Variant report

Variant	rs7862677
Chromosome Location	chr9:95299395-95299396
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10115976	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10117603	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10283718	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10820970	0.84[EUR][1000 genomes]
rs10820973	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10820978	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10820982	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10820995	0.87[EUR][1000 genomes]
rs10992308	0.84[EUR][1000 genomes]
rs10992312	0.84[EUR][1000 genomes]
rs10992348	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992350	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992359	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12347857	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12350198	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12378023	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1951849	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744140	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56168105	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6479425	0.87[EUR][1000 genomes]
rs7027998	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7036078	0.84[EUR][1000 genomes]
rs7036459	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7037068	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7860297	0.84[EUR][1000 genomes]
rs7872739	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7875681	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9695754	0.87[AMR][1000 genomes];0.86[EUR][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	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
rs7862677	CENPP	cis	Artery Tibial	GTEx
rs7862677	CENPP	cis	Thyroid	GTEx
rs7862677	CENPP	cis	Muscle Skeletal	GTEx
rs7862677	CENPP	cis	Nerve Tibial	GTEx
rs7862677	CENPP	cis	Esophagus Muscularis	GTEx
rs7862677	CENPP	cis	Adipose Subcutaneous	GTEx
rs7862677	CENPP	cis	Artery Aorta	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95294800-95301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:95296000-95301800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:95296400-95299600	Enhancers	HepG2	liver
4	chr9:95297200-95301000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:95297400-95299400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:95297400-95300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:95297400-95300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:95297400-95304600	Weak transcription	Left Ventricle	heart
9	chr9:95298000-95299600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr9:95298600-95299600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr9:95298600-95300200	Weak transcription	NH-A	brain
12	chr9:95298800-95299400	Enhancers	Fetal Muscle Leg	muscle
13	chr9:95298800-95299400	Enhancers	HSMM	muscle
14	chr9:95298800-95301400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:95299000-95299400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr9:95299000-95300200	Enhancers	Fetal Intestine Large	intestine
17	chr9:95299000-95300200	Weak transcription	HSMMtube	muscle
18	chr9:95299000-95300200	Weak transcription	NHLF	lung
19	chr9:95299000-95300400	Enhancers	Fetal Intestine Small	intestine
20	chr9:95299000-95300800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:95299000-95301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:95299000-95301200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:95299000-95301400	Enhancers	Osteobl	bone
24	chr9:95299000-95301600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:95299200-95299400	Enhancers	Ovary	ovary
26	chr9:95299200-95299400	Enhancers	Pancreas	Pancrea
27	chr9:95299200-95299600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:95299200-95299800	Weak transcription	NHDF-Ad	bronchial
29	chr9:95299200-95300000	Weak transcription	Adipose Nuclei	Adipose
30	chr9:95299200-95300000	Weak transcription	Liver	Liver
31	chr9:95299200-95301400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:95299200-95301400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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