Variant report

Variant	rs296688
Chromosome Location	chr9:93727875-93727876
allele	C/T
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	SRF	chr9:93727574-93728023	ECC-1	luminal epithelium:	n/a	n/a
2	SRF	chr9:93727511-93728024	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF143	chr9:93727845-93728274	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr9:93727343-93728125	H1-neurons	neurons:	n/a	chr9:93727402-93727420
5	POLR2A	chr9:93727358-93728125	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr9:93727860-93728010	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93725779..93727886-chr9:94185947..94188539,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228216	TF binding region
ENSG00000165030	Chromatin interaction
ENSG00000233081	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1572300	0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs169851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296690	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs296691	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296693	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs296721	0.85[CEU][hapmap]
rs379129	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386034	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426870	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs431158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034608	0.81[CEU][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
rs296688	RP11-367F23.1	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93724200-93728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:93724200-93728200	Weak transcription	HMEC	breast
3	chr9:93724200-93728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:93724200-93736000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:93724400-93728600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:93726200-93730600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr9:93726200-93731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:93726400-93728000	Active TSS	Colon Smooth Muscle	Colon
9	chr9:93726400-93728000	Enhancers	Fetal Lung	lung
10	chr9:93726400-93729600	Enhancers	NHDF-Ad	bronchial
11	chr9:93726400-93730200	Enhancers	NH-A	brain
12	chr9:93726400-93730400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr9:93726600-93728200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr9:93726600-93729600	Enhancers	Esophagus	oesophagus
15	chr9:93726800-93728000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:93726800-93730800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:93727000-93728000	Weak transcription	Fetal Heart	heart
18	chr9:93727000-93728000	Weak transcription	Osteobl	bone
19	chr9:93727000-93729200	Weak transcription	GM12878-XiMat	blood
20	chr9:93727200-93728200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:93727200-93729200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:93727200-93735800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:93727400-93729000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:93727400-93729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:93727600-93728000	Weak transcription	Aorta	Aorta
26	chr9:93727600-93728000	Enhancers	Brain Cingulate Gyrus	brain
27	chr9:93727600-93728000	Enhancers	Placenta	Placenta
28	chr9:93727600-93728000	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr9:93727600-93728400	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr9:93727600-93728600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:93727600-93728600	Enhancers	Fetal Stomach	stomach
32	chr9:93727600-93728800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:93727600-93729200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:93727600-93729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:93727600-93729200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:93727600-93729600	Enhancers	NHEK	skin
37	chr9:93727600-93729800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:93727800-93728000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr9:93727800-93728800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:93727800-93730400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links