Variant report

Variant	rs718452
Chromosome Location	chr9:18827034-18827035
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	chr9:18826203..18828034-chr9:18832223..18834749,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10156461	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10811041	0.83[JPT][hapmap]
rs10811043	0.87[JPT][hapmap]
rs10963783	0.80[ASN][1000 genomes]
rs10963784	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10963785	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10963786	0.87[JPT][hapmap]
rs12551997	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1433812	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1952293	0.86[AMR][1000 genomes]
rs2163999	0.82[AMR][1000 genomes]
rs4567124	0.81[ASN][1000 genomes]
rs6475255	0.83[AMR][1000 genomes]
rs7019871	0.80[ASN][1000 genomes]
rs7026429	0.81[GIH][hapmap]
rs7874702	0.87[JPT][hapmap]
rs934469	0.84[AMR][1000 genomes]
rs9792651	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs718452	IFNA13	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18815400-18829200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:18818000-18845200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:18818200-18828800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:18823000-18834400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:18824000-18827400	Enhancers	Primary T cells from cord blood	blood
6	chr9:18824000-18827800	Enhancers	Fetal Thymus	thymus
7	chr9:18825200-18827800	Strong transcription	NH-A	brain
8	chr9:18825400-18827400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:18825400-18828200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:18825400-18829800	Weak transcription	Aorta	Aorta
11	chr9:18825400-18829800	Weak transcription	Psoas Muscle	Psoas
12	chr9:18825400-18833000	Strong transcription	HSMM	muscle
13	chr9:18825400-18833400	Weak transcription	Right Ventricle	heart
14	chr9:18825400-18845200	Weak transcription	HSMMtube	muscle
15	chr9:18825400-18857200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:18825600-18830200	Weak transcription	NHLF	lung
17	chr9:18825600-18833600	Strong transcription	NHDF-Ad	bronchial
18	chr9:18825600-18857400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:18825800-18827800	Weak transcription	Adipose Nuclei	Adipose
20	chr9:18825800-18828600	Strong transcription	Osteobl	bone
21	chr9:18825800-18829800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:18825800-18829800	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:18826000-18827600	Strong transcription	Fetal Stomach	stomach
24	chr9:18826000-18827800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:18826000-18832600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr9:18826200-18827800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:18826200-18827800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:18826200-18833600	Weak transcription	HUVEC	blood vessel
29	chr9:18826400-18827200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr9:18826400-18827600	Enhancers	Dnd41	blood
31	chr9:18826600-18830400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:18826800-18830600	Weak transcription	Gastric	stomach
33	chr9:18826800-18834600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links