Variant report

Variant	rs9372889
Chromosome Location	chr6:128690470-128690471
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	chr6:128672173..128673690-chr6:128688740..128690797,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12055766	0.83[JPT][hapmap]
rs1339191	0.88[JPT][hapmap]
rs1339193	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3822945	0.81[CHB][hapmap]
rs4085784	0.81[CHB][hapmap]
rs4296904	0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57546390	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6934873	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7744436	0.88[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9385457	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388629	0.93[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9402037	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9491939	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs953549	0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs964179	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128678800-128697000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:128679600-128732000	Weak transcription	Left Ventricle	heart
3	chr6:128679800-128697600	Weak transcription	HSMMtube	muscle
4	chr6:128680000-128691400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:128681800-128695600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:128684600-128696600	Weak transcription	HSMM	muscle
7	chr6:128684800-128696400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:128686200-128692600	Enhancers	HepG2	liver
9	chr6:128686600-128696600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:128686800-128695400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:128687000-128693000	Enhancers	Fetal Intestine Large	intestine
12	chr6:128687000-128693000	Enhancers	Fetal Intestine Small	intestine
13	chr6:128688200-128692000	Enhancers	HUVEC	blood vessel
14	chr6:128688200-128697000	Weak transcription	Colonic Mucosa	Colon
15	chr6:128688600-128692200	Enhancers	Brain Hippocampus Middle	brain
16	chr6:128688800-128691200	Weak transcription	Small Intestine	intestine
17	chr6:128688800-128697200	Weak transcription	Pancreas	Pancrea
18	chr6:128688800-128697200	Weak transcription	HMEC	breast
19	chr6:128688800-128706800	Weak transcription	Gastric	stomach
20	chr6:128688800-128738800	Weak transcription	Psoas Muscle	Psoas
21	chr6:128689200-128691000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:128689200-128691600	Enhancers	Brain Anterior Caudate	brain
23	chr6:128689400-128691000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:128689400-128691000	Enhancers	Stomach Mucosa	stomach
25	chr6:128689400-128691600	Enhancers	A549	lung
26	chr6:128689400-128692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:128689600-128690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:128689600-128690800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:128689600-128691200	Weak transcription	NH-A	brain
30	chr6:128689800-128691000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:128689800-128691000	Weak transcription	Liver	Liver
32	chr6:128689800-128691000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:128689800-128691000	Weak transcription	Fetal Lung	lung
34	chr6:128689800-128693800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:128690000-128690800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:128690000-128690800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:128690000-128690800	Weak transcription	NHDF-Ad	bronchial
38	chr6:128690000-128691000	Weak transcription	NHLF	lung
39	chr6:128690000-128691000	Weak transcription	Osteobl	bone
40	chr6:128690000-128692000	Weak transcription	Fetal Heart	heart
41	chr6:128690000-128696400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:128690000-128697200	Weak transcription	Ovary	ovary
43	chr6:128690000-128697200	Weak transcription	NHEK	skin
44	chr6:128690000-128704400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:128690200-128690600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:128690400-128691400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:128690400-128701800	Weak transcription	Rectal Mucosa Donor 29	rectum

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