Variant report

Variant	rs62028398
Chromosome Location	chr16:12527849-12527850
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	chr16:12523717..12525761-chr16:12526587..12528260,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1035578	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11075072	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11643639	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11647957	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11649076	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11859542	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12051092	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12448347	0.81[EUR][1000 genomes]
rs12924190	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12926226	0.81[EUR][1000 genomes]
rs12931371	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34920830	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36011100	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780435	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4780436	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4780437	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4780438	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4781231	0.81[EUR][1000 genomes]
rs4781234	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781236	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4781237	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4781238	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4781239	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1036612	chr16:12518604-12565232	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12476000-12531600	Weak transcription	Right Ventricle	heart
2	chr16:12497800-12539800	Weak transcription	Left Ventricle	heart
3	chr16:12498000-12541200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:12498400-12564600	Weak transcription	Esophagus	oesophagus
5	chr16:12506200-12529600	Weak transcription	Gastric	stomach
6	chr16:12511400-12552000	Weak transcription	Lung	lung
7	chr16:12513200-12536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr16:12514800-12529600	Weak transcription	Fetal Brain Female	brain
9	chr16:12517000-12550800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr16:12517400-12537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:12517400-12537000	Weak transcription	Aorta	Aorta
12	chr16:12517600-12531600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:12518400-12537000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr16:12519800-12530200	Weak transcription	Placenta	Placenta
15	chr16:12520200-12529600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:12520400-12528800	Weak transcription	Fetal Brain Male	brain
17	chr16:12520400-12529600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:12520400-12533600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:12522000-12537600	Weak transcription	Primary B cells from cord blood	blood
20	chr16:12523600-12529600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:12523800-12528800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr16:12524000-12529200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr16:12524000-12529800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr16:12524000-12529800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:12524000-12530000	Weak transcription	Fetal Thymus	thymus
26	chr16:12524000-12536800	Weak transcription	Primary T cells from cord blood	blood
27	chr16:12524000-12551400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr16:12525400-12530400	Enhancers	Primary hematopoietic stem cells	blood
29	chr16:12526000-12529200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr16:12526200-12529200	Enhancers	Brain Hippocampus Middle	brain
31	chr16:12526400-12528600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr16:12526600-12529000	Enhancers	Brain Anterior Caudate	brain
33	chr16:12526600-12529600	Enhancers	Brain Substantia Nigra	brain
34	chr16:12526800-12528000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr16:12526800-12528000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr16:12526800-12528800	Enhancers	Brain Angular Gyrus	brain
37	chr16:12527000-12528200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:12527000-12528600	Enhancers	Primary B cells from peripheral blood	blood
39	chr16:12527000-12528600	Enhancers	Fetal Lung	lung
40	chr16:12527000-12529200	Enhancers	Brain Cingulate Gyrus	brain
41	chr16:12527400-12528000	Enhancers	Fetal Muscle Leg	muscle
42	chr16:12527600-12528000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr16:12527600-12528000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:12527600-12528000	Enhancers	Brain Germinal Matrix	brain
45	chr16:12527600-12528400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr16:12527600-12528400	Enhancers	Spleen	Spleen
47	chr16:12527600-12528800	Enhancers	GM12878-XiMat	blood
48	chr16:12527600-12528800	Enhancers	HepG2	liver
49	chr16:12527600-12529600	Enhancers	Fetal Muscle Trunk	muscle
50	chr16:12527800-12528400	Enhancers	Ovary	ovary

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