Variant report

Variant	rs12350198
Chromosome Location	chr9:95304235-95304236
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10115976	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10117603	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10283718	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10820970	0.84[EUR][1000 genomes]
rs10820973	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10820978	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10820982	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10820995	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992308	0.84[EUR][1000 genomes]
rs10992312	0.84[EUR][1000 genomes]
rs10992348	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992350	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992359	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12347857	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12378023	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1951849	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744140	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56168105	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6479425	0.87[EUR][1000 genomes]
rs7027998	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7036459	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7037068	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7860297	0.84[EUR][1000 genomes]
rs7862677	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872739	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7875681	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9695754	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12350198	CENPP	cis	Artery Tibial	GTEx
rs12350198	CENPP	cis	Artery Aorta	GTEx
rs12350198	CENPP	cis	Nerve Tibial	GTEx
rs12350198	CENPP	cis	Thyroid	GTEx
rs12350198	CENPP	cis	Muscle Skeletal	GTEx
rs12350198	CENPP	cis	Esophagus Muscularis	GTEx
rs12350198	CENPP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95297400-95304600	Weak transcription	Left Ventricle	heart
2	chr9:95300400-95304800	Weak transcription	Fetal Intestine Small	intestine
3	chr9:95301400-95305000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:95302000-95320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:95303800-95304400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr9:95303800-95304400	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links