Variant report

Variant	rs6479431
Chromosome Location	chr9:95546889-95546890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95501028..95504984-chr9:95544023..95547039,4	MCF-7	breast:
2	chr9:95540552..95544510-chr9:95545450..95549411,3	K562	blood:
3	chr9:95525056..95529006-chr9:95542998..95547069,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10120856	0.84[AFR][1000 genomes]
rs10120915	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121597	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10122383	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124058	0.93[EUR][1000 genomes]
rs10125587	0.93[EUR][1000 genomes]
rs1022844	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10491804	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821008	0.93[EUR][1000 genomes]
rs10992393	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10992424	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992450	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992457	0.93[EUR][1000 genomes]
rs13284038	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13284106	0.93[EUR][1000 genomes]
rs13286566	0.93[EUR][1000 genomes]
rs2181585	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2296669	0.85[EUR][1000 genomes]
rs2296671	1.00[ASN][1000 genomes]
rs41273372	1.00[ASN][1000 genomes]
rs4743875	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4743876	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744143	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7020104	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7043984	0.93[EUR][1000 genomes]
rs7046335	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724102	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs755209	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852698	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7865118	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7869521	0.87[AMR][1000 genomes];0.93[EUR][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	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479431	CENPP	cis	Esophagus Muscularis	GTEx
rs6479431	CENPP	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95541400-95558600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:95546000-95553000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:95546000-95553000	Weak transcription	NHEK	skin

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