Variant report

Variant	rs3733093
Chromosome Location	chr3:47287883-47287884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47287521..47289047-chr3:47290357..47292031,2	K562	blood:
2	chr3:47276538..47278116-chr3:47285524..47288270,2	K562	blood:
3	chr3:47286980..47288792-chr3:47322744..47324796,2	K562	blood:
4	chr3:47192656..47195424-chr3:47287048..47290020,2	K562	blood:
5	chr3:47285945..47288434-chr3:47322946..47325919,2	MCF-7	breast:
6	chr3:47285472..47289397-chr3:47290230..47292753,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47284469-47287987	NONHSAT089488
2	lnc-KLHL18-1	chr3:47284469-47288091	ENSG00000227398.3

No data

Variant related genes	Relation type
ENSG00000114648	Chromatin interaction
ENSG00000239128	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11712779	1.00[ASN][1000 genomes]
rs12487863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs12490251	0.82[AMR][1000 genomes]
rs12490467	0.81[EUR][1000 genomes]
rs12493011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12495173	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12495438	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12636235	1.00[CEU][hapmap]
rs17079512	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17079543	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17079580	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs17079634	1.00[CHD][hapmap]
rs2291721	0.84[AMR][1000 genomes]
rs3821879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627772	0.90[AMR][1000 genomes]
rs4683321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs4683328	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4858889	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs58206566	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7638049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
9	chr3:47277000-47288200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:47277000-47292000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:47277600-47300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:47279800-47288800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:47282200-47291800	Weak transcription	HepG2	liver
14	chr3:47282200-47300400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:47282200-47300600	Weak transcription	Lung	lung
16	chr3:47282600-47292400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:47283400-47293200	Weak transcription	Psoas Muscle	Psoas
19	chr3:47284800-47300400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
21	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:47285800-47289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:47286400-47299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:47286600-47288000	Weak transcription	Fetal Stomach	stomach
25	chr3:47287200-47293200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:47287400-47292000	Weak transcription	K562	blood
27	chr3:47287400-47299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links