Variant report

Variant	rs10283718
Chromosome Location	chr9:95172242-95172243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:240321650..240323210-chr9:95170170..95172647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222020	Chromatin interaction
ENSG00000068024	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10081693	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115976	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10117603	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119535	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10123080	0.91[ASN][1000 genomes]
rs10156530	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10820954	1.00[ASN][1000 genomes]
rs10820956	1.00[ASN][1000 genomes]
rs10820962	1.00[ASN][1000 genomes]
rs10820963	1.00[ASN][1000 genomes]
rs10820970	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820973	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820978	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820982	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10992265	0.91[ASN][1000 genomes]
rs10992266	1.00[ASN][1000 genomes]
rs10992267	1.00[ASN][1000 genomes]
rs10992270	1.00[ASN][1000 genomes]
rs10992308	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992312	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992314	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992334	1.00[ASN][1000 genomes]
rs10992348	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992350	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992359	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12347857	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12350198	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs12378023	0.81[AMR][1000 genomes]
rs1447114	1.00[ASN][1000 genomes]
rs1951849	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889951	1.00[ASN][1000 genomes]
rs4744140	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56168105	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58391046	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	1.00[ASN][1000 genomes]
rs6479413	1.00[ASN][1000 genomes]
rs7027998	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7036078	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036459	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7037068	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7860297	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862677	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7863859	1.00[ASN][1000 genomes]
rs7872739	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873882	1.00[ASN][1000 genomes]
rs7875681	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9695754	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1053205	chr9:95119195-95182612	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10283718	CENPP	cis	Adipose Subcutaneous	GTEx
rs10283718	CENPP	cis	Thyroid	GTEx
rs10283718	CENPP	cis	Heart Left Ventricle	GTEx
rs10283718	CENPP	cis	Muscle Skeletal	GTEx
rs10283718	CENPP	cis	Nerve Tibial	GTEx
rs10283718	CENPP	cis	Esophagus Muscularis	GTEx
rs10283718	CENPP	cis	Artery Aorta	GTEx
rs10283718	CENPP	cis	Artery Tibial	GTEx
rs10283718	CENPP	cis	lung	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95167200-95172600	Weak transcription	Osteobl	bone
2	chr9:95169000-95172600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:95169000-95172600	Weak transcription	Ovary	ovary
4	chr9:95169000-95172600	Weak transcription	Right Atrium	heart
5	chr9:95169000-95173000	Weak transcription	Fetal Kidney	kidney
6	chr9:95169000-95173600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:95169200-95172400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:95169200-95172600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:95169200-95172600	Weak transcription	NHDF-Ad	bronchial
10	chr9:95169200-95173600	Weak transcription	K562	blood
11	chr9:95169400-95172600	Weak transcription	Fetal Heart	heart
12	chr9:95169400-95172600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:95169400-95172800	Weak transcription	GM12878-XiMat	blood
14	chr9:95169400-95183800	Weak transcription	Aorta	Aorta
15	chr9:95169600-95172400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:95169600-95172600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:95169800-95172400	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:95169800-95175600	Weak transcription	Dnd41	blood
19	chr9:95169800-95176400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:95170000-95177600	Weak transcription	Thymus	Thymus
21	chr9:95170200-95172600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:95171200-95172600	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:95171400-95173000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:95172000-95172800	Enhancers	NHLF	lung
25	chr9:95172000-95173200	Enhancers	Fetal Lung	lung
26	chr9:95172200-95172600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:95172200-95173600	Enhancers	Fetal Muscle Trunk	muscle
28	chr9:95172200-95173800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:95172200-95173800	Enhancers	Fetal Stomach	stomach
30	chr9:95172200-95174200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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