Variant report

Variant	rs56009009
Chromosome Location	chr12:58154817-58154818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58153606..58155197-chr12:58186466..58188523,2	K562	blood:
2	chr12:57910612..57912523-chr12:58153055..58155888,2	K562	blood:
3	chr12:58153870..58155501-chr12:58325931..58327914,2	K562	blood:
4	chr12:58153738..58156431-chr7:150562978..150565095,2	MCF-7	breast:
5	chr12:57910530..57914371-chr12:58151795..58155888,4	K562	blood:

Variant related genes	Relation type
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55640208	1.00[AFR][1000 genomes]
rs74093637	1.00[AFR][1000 genomes]
rs74094227	1.00[AFR][1000 genomes]
rs74095757	1.00[AFR][1000 genomes]
rs74096250	1.00[AFR][1000 genomes]
rs74097710	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58150400-58158400	Weak transcription	Right Atrium	heart
2	chr12:58150600-58156400	Weak transcription	Small Intestine	intestine
3	chr12:58150600-58156400	Weak transcription	Hela-S3	cervix
4	chr12:58150600-58158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:58150800-58156200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:58150800-58156800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:58151000-58155400	Strong transcription	Brain Germinal Matrix	brain
8	chr12:58151000-58156000	Strong transcription	Fetal Intestine Small	intestine
9	chr12:58151000-58156600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:58151600-58155000	Strong transcription	Primary B cells from cord blood	blood
11	chr12:58151600-58155200	Strong transcription	Primary T cells from cord blood	blood
12	chr12:58151600-58155800	Strong transcription	Fetal Brain Female	brain
13	chr12:58151600-58156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:58151800-58156200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:58152200-58156600	Weak transcription	Fetal Lung	lung
16	chr12:58152200-58160000	Weak transcription	K562	blood
17	chr12:58152400-58156400	Strong transcription	NHEK	skin
18	chr12:58152400-58157400	Weak transcription	HSMMtube	muscle
19	chr12:58152600-58156400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:58152600-58156800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:58152600-58157200	Weak transcription	Liver	Liver
22	chr12:58152800-58155200	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:58152800-58156400	Weak transcription	Brain Substantia Nigra	brain
24	chr12:58152800-58158000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:58153000-58155000	Weak transcription	Right Ventricle	heart
26	chr12:58153000-58155400	Weak transcription	Ovary	ovary
27	chr12:58153000-58156400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:58153000-58157200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:58153000-58157400	Weak transcription	Pancreas	Pancrea
30	chr12:58153000-58158000	Weak transcription	GM12878-XiMat	blood
31	chr12:58153000-58158200	Weak transcription	Gastric	stomach
32	chr12:58153200-58155000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:58153200-58155000	Weak transcription	Left Ventricle	heart
34	chr12:58153200-58155400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:58153200-58155800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:58153200-58156000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:58153200-58156200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:58153200-58156400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:58153200-58156400	Weak transcription	Brain Angular Gyrus	brain
40	chr12:58153200-58156400	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:58153200-58156400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:58153200-58156400	Weak transcription	Fetal Thymus	thymus
43	chr12:58153200-58156800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:58153200-58156800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:58153200-58157000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:58153200-58158000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:58153200-58158000	Weak transcription	Esophagus	oesophagus
48	chr12:58153200-58158000	Weak transcription	Lung	lung
49	chr12:58153400-58155000	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:58153400-58155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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