Variant report

Variant	rs14003
Chromosome Location	chr17:17104714-17104715
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	chr17:17103497..17105821-chr17:17140669..17142216,2	K562	blood:
2	chr17:17099063..17102775-chr17:17103264..17109484,6	K562	blood:
3	chr17:16943176..16945630-chr17:17102978..17105800,2	K562	blood:
4	chr17:17103562..17107466-chr17:17107503..17109938,5	MCF-7	breast:
5	chr17:17104294..17107636-chr17:17108280..17111234,4	MCF-7	breast:
6	chr16:31722921..31725637-chr17:17104707..17107535,2	MCF-7	breast:
7	chr17:17104671..17106490-chr17:17138945..17141485,2	MCF-7	breast:
8	chr17:17091439..17092954-chr17:17102481..17104887,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000179598	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000261731	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12453929	0.92[ASN][1000 genomes]
rs1736217	0.81[MEX][hapmap]
rs1736219	0.84[JPT][hapmap]
rs2009478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3803761	1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs4399589	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs4985749	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218795	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs8077299	0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8077796	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9894565	0.85[MEX][hapmap]
rs9908150	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs9908205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs14003	RAI1	cis	cerebellum	SCAN
rs14003	FLCN	cis	parietal	SCAN
rs14003	B9D1	cis	parietal	SCAN
rs14003	FLCN	cis	lymphoblastoid	seeQTL
rs14003	FLCN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17086400-17104800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:17086400-17106600	Weak transcription	Colonic Mucosa	Colon
3	chr17:17090200-17107000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:17090200-17107400	Weak transcription	Small Intestine	intestine
5	chr17:17090800-17106600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:17090800-17106600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:17090800-17107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:17091800-17107600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:17092200-17105400	Weak transcription	Gastric	stomach
10	chr17:17092400-17105600	Weak transcription	Brain Germinal Matrix	brain
11	chr17:17093000-17104800	Weak transcription	Hela-S3	cervix
12	chr17:17093600-17107400	Weak transcription	Dnd41	blood
13	chr17:17093600-17108400	Weak transcription	Thymus	Thymus
14	chr17:17093800-17105400	Weak transcription	Pancreas	Pancrea
15	chr17:17093800-17105600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:17093800-17105600	Weak transcription	Esophagus	oesophagus
17	chr17:17093800-17107400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:17093800-17107600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr17:17094000-17107200	Weak transcription	Aorta	Aorta
20	chr17:17094200-17104800	Weak transcription	HepG2	liver
21	chr17:17095000-17104800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:17095000-17104800	Weak transcription	Right Ventricle	heart
23	chr17:17095000-17105600	Weak transcription	Right Atrium	heart
24	chr17:17095200-17105800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:17095200-17108400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr17:17095400-17108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:17095600-17104800	Weak transcription	A549	lung
28	chr17:17095600-17106600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr17:17095600-17107200	Weak transcription	Brain Angular Gyrus	brain
30	chr17:17095600-17107400	Weak transcription	HMEC	breast
31	chr17:17095600-17107600	Weak transcription	Osteobl	bone
32	chr17:17096000-17107400	Weak transcription	Fetal Heart	heart
33	chr17:17096200-17107200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr17:17096800-17106000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr17:17096800-17107400	Weak transcription	Primary B cells from cord blood	blood
36	chr17:17098600-17105400	Weak transcription	GM12878-XiMat	blood
37	chr17:17100800-17107600	Weak transcription	NHDF-Ad	bronchial
38	chr17:17101200-17105400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:17101200-17106400	Weak transcription	Fetal Brain Male	brain
40	chr17:17101200-17107800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr17:17102400-17107400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:17102800-17105400	Enhancers	Adipose Nuclei	Adipose
43	chr17:17103200-17104800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:17103200-17105000	Enhancers	Placenta	Placenta
45	chr17:17103200-17105600	Enhancers	Fetal Lung	lung
46	chr17:17103200-17106400	Strong transcription	Primary T cells from cord blood	blood
47	chr17:17103400-17104800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:17103400-17105000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr17:17103400-17105200	Enhancers	Fetal Muscle Trunk	muscle
50	chr17:17103400-17105200	Enhancers	NHLF	lung

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