Variant report

Variant	rs4271908
Chromosome Location	chr3:116110216-116110217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1030577	0.92[ASN][1000 genomes]
rs11924642	0.90[ASN][1000 genomes]
rs11928524	0.90[ASN][1000 genomes]
rs12695326	0.90[ASN][1000 genomes]
rs13068349	0.88[ASN][1000 genomes]
rs13073414	0.92[ASN][1000 genomes]
rs13077694	0.94[EUR][1000 genomes]
rs13088599	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13323946	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1367770	0.90[ASN][1000 genomes]
rs1583183	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17647091	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1920183	0.93[EUR][1000 genomes]
rs34642483	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35061171	0.92[EUR][1000 genomes]
rs4831133	0.94[EUR][1000 genomes]
rs4831134	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4831136	0.94[EUR][1000 genomes]
rs6438315	0.90[ASN][1000 genomes]
rs6775240	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786130	0.88[ASN][1000 genomes]
rs71323440	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71625206	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7619907	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630011	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7634137	0.90[ASN][1000 genomes]
rs7652554	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7652923	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9289050	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9289051	0.94[EUR][1000 genomes]
rs9823016	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9827984	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9833356	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9860260	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861474	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9989972	0.93[EUR][1000 genomes]
rs9990359	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	esv3463484	chr3:116098674-116110408	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3463485	chr3:116098674-116110408	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4271908	RNF152	trans	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116103000-116142000	Weak transcription	Fetal Lung	lung
2	chr3:116103800-116110600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:116108000-116110400	Weak transcription	Fetal Brain Male	brain
4	chr3:116108000-116113400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:116108200-116110600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:116108200-116110600	Weak transcription	Fetal Stomach	stomach
7	chr3:116108200-116115200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:116108400-116112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:116108400-116113400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:116108400-116113600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:116108600-116110600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:116108600-116110800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:116108600-116113200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:116108600-116113800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:116108600-116114200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:116109200-116118600	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:116109400-116110600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:116109600-116118400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:116110200-116110600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links