Variant report

Variant	rs12460101
Chromosome Location	chr19:52914233-52914234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52901728..52903647-chr19:52912630..52914410,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12459721	0.89[YRI][hapmap]
rs12460065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12462502	0.89[YRI][hapmap]
rs34031698	1.00[AMR][1000 genomes]
rs35257609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8102941	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3412133	chr19:52907745-52935907	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52902200-52917400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:52902200-52919200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:52902400-52917600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:52902600-52917600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:52902600-52918200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:52902800-52915600	Strong transcription	HSMMtube	muscle
7	chr19:52902800-52924200	ZNF genes & repeats	Liver	Liver
8	chr19:52903000-52916200	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:52903200-52916800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:52904200-52917200	Strong transcription	Brain Germinal Matrix	brain
11	chr19:52904200-52917600	Strong transcription	Right Ventricle	heart
12	chr19:52904400-52916200	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr19:52904400-52916200	Strong transcription	Brain Angular Gyrus	brain
14	chr19:52904400-52916600	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr19:52905000-52916000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:52905000-52916800	ZNF genes & repeats	Spleen	Spleen
17	chr19:52905000-52920800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:52905000-52923800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:52905200-52917800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:52905400-52915600	Strong transcription	Osteobl	bone
21	chr19:52906400-52916000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:52906400-52920600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
23	chr19:52906600-52921000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr19:52906800-52916200	Weak transcription	NHLF	lung
25	chr19:52907000-52915600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr19:52907200-52914400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:52907400-52918000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr19:52907400-52919000	ZNF genes & repeats	Aorta	Aorta
29	chr19:52908200-52919400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:52908400-52915200	ZNF genes & repeats	Small Intestine	intestine
31	chr19:52908400-52915600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:52908600-52915800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
33	chr19:52908600-52917000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
34	chr19:52908600-52920800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:52909200-52915000	ZNF genes & repeats	Placenta	Placenta
36	chr19:52909400-52914400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:52910400-52914800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
38	chr19:52910600-52914400	Weak transcription	NH-A	brain
39	chr19:52910600-52914600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:52911200-52917000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
41	chr19:52911200-52918000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:52911400-52917000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
43	chr19:52911400-52922000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
44	chr19:52911800-52916000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:52911800-52923600	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr19:52912000-52919600	ZNF genes & repeats	Left Ventricle	heart
47	chr19:52912200-52918400	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr19:52912200-52918600	ZNF genes & repeats	Colon Smooth Muscle	Colon
49	chr19:52912200-52920000	ZNF genes & repeats	Fetal Lung	lung
50	chr19:52912400-52915000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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