Variant report

Variant	rs7048497
Chromosome Location	chr9:108048933-108048934
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108048778..108051200-chr9:108054042..108056380,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12341869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688962	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57877883	1.00[AMR][1000 genomes]
rs59290851	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479300	1.00[AFR][1000 genomes]
rs6479301	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479302	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479303	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7024012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7033929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046185	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72744219	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72744225	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847744	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847952	0.94[AFR][1000 genomes]
rs7853038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853709	0.83[AMR][1000 genomes]
rs7854064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854282	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7857088	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7860356	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7869261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7873924	0.83[AMR][1000 genomes]
rs7874307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9777083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108022400-108053600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:108027200-108051000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:108028400-108053000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:108033200-108056200	Weak transcription	Primary T cells from cord blood	blood
5	chr9:108033800-108049400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:108033800-108052800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:108034000-108049800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:108034200-108053600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:108043600-108057400	Weak transcription	HSMM	muscle
10	chr9:108043600-108059400	Weak transcription	NHLF	lung
11	chr9:108043600-108059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:108044000-108053600	Weak transcription	Gastric	stomach
13	chr9:108044000-108053600	Weak transcription	Left Ventricle	heart
14	chr9:108044200-108052400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:108044800-108052000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:108044800-108052400	Weak transcription	HMEC	breast
17	chr9:108044800-108056600	Weak transcription	Hela-S3	cervix
18	chr9:108045600-108052800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr9:108045600-108053000	Weak transcription	A549	lung
20	chr9:108046200-108052400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:108046200-108053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:108046400-108049200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:108046400-108049400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:108046400-108049600	Weak transcription	HepG2	liver
25	chr9:108046400-108049800	Weak transcription	Brain Angular Gyrus	brain
26	chr9:108046400-108049800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:108046400-108049800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:108046400-108051000	Weak transcription	Brain Substantia Nigra	brain
29	chr9:108046400-108051600	Weak transcription	Stomach Mucosa	stomach
30	chr9:108046400-108052000	Weak transcription	Fetal Intestine Large	intestine
31	chr9:108046400-108052800	Weak transcription	Brain Anterior Caudate	brain
32	chr9:108046400-108053000	Weak transcription	Small Intestine	intestine
33	chr9:108046400-108053200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:108046400-108053600	Weak transcription	Pancreas	Pancrea
35	chr9:108046600-108049000	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:108046800-108050600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr9:108047800-108050200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr9:108047800-108050200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr9:108047800-108050200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:108048000-108049200	Enhancers	Placenta	Placenta
41	chr9:108048400-108050000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr9:108048400-108050200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr9:108048600-108049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:108048800-108049200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:108048800-108049800	Weak transcription	Brain Cingulate Gyrus	brain

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