Variant report

Variant	rs1417896
Chromosome Location	chr6:128880225-128880226
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128839509..128841677-chr6:128878813..128880838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10872332	0.87[ASN][1000 genomes]
rs11154440	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11753496	0.99[EUR][1000 genomes]
rs11758690	0.99[EUR][1000 genomes]
rs11969975	0.87[ASN][1000 genomes]
rs12176375	0.87[ASN][1000 genomes]
rs12524679	0.90[EUR][1000 genomes]
rs12525214	0.96[EUR][1000 genomes]
rs12526634	1.00[EUR][1000 genomes]
rs12527086	0.86[CEU][hapmap];1.00[EUR][1000 genomes]
rs12527265	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12529229	0.90[EUR][1000 genomes]
rs12529511	0.99[EUR][1000 genomes]
rs12529947	0.90[EUR][1000 genomes]
rs12529948	0.99[EUR][1000 genomes]
rs1341584	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1341585	0.86[CEU][hapmap];0.96[EUR][1000 genomes]
rs1341588	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417894	0.87[ASN][1000 genomes]
rs1417895	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1572964	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs17055938	1.00[CHB][hapmap]
rs17056043	0.96[EUR][1000 genomes]
rs17461759	0.86[CEU][hapmap]
rs2144376	1.00[CEU][hapmap]
rs62426796	0.89[EUR][1000 genomes]
rs62426798	0.92[EUR][1000 genomes]
rs62426801	0.99[EUR][1000 genomes]
rs62426804	1.00[EUR][1000 genomes]
rs62426805	1.00[EUR][1000 genomes]
rs62426806	1.00[EUR][1000 genomes]
rs62426840	1.00[EUR][1000 genomes]
rs62426841	1.00[EUR][1000 genomes]
rs62426842	1.00[EUR][1000 genomes]
rs62426844	1.00[EUR][1000 genomes]
rs62426845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62426846	0.96[EUR][1000 genomes]
rs62426847	0.96[EUR][1000 genomes]
rs62426848	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62426849	0.87[EUR][1000 genomes]
rs62426850	0.87[EUR][1000 genomes]
rs62427780	0.85[EUR][1000 genomes]
rs6569533	1.00[ASN][1000 genomes]
rs6569535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916193	1.00[ASN][1000 genomes]
rs6916294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6919106	0.87[ASN][1000 genomes]
rs6920943	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6923822	1.00[CHB][hapmap]
rs6924111	1.00[ASN][1000 genomes]
rs6935611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs714782	0.85[EUR][1000 genomes]
rs717617	0.87[CEU][hapmap]
rs7356823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7454742	0.96[EUR][1000 genomes]
rs7738739	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745291	1.00[ASN][1000 genomes]
rs7751094	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7751265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754729	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760287	1.00[EUR][1000 genomes]
rs7760330	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7760572	1.00[EUR][1000 genomes]
rs7760682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7768240	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7773021	0.87[ASN][1000 genomes]
rs9321121	1.00[CHB][hapmap]
rs9321122	0.81[EUR][1000 genomes]
rs9372893	0.87[ASN][1000 genomes]
rs9372894	1.00[ASN][1000 genomes]
rs9375570	1.00[CHB][hapmap]
rs9375572	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9375575	1.00[ASN][1000 genomes]
rs9375577	0.87[ASN][1000 genomes]
rs9375578	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375579	0.87[ASN][1000 genomes]
rs9385464	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388638	1.00[CHB][hapmap]
rs9388639	0.87[ASN][1000 genomes]
rs9388640	0.87[ASN][1000 genomes]
rs9388645	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388646	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388647	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388648	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388649	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388651	1.00[ASN][1000 genomes]
rs9388652	1.00[ASN][1000 genomes]
rs9388654	1.00[ASN][1000 genomes]
rs9398873	0.87[ASN][1000 genomes]
rs9398876	0.87[ASN][1000 genomes]
rs9402051	0.87[ASN][1000 genomes]
rs9402052	0.87[ASN][1000 genomes]
rs9402054	0.87[ASN][1000 genomes]
rs9402055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402056	0.87[ASN][1000 genomes]
rs9402057	1.00[CHB][hapmap]
rs9482902	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9491990	0.89[ASN][1000 genomes]
rs9491997	1.00[ASN][1000 genomes]
rs9491999	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492000	0.86[CEU][hapmap];1.00[EUR][1000 genomes]
rs9492001	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492002	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9492003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492004	1.00[EUR][1000 genomes]
rs9492005	1.00[EUR][1000 genomes]
rs9492008	1.00[EUR][1000 genomes]
rs9492011	0.97[EUR][1000 genomes]
rs9492017	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9492018	0.80[AMR][1000 genomes];0.96[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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128879000-128881600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:128879000-128882000	Weak transcription	Fetal Heart	heart

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