Variant report

Variant	rs28690392
Chromosome Location	chr12:123863576-123863577
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	EGR1	chr12:123863504-123863722	K562	blood:	n/a	n/a
2	EGR1	chr12:123863469-123863751	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123847741..123850160-chr12:123863172..123865699,2	MCF-7	breast:
2	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
3	chr12:123862454..123865045-chr12:123865570..123867094,2	K562	blood:

Variant related genes	Relation type
SETD8	TF binding region
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10846516	1.00[AMR][1000 genomes]
rs11057252	1.00[AMR][1000 genomes]
rs11057257	1.00[AMR][1000 genomes]
rs11057265	1.00[AMR][1000 genomes]
rs11057272	1.00[AMR][1000 genomes]
rs11057278	1.00[AMR][1000 genomes]
rs11057281	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057282	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28553365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28624763	0.88[EUR][1000 genomes]
rs28664930	0.88[EUR][1000 genomes]
rs28698461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828722	0.94[EUR][1000 genomes]
rs28836481	0.85[EUR][1000 genomes]
rs28875264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3881293	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55634633	1.00[AMR][1000 genomes]
rs55932027	1.00[EUR][1000 genomes]
rs73216930	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73216932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73231994	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73233508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7486351	1.00[AMR][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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv826534	chr12:123859610-123876354	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
3	chr12:123859200-123867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:123861400-123866800	Weak transcription	K562	blood
5	chr12:123863200-123864600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:123863400-123864000	Enhancers	HepG2	liver
7	chr12:123863400-123864200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:123863400-123864200	Enhancers	A549	lung
9	chr12:123863400-123864400	Enhancers	NHEK	skin

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