Variant report

Variant	rs296693
Chromosome Location	chr9:93730496-93730497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr9:93730320-93730734	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr9:93730361-93730704	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93728320..93731079-chr9:93741313..93742989,2	MCF-7	breast:
2	chr9:93729468..93731137-chr9:93737514..93740454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228216	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1380950	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1380951	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1380952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs169851	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs296610	0.86[CHD][hapmap]
rs296688	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs296690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296691	0.81[EUR][1000 genomes]
rs296696	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296708	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs296710	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs296714	0.83[EUR][1000 genomes]
rs296715	0.83[EUR][1000 genomes]
rs296716	0.83[EUR][1000 genomes]
rs296717	0.82[EUR][1000 genomes]
rs296718	0.80[EUR][1000 genomes]
rs296721	0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs379129	0.81[EUR][1000 genomes]
rs386034	0.81[EUR][1000 genomes]
rs431158	0.82[EUR][1000 genomes]
rs452395	0.82[EUR][1000 genomes]
rs7034608	0.85[CEU][hapmap];0.85[TSI][hapmap]

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
rs296693	RP11-367F23.1	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 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	chr9:93726200-93730600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr9:93726200-93731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:93726800-93730800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:93727200-93735800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:93728200-93730600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:93728200-93733400	Weak transcription	Aorta	Aorta
8	chr9:93728600-93732800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:93728600-93732800	Weak transcription	Fetal Stomach	stomach
10	chr9:93729200-93730600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:93729200-93732800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:93729400-93730600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:93729400-93732400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:93729400-93734400	Weak transcription	Osteobl	bone
15	chr9:93729600-93731000	Weak transcription	NHEK	skin
16	chr9:93729600-93731200	Weak transcription	HMEC	breast
17	chr9:93729600-93732400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:93729600-93732400	Weak transcription	Esophagus	oesophagus
19	chr9:93729600-93732400	Weak transcription	NHDF-Ad	bronchial
20	chr9:93729600-93732800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:93729600-93733800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:93729600-93734400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:93729600-93737600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:93729800-93731000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:93729800-93731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:93729800-93731600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:93730200-93732800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:93730200-93734400	Weak transcription	NH-A	brain
29	chr9:93730200-93734600	Weak transcription	Fetal Brain Female	brain
30	chr9:93730400-93730800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:93730400-93741600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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