Variant report

Variant	rs9838534
Chromosome Location	chr3:116113609-116113610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10212415	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212559	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1030577	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10513826	0.85[CHD][hapmap]
rs11924642	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11928524	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494652	0.80[MEX][hapmap]
rs12695326	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13068349	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13069948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13070962	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13073414	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13075678	0.92[JPT][hapmap]
rs13077535	0.91[JPT][hapmap]
rs13077694	0.99[ASN][1000 genomes]
rs13088599	0.85[ASN][1000 genomes]
rs13323946	0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs1367770	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1583183	1.00[ASN][1000 genomes]
rs16824787	0.88[CEU][hapmap];0.88[CHB][hapmap]
rs1731596	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17647091	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs1920183	0.97[ASN][1000 genomes]
rs1920190	0.86[JPT][hapmap]
rs2100807	0.80[MEX][hapmap]
rs2867100	0.88[CEU][hapmap];0.88[CHB][hapmap]
rs34642483	0.86[ASN][1000 genomes]
rs35061171	0.97[ASN][1000 genomes]
rs41442746	0.86[CHD][hapmap]
rs4831096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4831097	0.86[CHD][hapmap]
rs4831133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs4831134	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4831136	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs4831138	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4831139	0.92[JPT][hapmap]
rs6438315	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775240	0.82[ASN][1000 genomes]
rs6786130	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71323440	0.86[ASN][1000 genomes]
rs71625206	0.97[ASN][1000 genomes]
rs7619907	1.00[ASN][1000 genomes]
rs7629472	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630011	1.00[ASN][1000 genomes]
rs7634137	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7637573	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652554	1.00[ASN][1000 genomes]
rs7652923	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs9289050	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs9289051	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9823016	0.96[ASN][1000 genomes]
rs9827984	1.00[ASN][1000 genomes]
rs9833356	0.87[ASN][1000 genomes]
rs9857124	0.81[CHD][hapmap]
rs9860105	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860236	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9860260	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9861474	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs9989972	0.99[ASN][1000 genomes]
rs9990359	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9838534	GTF2E1	cis	cerebellum	SCAN
rs9838534	NR1I2	cis	cerebellum	SCAN
rs9838534	KTELC1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116103000-116142000	Weak transcription	Fetal Lung	lung
2	chr3:116108200-116115200	Weak transcription	Brain Anterior Caudate	brain
3	chr3:116108600-116113800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:116108600-116114200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:116109200-116118600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:116109600-116118400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:116111400-116116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:116112600-116114200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:116112600-116132800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:116113200-116113800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:116113200-116114600	Enhancers	Brain Substantia Nigra	brain
12	chr3:116113400-116113800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:116113400-116114600	Enhancers	Brain Angular Gyrus	brain
14	chr3:116113600-116114000	Enhancers	Pancreatic Islets	Pancreatic Islet

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