Variant report

Variant	rs2456445
Chromosome Location	chr12:56450577-56450578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56450540..56452685-chr12:56472771..56474484,2	MCF-7	breast:
2	chr12:56435629..56437260-chr12:56449751..56452127,2	K562	blood:

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000065361	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11171736	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1581007	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1619653	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689507	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689516	0.85[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1701705	0.85[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702870	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702875	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1995742	1.00[MEX][hapmap]
rs2452822	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2452826	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2456446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2629449	1.00[MEX][hapmap]
rs35382885	1.00[MEX][hapmap]
rs705706	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7301099	1.00[MEX][hapmap];0.80[MKK][hapmap]
rs7309340	0.85[AFR][1000 genomes]
rs772917	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs772924	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs772925	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs772926	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs773118	0.91[AFR][1000 genomes]
rs773644	1.00[MEX][hapmap]
rs7977521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs808896	0.85[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs808905	0.85[AFR][1000 genomes]
rs9645818	0.88[AFR][1000 genomes]
rs9738150	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56440800-56454000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56440800-56455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:56449000-56453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:56449000-56454000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:56449000-56454000	Weak transcription	HMEC	breast
7	chr12:56449000-56454000	Weak transcription	NHEK	skin
8	chr12:56449200-56456400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:56449400-56454000	Weak transcription	Osteobl	bone
10	chr12:56449600-56450600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:56449600-56453600	Weak transcription	Placenta	Placenta

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