Variant report

Variant	rs28716857
Chromosome Location	chr9:137040133-137040134
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:137039283..137042109-chr9:137094336..137097224,2	MCF-7	breast:
2	chr9:137036260..137041614-chr9:137266040..137272215,8	MCF-7	breast:
3	chr9:136999557..137002222-chr9:137037334..137040252,2	MCF-7	breast:
4	chr9:137034179..137042512-chr9:137212832..137221430,18	MCF-7	breast:
5	chr9:137035658..137041824-chr9:137247104..137250799,8	MCF-7	breast:
6	chr9:137038333..137040512-chr9:137180843..137183627,2	MCF-7	breast:
7	chr9:137038640..137040595-chr9:137096986..137098760,2	K562	blood:
8	chr9:137036050..137037588-chr9:137038508..137040395,2	MCF-7	breast:
9	chr9:137028423..137041755-chr9:137210581..137221866,35	MCF-7	breast:
10	chr9:137038631..137040685-chr9:137274771..137277187,2	MCF-7	breast:
11	chr9:137030110..137032230-chr9:137037095..137040393,3	MCF-7	breast:
12	chr9:137039371..137041511-chr9:137333883..137336419,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186350	Chromatin interaction
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction
ENSG00000263897	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1134852	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28513414	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28549809	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28650068	0.82[ASN][1000 genomes]
rs34640256	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats 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	57 gene(s)	inside rSNPs	diseases
5	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
6	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137031000-137040200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:137031200-137040600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:137034600-137041200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:137035200-137041200	Enhancers	Spleen	Spleen
5	chr9:137035400-137041200	Enhancers	Ovary	ovary
6	chr9:137036000-137041000	Enhancers	Primary hematopoietic stem cells	blood
7	chr9:137036000-137041000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:137036000-137041200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr9:137036000-137041200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:137036400-137040200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:137036400-137040200	Weak transcription	Pancreas	Pancrea
12	chr9:137037800-137041200	Enhancers	Adipose Nuclei	Adipose
13	chr9:137038000-137040200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:137038200-137040800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:137038200-137041200	Bivalent Enhancer	Fetal Stomach	stomach
16	chr9:137038400-137041200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr9:137038600-137040600	Enhancers	Primary B cells from cord blood	blood
18	chr9:137038600-137041000	Enhancers	Primary B cells from peripheral blood	blood
19	chr9:137038600-137041000	Bivalent Enhancer	Placenta	Placenta
20	chr9:137038800-137041000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr9:137039000-137040200	Bivalent Enhancer	HepG2	liver
22	chr9:137039000-137040800	Enhancers	Fetal Thymus	thymus
23	chr9:137039000-137041000	Enhancers	Left Ventricle	heart
24	chr9:137039000-137041000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr9:137039000-137041200	Enhancers	Right Ventricle	heart
26	chr9:137039200-137040200	Enhancers	Liver	Liver
27	chr9:137039200-137040400	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr9:137039200-137041000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:137039200-137041000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
30	chr9:137039200-137041000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr9:137039200-137041200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr9:137039400-137041200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
33	chr9:137039600-137040200	Enhancers	Brain Hippocampus Middle	brain
34	chr9:137039600-137041000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:137039800-137040400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:137039800-137041000	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr9:137039800-137041200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr9:137039800-137041200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:137039800-137041200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:137039800-137041200	Bivalent Enhancer	Colonic Mucosa	Colon
41	chr9:137039800-137041200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr9:137040000-137040200	Bivalent Enhancer	Colon Smooth Muscle	Colon
43	chr9:137040000-137040200	Enhancers	Right Atrium	heart
44	chr9:137040000-137040400	Weak transcription	Lung	lung
45	chr9:137040000-137040400	Enhancers	Small Intestine	intestine
46	chr9:137040000-137040600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:137040000-137040800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:137040000-137040800	Enhancers	Fetal Intestine Large	intestine
49	chr9:137040000-137040800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr9:137040000-137040800	Enhancers	HMEC	breast

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