Variant report

Variant	rs7872739
Chromosome Location	chr9:95217930-95217931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95096545..95099095-chr9:95217061..95218841,2	MCF-7	breast:
2	chr9:95087278..95089387-chr9:95217797..95220254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10115976	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10117603	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119535	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs10156530	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10283718	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820954	1.00[ASN][1000 genomes]
rs10820956	1.00[ASN][1000 genomes]
rs10820962	1.00[ASN][1000 genomes]
rs10820963	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs10820970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820982	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10820995	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10992308	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992312	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992314	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992334	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992348	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992350	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992359	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12347857	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12350198	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12350842	1.00[CEU][hapmap]
rs12352447	1.00[ASN][1000 genomes]
rs12378023	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1447114	1.00[ASN][1000 genomes]
rs1951849	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744140	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56168105	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58391046	1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	1.00[ASN][1000 genomes]
rs6479413	1.00[ASN][1000 genomes]
rs6479425	0.81[EUR][1000 genomes]
rs7027998	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7036078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036459	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037068	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7860297	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862677	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7873882	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7875681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9695754	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7872739	CENPP	cis	Artery Aorta	GTEx
rs7872739	CENPP	cis	parietal	SCAN
rs7872739	CENPP	cis	Nerve Tibial	GTEx
rs7872739	IPPK	cis	cerebellum	SCAN
rs7872739	CENPP	cis	Adipose Subcutaneous	GTEx
rs7872739	CENPP	cis	Muscle Skeletal	GTEx
rs7872739	ZNF484	cis	parietal	SCAN
rs7872739	CENPP	cis	lung	GTEx
rs7872739	CENPP	cis	Artery Tibial	GTEx
rs7872739	OMD	cis	cerebellum	SCAN
rs7872739	NOL8	cis	cerebellum	SCAN
rs7872739	CENPP	cis	cerebellum	SCAN
rs7872739	CENPP	cis	Thyroid	GTEx
rs7872739	CENPP	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95217000-95225000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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