Variant report

Variant	rs10117603
Chromosome Location	chr9:95276587-95276588
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	chr9:95275292..95277875-chr9:95279129..95280868,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10115976	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10119535	0.90[ASN][1000 genomes]
rs10156530	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10283718	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820962	0.90[ASN][1000 genomes]
rs10820963	0.90[ASN][1000 genomes]
rs10820970	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820973	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820978	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820982	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10820995	0.86[EUR][1000 genomes]
rs10992308	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992312	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992314	0.90[ASN][1000 genomes]
rs10992334	0.90[ASN][1000 genomes]
rs10992348	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992350	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992359	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12347857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349712	0.90[ASN][1000 genomes]
rs12350198	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12352447	0.90[ASN][1000 genomes]
rs12378023	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1951849	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744140	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56168105	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58391046	0.90[ASN][1000 genomes]
rs6479425	0.86[EUR][1000 genomes]
rs7027998	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7036078	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036459	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7037068	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7860297	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7862677	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7872739	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7873882	0.90[ASN][1000 genomes]
rs7875681	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695754	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	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	esv1822933	chr9:95255176-95293308	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3374324	chr9:95276346-95276602	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10117603	CENPP	cis	Artery Aorta	GTEx
rs10117603	CENPP	cis	Artery Tibial	GTEx
rs10117603	CENPP	cis	Nerve Tibial	GTEx
rs10117603	CENPP	cis	Adipose Subcutaneous	GTEx
rs10117603	CENPP	cis	lung	GTEx
rs10117603	CENPP	cis	Thyroid	GTEx
rs10117603	CENPP	cis	Muscle Skeletal	GTEx
rs10117603	CENPP	cis	Esophagus Muscularis	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95268600-95278600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:95269800-95298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:95270400-95281000	Weak transcription	Thymus	Thymus
4	chr9:95270800-95278400	Weak transcription	Esophagus	oesophagus
5	chr9:95270800-95284800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:95271200-95284800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:95271600-95279200	Weak transcription	Gastric	stomach
8	chr9:95271600-95285600	Weak transcription	Left Ventricle	heart
9	chr9:95273400-95279400	Weak transcription	Pancreas	Pancrea
10	chr9:95274400-95281800	Strong transcription	Adipose Nuclei	Adipose
11	chr9:95274600-95276800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:95274600-95278400	Strong transcription	Liver	Liver
13	chr9:95275400-95277400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:95275400-95279200	Weak transcription	Fetal Lung	lung
15	chr9:95275400-95279600	Weak transcription	Osteobl	bone
16	chr9:95275400-95282400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:95275600-95278200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:95275600-95279200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:95275600-95282200	Weak transcription	Fetal Stomach	stomach
20	chr9:95275800-95277000	Weak transcription	Right Ventricle	heart
21	chr9:95275800-95278400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:95275800-95279000	Weak transcription	Aorta	Aorta
23	chr9:95275800-95279200	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:95275800-95280000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:95275800-95285800	Weak transcription	Fetal Intestine Small	intestine
26	chr9:95276000-95281800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:95276000-95296600	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:95276200-95276800	Weak transcription	Ovary	ovary

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