Variant report

Variant	rs12378023
Chromosome Location	chr9:95354255-95354256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10115976	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10117603	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10283718	0.81[AMR][1000 genomes]
rs10820973	0.81[EUR][1000 genomes]
rs10820978	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10820982	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10820995	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992350	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992359	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12347857	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12350198	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1951849	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744140	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56168105	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479425	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7027998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7036459	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7037068	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7862677	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7872739	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7875681	0.86[EUR][1000 genomes]
rs9695754	0.81[AMR][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	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
2	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12378023	CENPP	cis	Adipose Subcutaneous	GTEx
rs12378023	CENPP	cis	Artery Aorta	GTEx
rs12378023	CENPP	cis	Muscle Skeletal	GTEx
rs12378023	CENPP	cis	Esophagus Muscularis	GTEx
rs12378023	CENPP	cis	Thyroid	GTEx
rs12378023	CENPP	cis	Artery Tibial	GTEx
rs12378023	CENPP	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95347600-95365800	Weak transcription	Thymus	Thymus
2	chr9:95347800-95364000	Weak transcription	Left Ventricle	heart
3	chr9:95348800-95355200	Weak transcription	Aorta	Aorta
4	chr9:95351800-95356600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:95352800-95355000	Weak transcription	Fetal Stomach	stomach
6	chr9:95352800-95356200	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:95353000-95355000	Weak transcription	HSMMtube	muscle
8	chr9:95353000-95355200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:95353000-95355200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:95353000-95355400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:95353000-95362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:95353200-95355000	Weak transcription	Osteobl	bone
13	chr9:95353200-95355400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:95353200-95355400	Weak transcription	NHDF-Ad	bronchial
15	chr9:95353200-95359400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:95353200-95360600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:95353400-95355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:95353400-95355200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:95353400-95355400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:95353400-95355400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:95353600-95355600	Weak transcription	Adipose Nuclei	Adipose
24	chr9:95353800-95355200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:95354000-95355000	Weak transcription	Fetal Lung	lung
26	chr9:95354000-95358400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:95354000-95358600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr9:95354000-95362200	Weak transcription	Rectal Smooth Muscle	rectum

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