Variant report

Variant	rs7208065
Chromosome Location	chr17:17120204-17120205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1029830	0.95[JPT][hapmap]
rs1029832	0.95[JPT][hapmap]
rs12947291	0.81[ASN][1000 genomes]
rs1613416	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1624963	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1708618	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1708619	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1708620	0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1708623	0.95[JPT][hapmap]
rs1708626	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1708627	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1708629	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1736200	0.95[JPT][hapmap]
rs1736202	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1736203	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1736206	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1736207	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1736210	0.80[ASN][1000 genomes]
rs1736213	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736214	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736215	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1736219	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736221	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2009478	0.83[JPT][hapmap]
rs3182911	0.93[ASW][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3803761	0.85[CHD][hapmap]
rs4399589	0.88[CHD][hapmap]
rs4985705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985761	0.95[JPT][hapmap]
rs7218795	0.88[CHD][hapmap]
rs7220275	0.95[JPT][hapmap]
rs8065832	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8072402	0.90[JPT][hapmap]
rs8072869	0.90[JPT][hapmap]
rs8080386	1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9890657	0.81[ASN][1000 genomes]
rs9903294	0.90[JPT][hapmap]
rs9908150	0.85[CEU][hapmap];0.88[CHD][hapmap];0.91[TSI][hapmap]
rs9908205	0.81[CEU][hapmap]

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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs7208065	RASD1	cis	parietal	SCAN
rs7208065	FLCN	cis	Skin Sun Exposed Lower leg	GTEx
rs7208065	FLCN	cis	Artery Tibial	GTEx
rs7208065	FLCN	cis	Esophagus Muscularis	GTEx
rs7208065	FLCN	cis	lymphoblastoid	seeQTL
rs7208065	FLCN	cis	Artery Aorta	GTEx
rs7208065	COPS3	cis	multi-tissue	Pritchard
rs7208065	FLCN	cis	lung	GTEx
rs7208065	M-RIP	cis	multi-tissue	Pritchard
rs7208065	FLCN	cis	Adipose Subcutaneous	GTEx
rs7208065	FLCN	cis	Nerve Tibial	GTEx
rs7208065	FLCN	cis	Esophagus Mucosa	GTEx
rs7208065	FLCN	cis	cerebellum	SCAN
rs7208065	FLCN	cis	Stomach	GTEx
rs7208065	RAI1	cis	cerebellum	SCAN
rs7208065	FLCN	cis	parietal	SCAN
rs7208065	COPS3	cis	Whole Blood	GTEx
rs7208065	PLD6	cis	cerebellum	SCAN
rs7208065	FLCN	cis	multi-tissue	Pritchard
rs7208065	FLCN	cis	Thyroid	GTEx
rs7208065	MPRIP	cis	cerebellum	SCAN
rs7208065	FLCN	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17109400-17120400	Weak transcription	Fetal Kidney	kidney
2	chr17:17109400-17131600	Weak transcription	Fetal Heart	heart
3	chr17:17109600-17124200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:17109800-17123200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:17110000-17121000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:17110400-17120400	Weak transcription	Hela-S3	cervix
7	chr17:17111800-17120600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:17113200-17135200	Strong transcription	Fetal Intestine Small	intestine
9	chr17:17113200-17136600	Strong transcription	Fetal Stomach	stomach
10	chr17:17113400-17131400	Strong transcription	Brain Anterior Caudate	brain
11	chr17:17113400-17131400	Strong transcription	Brain Substantia Nigra	brain
12	chr17:17113400-17134600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:17113400-17136200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:17113800-17134600	Strong transcription	Fetal Muscle Leg	muscle
15	chr17:17113800-17137600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr17:17114000-17122600	Strong transcription	A549	lung
17	chr17:17114000-17131200	Strong transcription	Liver	Liver
18	chr17:17114000-17131200	Strong transcription	Left Ventricle	heart
19	chr17:17114000-17134800	Strong transcription	Fetal Intestine Large	intestine
20	chr17:17114000-17135200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:17114000-17136200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:17114000-17136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:17114000-17136400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:17114000-17136400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:17114000-17136400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:17114000-17136400	Strong transcription	Placenta	Placenta
27	chr17:17114000-17136600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:17114200-17131600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:17114200-17131600	Strong transcription	Spleen	Spleen
30	chr17:17114200-17136600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:17114400-17131400	Strong transcription	Lung	lung
32	chr17:17114400-17136200	Strong transcription	Primary T cells from cord blood	blood
33	chr17:17114400-17136200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:17114400-17136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:17114400-17136600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:17114600-17121000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:17114600-17121600	Strong transcription	Primary B cells from cord blood	blood
38	chr17:17114600-17134800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr17:17114600-17136000	Strong transcription	Fetal Brain Female	brain
40	chr17:17114600-17136200	Strong transcription	NHLF	lung
41	chr17:17114600-17136400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:17114600-17136400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:17114600-17136400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr17:17114600-17136400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:17114600-17136400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr17:17114600-17136400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr17:17114600-17136600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:17114800-17131800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:17114800-17136400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:17114800-17136400	Strong transcription	Osteobl	bone

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