Variant report

Variant	rs58819288
Chromosome Location	chr16:72550207-72550208
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	chr16:72533574..72535315-chr16:72549246..72551228,2	MCF-7	breast:

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs11075927	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075928	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11859210	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11860511	1.00[AMR][1000 genomes]
rs11860913	1.00[AMR][1000 genomes]
rs11861074	0.83[AMR][1000 genomes]
rs11861672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11863759	1.00[EUR][1000 genomes]
rs11866292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12103150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13331987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13332257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13333424	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333480	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336634	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13338662	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13339625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1429069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1429070	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970828	1.00[AMR][1000 genomes]
rs16970897	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970987	0.88[AFR][1000 genomes]
rs16970996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971006	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971145	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1864230	0.91[AFR][1000 genomes]
rs2017748	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053234	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2107154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2163066	0.92[AFR][1000 genomes]
rs2189339	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336436	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28393088	1.00[AMR][1000 genomes]
rs2840012	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28473657	1.00[AMR][1000 genomes]
rs28514442	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28568963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28569075	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28616025	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28634932	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28706881	0.83[AMR][1000 genomes]
rs28712432	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28828717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35917623	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4255793	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4624185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55777547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806458	1.00[AMR][1000 genomes]
rs57841266	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58363387	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59875457	1.00[AMR][1000 genomes]
rs61192283	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61398692	1.00[EUR][1000 genomes]
rs6499589	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7184113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7184224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185566	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7187532	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7187768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7192337	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7197250	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7199507	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7199594	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203819	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73583002	1.00[EUR][1000 genomes]
rs73583171	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73583174	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73583188	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73583198	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73584928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73584931	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73584955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73585209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73585273	1.00[EUR][1000 genomes]
rs73585295	1.00[EUR][1000 genomes]
rs73587415	0.83[AMR][1000 genomes]
rs73599411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73601423	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73601436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8043976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8045319	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8045813	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8046375	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8046891	1.00[AMR][1000 genomes]
rs8048860	1.00[AMR][1000 genomes]
rs8050489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051123	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051595	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8052117	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8053288	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8053566	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8053837	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8059369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8061838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8063144	0.83[AMR][1000 genomes]
rs9302636	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9889208	1.00[AMR][1000 genomes]
rs9921921	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922597	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922853	1.00[AMR][1000 genomes]
rs9923235	1.00[AMR][1000 genomes]
rs9926141	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9927677	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928119	0.83[AMR][1000 genomes]
rs9928673	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9929006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9930862	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9933062	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934152	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9934457	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935400	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9935826	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9937525	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9938038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv523524	chr16:72464460-72635674	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1055142	chr16:72473520-72627783	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv542950	chr16:72473520-72627783	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv530712	chr16:72499171-72744114	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1064928	chr16:72509626-72627783	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1065173	chr16:72509626-72693970	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv542951	chr16:72509626-72693970	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv518234	chr16:72544447-72635674	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72530600-72555400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr16:72542000-72554800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:72545000-72556000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:72545000-72588800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr16:72545200-72555400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:72549200-72556200	Weak transcription	Esophagus	oesophagus
7	chr16:72549600-72551800	Weak transcription	A549	lung
8	chr16:72550000-72550600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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