Variant report

Variant	rs4894329
Chromosome Location	chr3:138640139-138640140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138311406..138314076-chr3:138638843..138641215,2	MCF-7	breast:
2	chr3:138633449..138636346-chr3:138637626..138640163,2	K562	blood:
3	chr3:138551660..138555221-chr3:138637587..138640487,3	K562	blood:
4	chr3:138633432..138635539-chr3:138639300..138641799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction
ENSG00000114107	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11706291	0.83[EUR][1000 genomes]
rs11716946	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720941	0.83[ASN][1000 genomes]
rs28826701	0.81[EUR][1000 genomes]
rs35514824	0.83[EUR][1000 genomes]
rs36033442	0.83[ASN][1000 genomes]
rs6439828	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634571	0.81[EUR][1000 genomes]
rs9817734	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832447	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846784	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850990	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857349	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858062	0.83[ASN][1000 genomes]
rs9870355	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4894329	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs4894329	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138635200-138640200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:138635200-138640200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:138635200-138640200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:138635200-138640200	Weak transcription	NH-A	brain
5	chr3:138635200-138642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:138635200-138642600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:138635200-138642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:138635200-138652600	Weak transcription	Ovary	ovary
9	chr3:138635200-138654800	Weak transcription	Right Atrium	heart
10	chr3:138635400-138640400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:138635600-138640200	Weak transcription	NHLF	lung
12	chr3:138635800-138640200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:138636000-138640200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:138636000-138640200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:138636000-138640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:138636000-138640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:138636000-138640200	Weak transcription	A549	lung
18	chr3:138636000-138640200	Weak transcription	Hela-S3	cervix
19	chr3:138636000-138640200	Weak transcription	HUVEC	blood vessel
20	chr3:138636000-138640200	Weak transcription	NHDF-Ad	bronchial
21	chr3:138636000-138640200	Weak transcription	NHEK	skin
22	chr3:138636000-138642400	Weak transcription	K562	blood
23	chr3:138636200-138640200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:138638800-138640200	Weak transcription	HepG2	liver
25	chr3:138640000-138640400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:138640000-138640400	Enhancers	Osteobl	bone
27	chr3:138640000-138641600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:138640000-138641600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links