Variant report

Variant	rs1152759
Chromosome Location	chr9:95129359-95129360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95128615..95130359-chr9:95138980..95141028,2	MCF-7	breast:
2	chr9:95123897..95125833-chr9:95129339..95132296,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10283572	0.84[JPT][hapmap]
rs10453241	0.82[JPT][hapmap]
rs10491806	1.00[YRI][hapmap]
rs1053441	0.81[JPT][hapmap]
rs1053446	0.82[JPT][hapmap]
rs10739927	0.81[JPT][hapmap]
rs10761149	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761152	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10761154	0.85[JPT][hapmap]
rs10761156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761158	0.81[JPT][hapmap]
rs10820950	0.85[EUR][1000 genomes]
rs10820951	0.84[EUR][1000 genomes]
rs10820952	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs10820964	0.81[JPT][hapmap]
rs10820969	0.82[JPT][hapmap]
rs10820971	0.82[JPT][hapmap]
rs10992322	0.81[JPT][hapmap]
rs10992347	0.82[JPT][hapmap]
rs10992367	1.00[YRI][hapmap]
rs1152757	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1175788	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12552866	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535754	0.81[JPT][hapmap]
rs1760318	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1923599	0.93[CEU][hapmap]
rs1924243	0.82[JPT][hapmap]
rs2025388	0.81[JPT][hapmap]
rs2025389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2031262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131919	1.00[YRI][hapmap]
rs2147060	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2181712	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274966	0.81[JPT][hapmap]
rs230222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2398751	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516567	0.81[JPT][hapmap]
rs3174352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs331377	0.93[CEU][hapmap]
rs331379	0.93[CEU][hapmap]
rs331380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs331381	0.93[CEU][hapmap]
rs3736835	0.90[CEU][hapmap]
rs3780346	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3996311	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs471478	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743869	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744126	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744133	0.81[JPT][hapmap]
rs504708	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6479417	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6479419	0.81[JPT][hapmap]
rs6651532	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7020874	0.81[JPT][hapmap]
rs7022562	0.81[JPT][hapmap]
rs7023004	0.81[JPT][hapmap]
rs7026361	0.81[JPT][hapmap]
rs7037075	0.81[JPT][hapmap]
rs7037194	0.81[JPT][hapmap]
rs7040860	0.83[EUR][1000 genomes]
rs7045409	0.81[JPT][hapmap]
rs7047089	0.82[JPT][hapmap]
rs710162	0.81[JPT][hapmap]
rs710163	0.89[CEU][hapmap]
rs7467899	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847929	0.81[JPT][hapmap]
rs7850432	0.81[JPT][hapmap]
rs7853859	0.81[JPT][hapmap]
rs7863406	0.81[JPT][hapmap]
rs7867300	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7872375	0.82[JPT][hapmap]
rs7873932	0.82[JPT][hapmap]
rs9299402	0.84[EUR][1000 genomes]
rs9299404	0.81[JPT][hapmap]
rs9409664	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9409667	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	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
5	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	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
7	nsv1053205	chr9:95119195-95182612	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1152759	OGN	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95117000-95134800	Weak transcription	Ovary	ovary
2	chr9:95118000-95135000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:95120000-95131400	Weak transcription	Thymus	Thymus
4	chr9:95120400-95130600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:95122200-95138600	Weak transcription	Aorta	Aorta
6	chr9:95122400-95131200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:95122400-95132200	Weak transcription	Fetal Intestine Small	intestine
8	chr9:95122800-95130200	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:95122800-95131400	Weak transcription	GM12878-XiMat	blood
10	chr9:95122800-95134800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:95122800-95135400	Weak transcription	Fetal Thymus	thymus
12	chr9:95125600-95131200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:95125600-95131400	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:95127200-95130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:95127400-95129400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:95127400-95131400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:95128000-95130400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:95128000-95130600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:95128000-95141400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:95128400-95146600	Weak transcription	NHEK	skin
21	chr9:95128600-95129400	Strong transcription	Dnd41	blood
22	chr9:95128600-95129400	Strong transcription	K562	blood
23	chr9:95128800-95131200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:95129000-95129400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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