Variant report

Variant	rs7029939
Chromosome Location	chr9:95319891-95319892
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10114912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10114932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10116813	0.80[EUR][1000 genomes]
rs10117627	0.80[EUR][1000 genomes]
rs10117680	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10118107	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10118939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10124058	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10125450	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10125587	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10429459	0.83[EUR][1000 genomes]
rs10514815	0.84[EUR][1000 genomes]
rs1075397	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10761155	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10761160	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10761163	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761164	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820968	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10820980	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10820989	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820994	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10821008	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992304	0.80[EUR][1000 genomes]
rs10992347	0.81[EUR][1000 genomes]
rs10992349	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10992365	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992366	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992375	0.81[EUR][1000 genomes]
rs10992393	0.81[EUR][1000 genomes]
rs10992457	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1121978	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11788511	0.89[ASN][1000 genomes]
rs11788523	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11791001	0.82[ASN][1000 genomes]
rs11791339	0.96[ASN][1000 genomes]
rs11791805	0.89[ASN][1000 genomes]
rs11792019	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11792916	0.82[ASN][1000 genomes]
rs11793727	0.87[ASN][1000 genomes]
rs11794346	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12336415	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12336884	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12338938	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12341817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12342019	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12343820	0.82[EUR][1000 genomes]
rs13286566	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13301492	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13301537	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13301652	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1380	0.82[ASN][1000 genomes]
rs1535756	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1924244	0.81[EUR][1000 genomes]
rs1980848	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2026585	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2094281	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2104533	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2296666	0.88[EUR][1000 genomes]
rs2296669	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516568	0.81[AMR][1000 genomes]
rs2761677	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2761678	0.84[ASN][1000 genomes]
rs2761681	0.81[AMR][1000 genomes]
rs2895219	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3739606	0.82[EUR][1000 genomes]
rs3780347	0.84[EUR][1000 genomes]
rs3927488	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743873	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743874	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4743875	0.81[EUR][1000 genomes]
rs4744133	0.81[EUR][1000 genomes]
rs4744135	0.85[EUR][1000 genomes]
rs4744137	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744138	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744139	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744141	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744143	0.81[EUR][1000 genomes]
rs62572543	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479422	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6479423	0.84[EUR][1000 genomes]
rs7020104	0.81[EUR][1000 genomes]
rs7029879	0.82[ASN][1000 genomes]
rs7030920	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7031567	0.83[EUR][1000 genomes]
rs7033979	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7043984	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7045572	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs724102	0.83[EUR][1000 genomes]
rs747628	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747629	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7847534	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7848472	0.87[ASN][1000 genomes]
rs7849788	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7849927	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7850528	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7852698	0.83[EUR][1000 genomes]
rs7860786	0.85[EUR][1000 genomes]
rs7863049	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7864575	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7865019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7865118	0.81[EUR][1000 genomes]
rs7868013	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7869521	0.81[EUR][1000 genomes]
rs7872610	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7872644	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7873390	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7873397	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7874151	0.87[ASN][1000 genomes]
rs927865	0.85[EUR][1000 genomes]
rs9299405	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs968040	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs987553	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7029939	CENPP	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95302000-95320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:95307400-95320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:95308600-95324000	Weak transcription	Fetal Intestine Small	intestine
4	chr9:95310800-95323600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:95319200-95323000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:95319400-95320600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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