Variant report

Variant	rs12453929
Chromosome Location	chr17:17106701-17106702
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17106584..17108304-chr17:17112310..17114870,2	K562	blood:
2	chr17:17099063..17102775-chr17:17103264..17109484,6	K562	blood:
3	chr17:17103562..17107466-chr17:17107503..17109938,5	MCF-7	breast:
4	chr17:17104294..17107636-chr17:17108280..17111234,4	MCF-7	breast:
5	chr16:31722921..31725637-chr17:17104707..17107535,2	MCF-7	breast:
6	chr17:16890905..16892638-chr17:17106431..17108184,2	K562	blood:
7	chr17:17098202..17101244-chr17:17105252..17107774,3	MCF-7	breast:
8	chr17:17082040..17084851-chr17:17105255..17106821,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179598	Chromatin interaction
ENSG00000133030	Chromatin interaction
ENSG00000230969	Chromatin interaction
ENSG00000261731	Chromatin interaction
ENSG00000197302	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs14003	0.92[ASN][1000 genomes]
rs2009478	0.92[ASN][1000 genomes]
rs3803761	0.98[ASN][1000 genomes]
rs4399589	0.98[ASN][1000 genomes]
rs4985749	0.92[ASN][1000 genomes]
rs7218795	0.98[ASN][1000 genomes]
rs8077299	0.83[ASN][1000 genomes]
rs8077796	0.99[ASN][1000 genomes]
rs9908150	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9908205	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12453929	FLCN	cis	Artery Tibial	GTEx
rs12453929	FLCN	cis	Thyroid	GTEx
rs12453929	FLCN	cis	Esophagus Muscularis	GTEx
rs12453929	FLCN	cis	Heart Left Ventricle	GTEx
rs12453929	COPS3	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17090200-17107000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:17090200-17107400	Weak transcription	Small Intestine	intestine
3	chr17:17090800-17107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:17091800-17107600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr17:17093600-17107400	Weak transcription	Dnd41	blood
6	chr17:17093600-17108400	Weak transcription	Thymus	Thymus
7	chr17:17093800-17107400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:17093800-17107600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr17:17094000-17107200	Weak transcription	Aorta	Aorta
10	chr17:17095200-17108400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:17095400-17108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:17095600-17107200	Weak transcription	Brain Angular Gyrus	brain
13	chr17:17095600-17107400	Weak transcription	HMEC	breast
14	chr17:17095600-17107600	Weak transcription	Osteobl	bone
15	chr17:17096000-17107400	Weak transcription	Fetal Heart	heart
16	chr17:17096200-17107200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr17:17096800-17107400	Weak transcription	Primary B cells from cord blood	blood
18	chr17:17100800-17107600	Weak transcription	NHDF-Ad	bronchial
19	chr17:17101200-17107800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:17102400-17107400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:17103400-17106800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:17103600-17108200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:17104000-17106800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr17:17104000-17107600	Strong transcription	Fetal Intestine Small	intestine
25	chr17:17104200-17107400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:17104200-17108800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:17104200-17110400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:17104400-17106800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr17:17104400-17114000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:17104600-17106800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr17:17104600-17106800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:17104600-17107000	Strong transcription	K562	blood
33	chr17:17104600-17108800	Enhancers	Left Ventricle	heart
34	chr17:17104800-17106800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:17104800-17107200	Enhancers	Rectal Smooth Muscle	rectum
36	chr17:17104800-17114000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:17105000-17106800	Weak transcription	Placenta	Placenta
38	chr17:17105000-17107000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:17105000-17107600	Weak transcription	Fetal Kidney	kidney
40	chr17:17105000-17116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:17105400-17106800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:17105400-17106800	Genic enhancers	Brain Anterior Caudate	brain
43	chr17:17105400-17106800	Strong transcription	Fetal Thymus	thymus
44	chr17:17105400-17106800	Strong transcription	GM12878-XiMat	blood
45	chr17:17105400-17107000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:17105600-17106800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr17:17105600-17107400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:17105600-17107400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr17:17105600-17107600	Weak transcription	Fetal Lung	lung
50	chr17:17105600-17107600	Strong transcription	NHLF	lung

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