Variant report

Variant	rs9833356
Chromosome Location	chr3:116105501-116105502
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:115858694..115859203-chr3:116105156..116105712,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10212415	0.86[ASN][1000 genomes]
rs10212559	0.86[ASN][1000 genomes]
rs1030577	0.99[ASN][1000 genomes]
rs11924642	1.00[ASN][1000 genomes]
rs11928524	1.00[ASN][1000 genomes]
rs12695326	1.00[ASN][1000 genomes]
rs13068349	0.97[ASN][1000 genomes]
rs13069948	0.86[ASN][1000 genomes]
rs13070962	0.86[ASN][1000 genomes]
rs13073414	0.99[ASN][1000 genomes]
rs13077694	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088599	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367770	1.00[ASN][1000 genomes]
rs1583183	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1731596	0.85[ASN][1000 genomes]
rs17647091	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920183	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34642483	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35061171	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4271908	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4831096	0.86[ASN][1000 genomes]
rs4831133	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4831134	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4831136	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4831138	0.86[ASN][1000 genomes]
rs6438315	1.00[ASN][1000 genomes]
rs6775240	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786130	0.97[ASN][1000 genomes]
rs71323440	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71625206	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7619907	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629472	0.87[ASN][1000 genomes]
rs7630011	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7634137	1.00[ASN][1000 genomes]
rs7637573	0.86[ASN][1000 genomes]
rs7652554	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7652923	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9289050	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289051	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823016	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9827984	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9838534	0.87[ASN][1000 genomes]
rs9860105	0.86[ASN][1000 genomes]
rs9860236	0.89[ASN][1000 genomes]
rs9860260	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861474	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989972	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9990359	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv437338	chr3:116076289-116110635	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2757005	chr3:116085678-116121948	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv2759170	chr3:116085678-116121948	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1014989	chr3:116096198-116109192	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1003543	chr3:116096198-116111430	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3463484	chr3:116098674-116110408	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3463485	chr3:116098674-116110408	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv21066	chr3:116098946-116109977	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv516570	chr3:116099041-116108165	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1011591	chr3:116099041-116109192	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9833356	RNF152	trans	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116096400-116108000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:116103000-116107400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:116103000-116107400	Weak transcription	Fetal Brain Male	brain
4	chr3:116103000-116142000	Weak transcription	Fetal Lung	lung
5	chr3:116103600-116107200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:116103800-116107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:116103800-116107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:116103800-116107600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:116103800-116110600	Weak transcription	Brain Germinal Matrix	brain
10	chr3:116104200-116107400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:116104200-116107600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:116104400-116107600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:116104400-116107600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:116104600-116107000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:116105000-116110200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links