Variant report

Variant	rs296696
Chromosome Location	chr9:93733835-93733836
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	chr9:93733650..93736108-chr9:94185708..94187322,2	MCF-7	breast:
2	chr9:93731886..93734151-chr9:93736139..93738687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165030	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1380950	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1380951	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1380952	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs296690	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296693	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296708	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs296710	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs296714	0.87[EUR][1000 genomes]
rs296715	0.87[EUR][1000 genomes]
rs296716	0.87[EUR][1000 genomes]
rs296717	0.87[EUR][1000 genomes]
rs296718	0.84[EUR][1000 genomes]
rs296721	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs296696	RP11-367F23.1	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93724200-93736000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:93727200-93735800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:93729400-93734400	Weak transcription	Osteobl	bone
4	chr9:93729600-93734400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:93729600-93737600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:93730200-93734400	Weak transcription	NH-A	brain
7	chr9:93730200-93734600	Weak transcription	Fetal Brain Female	brain
8	chr9:93730400-93741600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:93730800-93737000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:93731000-93737400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:93731200-93735600	Enhancers	HMEC	breast
12	chr9:93731200-93737400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:93731400-93737600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:93732400-93735600	Enhancers	Esophagus	oesophagus
15	chr9:93732800-93736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:93733000-93736400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:93733000-93737600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:93733200-93734400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:93733200-93734400	Weak transcription	NHDF-Ad	bronchial
20	chr9:93733200-93735200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:93733200-93738200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:93733400-93734000	Enhancers	Aorta	Aorta
23	chr9:93733400-93734200	Enhancers	GM12878-XiMat	blood
24	chr9:93733400-93735600	Enhancers	NHEK	skin
25	chr9:93733800-93734000	Enhancers	Right Atrium	heart
26	chr9:93733800-93734400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:93733800-93734600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:93733800-93737000	Weak transcription	Fetal Stomach	stomach
29	chr9:93733800-93737800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links