Variant report

Variant	rs56232005
Chromosome Location	chr9:107894865-107894866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:107889900..107891931-chr9:107892522..107895026,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10991555	0.83[EUR][1000 genomes]
rs12003255	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4317634	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4381000	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55872032	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56202605	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59179413	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66488152	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022410	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033651	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607110	0.80[ASN][1000 genomes]
rs72607111	0.80[ASN][1000 genomes]
rs72607112	0.89[ASN][1000 genomes]
rs72607113	0.89[ASN][1000 genomes]
rs72607114	0.89[ASN][1000 genomes]
rs72607115	0.89[ASN][1000 genomes]
rs72607116	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607117	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607118	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607119	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607120	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607121	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607122	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607123	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72607124	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72607125	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7866729	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792436	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792586	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792666	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792667	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	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
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:107882400-107900600	Weak transcription	Brain Hippocampus Middle	brain
2	chr9:107888800-107900800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:107889600-107895200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:107890400-107895200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:107890600-107895000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:107891600-107903000	Weak transcription	Esophagus	oesophagus
7	chr9:107892000-107903000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:107892400-107900600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:107893600-107900400	Weak transcription	Fetal Thymus	thymus
10	chr9:107893600-107900600	Weak transcription	Primary T cells from cord blood	blood
11	chr9:107893600-107900800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:107893600-107907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:107893800-107895400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:107893800-107895800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:107893800-107895800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:107894000-107895000	Enhancers	Fetal Muscle Trunk	muscle
17	chr9:107894000-107895400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:107894000-107895400	Enhancers	NH-A	brain
19	chr9:107894000-107896200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:107894000-107897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:107894200-107895400	Enhancers	NHLF	lung
22	chr9:107894200-107895800	Enhancers	Placenta	Placenta
23	chr9:107894400-107896600	Enhancers	Hela-S3	cervix
24	chr9:107894600-107895600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:107894600-107895600	Enhancers	Osteobl	bone
26	chr9:107894600-107895800	Enhancers	NHDF-Ad	bronchial
27	chr9:107894600-107896000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:107894800-107895000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:107894800-107895200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:107894800-107895400	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links