Variant report

Variant	rs10816586
Chromosome Location	chr9:110672373-110672374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10739249	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759262	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759264	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759265	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759266	0.91[ASN][1000 genomes]
rs10816585	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339764	0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1339765	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1416839	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929277	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929279	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929280	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970403	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1999349	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094919	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104825	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4978644	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4978650	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978651	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7023709	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs7030786	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7031148	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040902	0.91[ASN][1000 genomes]
rs7047831	0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7853326	0.98[ASN][1000 genomes]
rs7858147	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873668	0.91[ASN][1000 genomes]
rs944473	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944475	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs944476	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051101	chr9:110548257-110697253	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv893701	chr9:110650482-110709587	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10816586	CHRNA1	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110671000-110674600	Weak transcription	Brain Hippocampus Middle	brain
2	chr9:110672200-110672400	ZNF genes & repeats	Psoas Muscle	Psoas
3	chr9:110672200-110675000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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