Variant report

Variant	rs9536090
Chromosome Location	chr13:53053195-53053196
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53049275..53051586-chr13:53052175..53054640,2	MCF-7	breast:

Extended variants
information (count: 178 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs1053245	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11148250	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11148251	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12184815	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28589286	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28756262	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34355831	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35975899	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41292810	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41292818	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55850688	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56173235	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56249382	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57412438	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57831032	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57904860	0.80[EUR][1000 genomes]
rs58655347	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61011708	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61171418	0.83[AMR][1000 genomes]
rs61677410	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61957967	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957980	0.83[AMR][1000 genomes]
rs61957981	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957982	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957983	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957984	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957986	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957987	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957988	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957989	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957993	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61957995	0.80[EUR][1000 genomes]
rs61957996	0.86[EUR][1000 genomes]
rs61957997	0.80[EUR][1000 genomes]
rs61958009	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958010	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958011	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958012	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958013	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958014	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958016	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958017	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958018	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958019	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958020	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958024	0.83[EUR][1000 genomes]
rs61958026	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958048	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958049	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958051	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958052	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958053	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61958055	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958057	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958058	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61958059	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959660	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959661	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959663	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959664	0.90[AMR][1000 genomes]
rs61959666	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959667	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959668	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959669	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959670	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959672	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959673	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959674	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959675	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959676	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959677	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959679	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61959698	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959702	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61959706	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61959707	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61959708	0.87[EUR][1000 genomes]
rs61959711	1.00[ASN][1000 genomes]
rs61959784	0.80[AMR][1000 genomes]
rs659848	0.86[ASN][1000 genomes]
rs664827	0.86[ASN][1000 genomes]
rs9526882	0.80[EUR][1000 genomes]
rs9526888	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526896	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526897	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526898	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526901	1.00[AMR][1000 genomes]
rs9526902	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526903	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526906	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526908	0.80[EUR][1000 genomes]
rs9526909	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9526910	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9526915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526916	0.90[AMR][1000 genomes]
rs9526924	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526926	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535975	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536003	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536004	0.80[EUR][1000 genomes]
rs9536005	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9536008	0.86[EUR][1000 genomes]
rs9536009	0.80[EUR][1000 genomes]
rs9536018	0.86[EUR][1000 genomes]
rs9536019	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536020	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536022	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536023	0.90[AMR][1000 genomes]
rs9536025	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536026	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536027	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536028	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536029	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536031	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536033	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536034	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536036	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536037	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536038	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536039	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536040	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536041	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536042	0.86[EUR][1000 genomes]
rs9536043	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536044	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536047	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536049	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536050	0.83[AMR][1000 genomes]
rs9536051	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536053	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536054	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536056	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536057	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536058	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536059	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536060	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536061	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536062	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536063	0.86[EUR][1000 genomes]
rs9536064	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536065	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536067	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536068	0.86[EUR][1000 genomes]
rs9536070	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536072	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536073	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536074	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536075	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536076	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536077	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536078	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536080	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536081	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536083	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9536084	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536085	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9536087	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536088	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9536097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536098	0.87[EUR][1000 genomes]
rs9536099	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9536153	1.00[ASN][1000 genomes]
rs9536167	1.00[ASN][1000 genomes]
rs9536168	1.00[ASN][1000 genomes]
rs9536169	1.00[ASN][1000 genomes]
rs9536170	1.00[ASN][1000 genomes]
rs9536172	0.86[ASN][1000 genomes]
rs9536173	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv976117	chr13:53051476-53058376	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2421964	chr13:53051526-53160234	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53030200-53053800	Weak transcription	Small Intestine	intestine
2	chr13:53030400-53055800	Weak transcription	Lung	lung
3	chr13:53034400-53054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:53038000-53053200	Weak transcription	Brain Angular Gyrus	brain
5	chr13:53038200-53055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:53041200-53053200	Weak transcription	Fetal Stomach	stomach
7	chr13:53042800-53054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:53048600-53053200	Weak transcription	Fetal Intestine Small	intestine
9	chr13:53049400-53054000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:53049600-53054000	Weak transcription	Liver	Liver
11	chr13:53050000-53053200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:53050000-53053400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:53050000-53055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:53050000-53058800	Weak transcription	HepG2	liver
15	chr13:53051000-53053600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:53051000-53055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr13:53051200-53053400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr13:53051400-53053200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:53051400-53054800	Weak transcription	Osteobl	bone
20	chr13:53051400-53055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:53051400-53055400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr13:53051400-53055400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr13:53051600-53053200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:53051600-53053200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr13:53051600-53053200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:53051600-53053200	Weak transcription	Fetal Intestine Large	intestine
27	chr13:53051600-53053400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:53051600-53053400	Weak transcription	Fetal Thymus	thymus
29	chr13:53051800-53053400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:53051800-53053400	Weak transcription	NH-A	brain
31	chr13:53051800-53053600	Weak transcription	Dnd41	blood
32	chr13:53051800-53055000	Weak transcription	HMEC	breast
33	chr13:53052000-53053600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:53052000-53053600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:53052000-53055200	Weak transcription	HSMM	muscle
36	chr13:53052200-53053800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:53052200-53053800	Weak transcription	Monocytes-CD14+_RO01746	blood

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