Variant report

Variant	rs10820989
Chromosome Location	chr9:95322020-95322021
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95321743..95324130-chr9:95360863..95362407,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10114912	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10114932	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10115290	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10117627	0.84[EUR][1000 genomes]
rs10117680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10118107	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10118939	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10120329	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123738	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10125450	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10429459	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10514815	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1075397	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761158	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761163	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820980	0.81[EUR][1000 genomes]
rs10820986	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820988	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820990	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820994	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992347	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992366	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992375	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11788523	0.81[EUR][1000 genomes]
rs11794346	0.81[EUR][1000 genomes]
rs12335553	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12338938	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12341817	0.81[EUR][1000 genomes]
rs12343820	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13301492	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13301652	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1924243	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1924244	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1980848	0.81[EUR][1000 genomes]
rs2026585	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2094281	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2104533	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296666	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2895219	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3739606	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3780347	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3927488	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4302908	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743873	0.81[EUR][1000 genomes]
rs4743874	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744133	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744135	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744137	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744138	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744139	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744141	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6479423	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7029939	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7031567	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs747628	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs747629	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7847534	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7849788	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7849927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7852510	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7860774	0.82[EUR][1000 genomes]
rs7860786	0.90[EUR][1000 genomes]
rs7863049	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7864575	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7865019	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7872610	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7872644	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7873390	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs927865	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9299405	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs968040	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs987553	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs987554	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[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
rs10820989	CENPP	cis	Esophagus Muscularis	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95308600-95324000	Weak transcription	Fetal Intestine Small	intestine
2	chr9:95310800-95323600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:95319200-95323000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:95320600-95324200	Weak transcription	Small Intestine	intestine
5	chr9:95321200-95323400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:95321200-95325400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:95321400-95324000	Weak transcription	Esophagus	oesophagus
8	chr9:95321600-95323400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:95321600-95323400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:95321600-95325400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:95321800-95326400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:95322000-95324200	Weak transcription	Adipose Nuclei	Adipose

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