	n/a	n/a
5	CTCF	chr12:48559480-48559630	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48559108..48559625-chr12:48848164..48848665,2	MCF-7	breast:
2	chr12:48477561..48478652-chr12:48558658..48559651,7	MCF-7	breast:
3	chr12:48477632..48478212-chr12:48558666..48559592,2	MCF-7	breast:
4	chr12:48559402..48559905-chr12:48574920..48575635,2	MCF-7	breast:
5	chr12:48559054..48559616-chr12:48570377..48571168,2	K562	blood:
6	chr12:48549808..48555740-chr12:48556420..48560606,6	K562	blood:
7	chr12:48239241..48242168-chr12:48557559..48560161,2	K562	blood:

Variant related genes	Relation type
ENSG00000258051	TF binding region
ENSG00000258051	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10467100	1.00[EUR][1000 genomes]
rs11168368	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830088	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830546	1.00[ASN][1000 genomes]
rs11833210	1.00[EUR][1000 genomes]
rs11833896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835145	1.00[ASN][1000 genomes]
rs11835282	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835720	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836542	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838217	1.00[EUR][1000 genomes]
rs12297117	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793947	1.00[EUR][1000 genomes]
rs34116679	1.00[EUR][1000 genomes]
rs34120080	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34698661	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445616	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35725325	1.00[EUR][1000 genomes]
rs35902603	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272745	1.00[EUR][1000 genomes]
rs41272751	1.00[EUR][1000 genomes]
rs41272757	1.00[EUR][1000 genomes]
rs41272761	1.00[EUR][1000 genomes]
rs56265470	1.00[EUR][1000 genomes]
rs57550917	1.00[EUR][1000 genomes]
rs57783574	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58279970	1.00[EUR][1000 genomes]
rs58373242	1.00[ASN][1000 genomes]
rs58573495	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60894356	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297147	1.00[EUR][1000 genomes]
rs73297150	1.00[EUR][1000 genomes]
rs73297159	1.00[EUR][1000 genomes]
rs73302878	0.94[AFR][1000 genomes]
rs73304908	0.88[AFR][1000 genomes]
rs74086446	1.00[EUR][1000 genomes]
rs74088715	1.00[EUR][1000 genomes]
rs74088779	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv976608	chr12:48558446-48563571	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48559400-48559600	Enhancers	HepG2	liver

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