Variant report

Variant	rs9388654
Chromosome Location	chr6:128889150-128889151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128837776..128844055-chr6:128888331..128895856,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10085247	0.92[EUR][1000 genomes]
rs10085248	0.92[EUR][1000 genomes]
rs10872332	0.87[ASN][1000 genomes]
rs11963575	0.85[EUR][1000 genomes]
rs11969975	0.87[ASN][1000 genomes]
rs12176375	0.87[ASN][1000 genomes]
rs12526667	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13209380	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1341588	1.00[ASN][1000 genomes]
rs13437323	0.89[EUR][1000 genomes]
rs1361595	0.90[EUR][1000 genomes]
rs1417894	0.87[ASN][1000 genomes]
rs1417895	0.87[ASN][1000 genomes]
rs1417896	1.00[ASN][1000 genomes]
rs17055952	0.92[EUR][1000 genomes]
rs2326702	0.90[EUR][1000 genomes]
rs62426794	0.87[EUR][1000 genomes]
rs62426851	0.86[EUR][1000 genomes]
rs6569533	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569535	1.00[ASN][1000 genomes]
rs6569536	1.00[ASN][1000 genomes]
rs6916193	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919106	0.87[ASN][1000 genomes]
rs6920943	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924111	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935611	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356823	1.00[ASN][1000 genomes]
rs7356912	0.92[EUR][1000 genomes]
rs7739600	0.85[EUR][1000 genomes]
rs7745291	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748742	0.89[EUR][1000 genomes]
rs7751265	1.00[ASN][1000 genomes]
rs7752487	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7754729	1.00[ASN][1000 genomes]
rs7760330	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765212	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7771701	0.88[EUR][1000 genomes]
rs7773021	0.87[ASN][1000 genomes]
rs9372893	0.87[ASN][1000 genomes]
rs9372894	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375572	0.87[ASN][1000 genomes]
rs9375575	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375577	0.87[ASN][1000 genomes]
rs9375578	1.00[ASN][1000 genomes]
rs9375579	0.87[ASN][1000 genomes]
rs9385464	0.87[ASN][1000 genomes]
rs9388639	0.87[ASN][1000 genomes]
rs9388640	0.87[ASN][1000 genomes]
rs9388645	0.87[ASN][1000 genomes]
rs9388646	0.87[ASN][1000 genomes]
rs9388647	1.00[ASN][1000 genomes]
rs9388648	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9388649	1.00[ASN][1000 genomes]
rs9388650	1.00[ASN][1000 genomes]
rs9388651	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];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	1.00[ASN][1000 genomes]
rs9402056	0.87[ASN][1000 genomes]
rs9482904	0.92[EUR][1000 genomes]
rs9491990	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9491997	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491999	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492001	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492003	1.00[ASN][1000 genomes]
rs9492013	0.96[EUR][1000 genomes]
rs9492014	0.94[EUR][1000 genomes]
rs9492020	0.88[EUR][1000 genomes]
rs9492021	0.88[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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128882400-128890600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:128882800-128890400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:128887400-128891200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:128887600-128892200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:128887800-128889200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:128887800-128891200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:128888600-128889600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:128888600-128889600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:128888600-128889600	Weak transcription	HMEC	breast
10	chr6:128888600-128890200	Weak transcription	A549	lung
11	chr6:128888800-128890000	Weak transcription	NHDF-Ad	bronchial
12	chr6:128888800-128890200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:128888800-128890200	Weak transcription	Osteobl	bone
14	chr6:128888800-128890600	Weak transcription	NH-A	brain
15	chr6:128888800-128891000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:128888800-128891200	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:128889000-128889400	Weak transcription	HSMM	muscle
18	chr6:128889000-128889400	Weak transcription	NHEK	skin

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