Variant report

Variant	rs9856462
Chromosome Location	chr3:70092775-70092776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10510994	0.82[EUR][1000 genomes]
rs11923982	0.87[AMR][1000 genomes]
rs12495615	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1491694	0.84[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1491696	0.87[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491697	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491700	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17729465	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17729489	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17785152	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17785756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2101636	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28462307	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2874269	0.80[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849467	0.84[AMR][1000 genomes]
rs4293707	0.81[EUR][1000 genomes]
rs4855334	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855335	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55966844	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60251138	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60403843	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60647884	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61645126	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6549267	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6763730	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6799525	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431273	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7611660	0.87[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs7619924	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7632596	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645353	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649560	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7651972	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9310181	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815027	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818798	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9818964	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9826811	0.82[AMR][1000 genomes]
rs9837453	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9840951	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9843867	0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9856462	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70063800-70098000	Weak transcription	Aorta	Aorta
2	chr3:70090000-70093600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:70091000-70092800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:70091000-70093800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:70091200-70093400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:70091600-70093400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:70092000-70093000	Enhancers	Fetal Brain Female	brain
8	chr3:70092000-70105000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:70092400-70092800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:70092400-70093800	Enhancers	Brain Germinal Matrix	brain
11	chr3:70092600-70093200	Weak transcription	Brain Angular Gyrus	brain

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