Variant report

Variant	rs9461144
Chromosome Location	chr6:25358069-25358070
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	chr6:25348848..25351253-chr6:25357378..25359021,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11491476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11965829	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16890448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16890454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56930318	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs57899991	0.97[ASN][1000 genomes]
rs60384851	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456670	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456671	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6456672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456673	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456674	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6456675	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456677	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932311	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73399971	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7750545	0.84[AFR][1000 genomes]
rs7750609	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7770521	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9461142	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9461143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467474	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986335	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9986525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986608	0.93[AFR][1000 genomes];0.97[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
3	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:25349200-25359200	Weak transcription	Ovary	ovary
7	chr6:25350800-25359200	Weak transcription	Lung	lung
8	chr6:25351000-25359600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:25351800-25359200	Weak transcription	HSMMtube	muscle
10	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:25353000-25359400	Weak transcription	Fetal Thymus	thymus
12	chr6:25353200-25359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:25353200-25359600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:25353400-25358200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:25353400-25358800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:25353400-25359200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:25353400-25359200	Weak transcription	Small Intestine	intestine
18	chr6:25353800-25359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:25354600-25359400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:25355000-25359200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:25355000-25359200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:25355000-25359200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:25355000-25359400	Weak transcription	NH-A	brain
24	chr6:25355200-25358200	Weak transcription	Fetal Lung	lung
25	chr6:25355200-25358800	Weak transcription	NHDF-Ad	bronchial
26	chr6:25355200-25359200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:25355200-25359200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:25355200-25359200	Weak transcription	Osteobl	bone
29	chr6:25355200-25359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:25355200-25359400	Weak transcription	Right Atrium	heart
31	chr6:25355400-25358200	Weak transcription	NHLF	lung
32	chr6:25355400-25359000	Weak transcription	Fetal Heart	heart
33	chr6:25355400-25359200	Weak transcription	Stomach Mucosa	stomach
34	chr6:25355400-25359400	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:25355600-25358800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:25355600-25359600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:25356000-25359400	Weak transcription	Fetal Intestine Large	intestine
38	chr6:25356000-25359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:25357000-25358800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:25357200-25358200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:25357200-25358200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:25357200-25359400	Weak transcription	Aorta	Aorta
43	chr6:25357400-25359000	Weak transcription	Brain Germinal Matrix	brain
44	chr6:25357400-25359400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:25357600-25359400	Enhancers	HMEC	breast
46	chr6:25357800-25358600	Enhancers	NHEK	skin
47	chr6:25357800-25359200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:25357800-25359400	Weak transcription	Left Ventricle	heart
49	chr6:25358000-25358400	Enhancers	Fetal Intestine Small	intestine

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