Variant report

Variant	rs9695754
Chromosome Location	chr9:95167578-95167579
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95086147..95089104-chr9:95166950..95169643,2	K562	blood:

Variant related genes	Relation type
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10081693	1.00[ASN][1000 genomes]
rs10115976	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10117603	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119535	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs10123080	0.91[ASN][1000 genomes]
rs10156530	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10283718	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820954	1.00[ASN][1000 genomes]
rs10820956	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10820962	1.00[ASN][1000 genomes]
rs10820963	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs10820970	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820973	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820978	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820982	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10820995	0.94[CEU][hapmap]
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	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992312	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992314	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992334	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992348	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992350	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992359	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12347857	0.95[CEU][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12350198	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12350842	0.95[CEU][hapmap]
rs12352447	1.00[ASN][1000 genomes]
rs12378023	0.81[AMR][1000 genomes]
rs1447114	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs1951849	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889951	1.00[ASN][1000 genomes]
rs4744140	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56168105	0.87[AMR][1000 genomes];0.84[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]
rs7027998	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7036078	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036459	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7037068	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7860297	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862677	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7863859	1.00[ASN][1000 genomes]
rs7872739	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]
rs7873882	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7875681	0.94[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9695754	CENPP	cis	Esophagus Muscularis	GTEx
rs9695754	CENPP	cis	Heart Left Ventricle	GTEx
rs9695754	CENPP	cis	Nerve Tibial	GTEx
rs9695754	CENPP	cis	Adipose Subcutaneous	GTEx
rs9695754	CENPP	cis	Artery Tibial	GTEx
rs9695754	CENPP	cis	Artery Aorta	GTEx
rs9695754	CENPP	cis	lung	GTEx
rs9695754	CENPP	cis	Muscle Skeletal	GTEx
rs9695754	CENPP	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95156200-95168200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:95163400-95168000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:95165000-95168200	Weak transcription	Thymus	Thymus
4	chr9:95165600-95168400	Enhancers	Primary T cells from cord blood	blood
5	chr9:95165600-95168600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:95165800-95168800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr9:95166000-95168000	Weak transcription	Fetal Kidney	kidney
8	chr9:95166400-95167600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr9:95166400-95169800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:95166600-95168000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:95166800-95168000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:95166800-95168200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:95167000-95167600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:95167000-95168000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:95167000-95168000	Weak transcription	Aorta	Aorta
16	chr9:95167000-95168000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:95167000-95168000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:95167000-95168200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:95167000-95168200	Weak transcription	Adipose Nuclei	Adipose
20	chr9:95167000-95168200	Weak transcription	Fetal Intestine Small	intestine
21	chr9:95167000-95168200	Weak transcription	Fetal Stomach	stomach
22	chr9:95167000-95168200	Weak transcription	Fetal Thymus	thymus
23	chr9:95167000-95168200	Weak transcription	NHDF-Ad	bronchial
24	chr9:95167000-95168200	Weak transcription	NHLF	lung
25	chr9:95167000-95168400	Weak transcription	Ovary	ovary
26	chr9:95167000-95169600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:95167000-95172200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:95167200-95167800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:95167200-95168000	Weak transcription	Fetal Intestine Large	intestine
30	chr9:95167200-95168200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr9:95167200-95168200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:95167200-95168200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:95167200-95168200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:95167200-95168200	Enhancers	Colon Smooth Muscle	Colon
35	chr9:95167200-95168200	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:95167200-95168200	Weak transcription	Right Atrium	heart
37	chr9:95167200-95168200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:95167200-95168200	Enhancers	Dnd41	blood
39	chr9:95167200-95168800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:95167200-95172600	Weak transcription	Osteobl	bone
41	chr9:95167400-95167800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:95167400-95167800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr9:95167400-95167800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr9:95167400-95167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:95167400-95167800	Weak transcription	Fetal Lung	lung
46	chr9:95167400-95168800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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