Variant report

Variant	rs12336884
Chromosome Location	chr9:95234183-95234184
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10114912	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10114932	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10115222	0.90[ASN][1000 genomes]
rs10115290	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10116813	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10117627	0.84[EUR][1000 genomes]
rs10118939	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10120980	0.83[ASN][1000 genomes]
rs10123342	0.90[ASN][1000 genomes]
rs10125474	0.90[ASN][1000 genomes]
rs10429459	0.81[EUR][1000 genomes]
rs10514815	0.83[EUR][1000 genomes]
rs10739928	0.90[ASN][1000 genomes]
rs10761150	0.90[ASN][1000 genomes]
rs10761151	0.87[ASN][1000 genomes]
rs10761155	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761158	0.83[EUR][1000 genomes]
rs10761160	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761163	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10820960	0.87[ASN][1000 genomes]
rs10820961	0.87[ASN][1000 genomes]
rs10820965	0.90[ASN][1000 genomes]
rs10820966	0.90[ASN][1000 genomes]
rs10820967	0.90[ASN][1000 genomes]
rs10820968	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820980	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820994	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992280	0.90[ASN][1000 genomes]
rs10992303	0.90[ASN][1000 genomes]
rs10992304	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992319	0.87[ASN][1000 genomes]
rs10992347	0.84[EUR][1000 genomes]
rs10992349	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992366	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1121978	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1121979	0.84[ASN][1000 genomes]
rs11788523	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11792019	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11792342	0.90[ASN][1000 genomes]
rs11793727	0.81[ASN][1000 genomes]
rs11794346	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12336415	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341817	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12342019	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12343820	0.84[EUR][1000 genomes]
rs13301537	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535754	0.83[EUR][1000 genomes]
rs1535756	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1924243	0.83[EUR][1000 genomes]
rs1924244	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1980848	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2094281	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2236341	0.87[ASN][1000 genomes]
rs2273862	0.87[ASN][1000 genomes]
rs2295941	0.87[ASN][1000 genomes]
rs2296666	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2516568	0.92[ASN][1000 genomes]
rs2761677	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2761681	0.92[ASN][1000 genomes]
rs3739606	0.84[EUR][1000 genomes]
rs3758229	0.90[ASN][1000 genomes]
rs3780347	0.82[EUR][1000 genomes]
rs4743873	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744133	0.84[EUR][1000 genomes]
rs4744135	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4744137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744138	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744141	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62572543	0.84[EUR][1000 genomes]
rs6479418	0.90[ASN][1000 genomes]
rs6479422	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479423	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7024190	0.87[ASN][1000 genomes]
rs7027595	0.90[ASN][1000 genomes]
rs7029939	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7030920	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7031567	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7033979	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7042335	0.87[ASN][1000 genomes]
rs7043152	0.90[ASN][1000 genomes]
rs7045572	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747628	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7847534	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7848055	0.90[ASN][1000 genomes]
rs7848472	0.81[ASN][1000 genomes]
rs7850528	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860774	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7860786	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7864575	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7865019	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7867909	0.90[ASN][1000 genomes]
rs7868013	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7872610	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7873397	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7874151	0.81[ASN][1000 genomes]
rs927865	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9299403	0.87[ASN][1000 genomes]
rs9299405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs968040	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs987553	0.86[AMR][1000 genomes];0.90[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	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12336884	CENPP	cis	Esophagus Muscularis	GTEx
rs12336884	CENPP	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95219000-95241600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:95220200-95242400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:95225600-95235400	Weak transcription	Pancreas	Pancrea
4	chr9:95227000-95235200	Weak transcription	Aorta	Aorta
5	chr9:95227000-95241200	Weak transcription	Ovary	ovary
6	chr9:95227400-95235200	Weak transcription	Psoas Muscle	Psoas
7	chr9:95227400-95240800	Weak transcription	Left Ventricle	heart
8	chr9:95227400-95240800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:95227600-95239000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:95227600-95239400	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:95230600-95242600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:95230800-95243400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:95231000-95241200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:95231800-95268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:95232000-95235400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:95232200-95235000	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:95232200-95241200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:95232200-95242600	Weak transcription	K562	blood
19	chr9:95234000-95235600	Strong transcription	Fetal Stomach	stomach

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