Variant report

Variant	rs4420548
Chromosome Location	chr16:12228370-12228371
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	chr16:12213304..12215275-chr16:12226853..12228529,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs57198466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57422395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59449747	1.00[AMR][1000 genomes]
rs61021038	0.81[AFR][1000 genomes]
rs7206034	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73517891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73517900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519837	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519839	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73519851	1.00[AFR][1000 genomes];1.00[AMR][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	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv528952	chr16:12222064-12234877	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv984231	chr16:12226828-12231741	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:12213200-12232600	Weak transcription	Colonic Mucosa	Colon
3	chr16:12213800-12228400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:12213800-12231400	Weak transcription	Small Intestine	intestine
5	chr16:12213800-12255400	Weak transcription	Gastric	stomach
6	chr16:12215000-12233200	Weak transcription	Fetal Lung	lung
7	chr16:12215200-12229200	Weak transcription	NHDF-Ad	bronchial
8	chr16:12215400-12231000	Weak transcription	HepG2	liver
9	chr16:12215400-12241600	Weak transcription	NH-A	brain
10	chr16:12215600-12234000	Weak transcription	Right Ventricle	heart
11	chr16:12215600-12234400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:12217800-12241800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:12218600-12241200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr16:12218800-12241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr16:12219200-12228400	Weak transcription	Fetal Kidney	kidney
16	chr16:12219400-12237600	Weak transcription	Fetal Intestine Large	intestine
17	chr16:12219600-12231800	Weak transcription	Liver	Liver
18	chr16:12220000-12236400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:12220200-12229800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:12220400-12230600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr16:12220400-12236000	Strong transcription	Primary B cells from cord blood	blood
22	chr16:12220600-12236800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:12220800-12229600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr16:12221000-12237200	Weak transcription	K562	blood
25	chr16:12221400-12230200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr16:12221400-12236200	Strong transcription	GM12878-XiMat	blood
27	chr16:12221400-12236400	Strong transcription	Primary T cells from cord blood	blood
28	chr16:12221600-12234200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr16:12221600-12241600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr16:12222000-12240800	Weak transcription	Brain Anterior Caudate	brain
31	chr16:12222800-12230200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr16:12223000-12229600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr16:12225000-12231000	Weak transcription	Pancreas	Pancrea
34	chr16:12226000-12230400	Weak transcription	Psoas Muscle	Psoas
35	chr16:12226200-12230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:12226600-12228400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr16:12226600-12231800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr16:12226600-12234200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr16:12226800-12228600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:12227000-12228800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr16:12227000-12234600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr16:12227000-12234800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr16:12227000-12235800	Weak transcription	Right Atrium	heart
44	chr16:12227200-12228400	Weak transcription	Ovary	ovary
45	chr16:12227200-12229000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr16:12227400-12229800	Strong transcription	Pancreatic Islets	Pancreatic Islet
47	chr16:12227400-12231000	Weak transcription	Fetal Heart	heart
48	chr16:12227400-12232000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr16:12227600-12228400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr16:12227600-12229000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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