Variant report

Variant	rs4399589
Chromosome Location	chr17:17114586-17114587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17114398-17114982	U87	brain:	n/a	n/a
2	POLR2A	chr17:17114404-17114976	U87	brain:	n/a	n/a
3	POLR2A	chr17:17114534-17114933	K562	blood:	n/a	n/a
4	JUND	chr17:17114463-17114846	A549	lung:	n/a	n/a
5	POLR2A	chr17:17114244-17115003	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:17114545-17114783	U87	brain:	n/a	n/a
7	POLR2A	chr17:17114576-17114594	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:17114431-17114948	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr17:17114526-17114900	K562	blood:	n/a	n/a
10	POLR2A	chr17:17114487-17115177	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr17:17114502-17115137	K562	blood:	n/a	n/a
12	POLR2A	chr17:17114528-17114783	U87	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17107906..17111698-chr17:17113566..17117634,4	K562	blood:
2	chr17:17110096..17111994-chr17:17113370..17116331,3	MCF-7	breast:
3	chr17:17106584..17108304-chr17:17112310..17114870,2	K562	blood:

No data

Variant related genes	Relation type
PLD6	TF binding region
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12453929	0.98[ASN][1000 genomes]
rs14003	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs1736208	0.88[MEX][hapmap]
rs1736211	0.88[MEX][hapmap]
rs1736219	0.88[CHD][hapmap]
rs2009478	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2018781	0.82[EUR][1000 genomes]
rs3803761	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985749	0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs4985752	0.88[CHD][hapmap]
rs7208065	0.88[CHD][hapmap]
rs7218795	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065832	0.88[CHD][hapmap]
rs8077299	0.81[ASN][1000 genomes]
rs8077796	0.99[ASN][1000 genomes]
rs9908150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9908205	1.00[CHB][hapmap];0.80[JPT][hapmap];0.90[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4399589	FLCN	cis	cerebellum	SCAN
rs4399589	RAI1	cis	cerebellum	SCAN
rs4399589	FLCN	cis	lymphoblastoid	seeQTL
rs4399589	UBB	cis	cerebellum	SCAN
rs4399589	FLCN	cis	parietal	SCAN
rs4399589	COPS3	cis	multi-tissue	Pritchard
rs4399589	FLCN	cis	Heart Left Ventricle	GTEx
rs4399589	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17105000-17116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:17109400-17114600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr17:17109400-17120400	Weak transcription	Fetal Kidney	kidney
4	chr17:17109400-17131600	Weak transcription	Fetal Heart	heart
5	chr17:17109600-17114600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr17:17109600-17114800	Weak transcription	Aorta	Aorta
7	chr17:17109600-17115400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:17109600-17115400	Weak transcription	GM12878-XiMat	blood
9	chr17:17109600-17116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:17109600-17116200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:17109600-17116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:17109600-17116200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:17109600-17116400	Weak transcription	Small Intestine	intestine
14	chr17:17109600-17118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:17109600-17124200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:17109800-17114600	Weak transcription	Primary B cells from cord blood	blood
17	chr17:17109800-17114600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:17109800-17114600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:17109800-17115600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:17109800-17116000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:17109800-17116200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:17109800-17116200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:17109800-17116600	Weak transcription	HUVEC	blood vessel
24	chr17:17109800-17117200	Weak transcription	Psoas Muscle	Psoas
25	chr17:17109800-17123200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:17110000-17114600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:17110000-17114600	Weak transcription	Fetal Brain Female	brain
28	chr17:17110000-17114800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:17110000-17114800	Weak transcription	Thymus	Thymus
30	chr17:17110000-17116600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:17110000-17121000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:17110200-17114600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:17110200-17114800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:17110200-17115000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:17110200-17116000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr17:17110200-17116200	Weak transcription	Brain Germinal Matrix	brain
37	chr17:17110200-17117000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:17110400-17114600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr17:17110400-17114600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:17110400-17114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:17110400-17114600	Weak transcription	NHLF	lung
42	chr17:17110400-17114800	Weak transcription	Brain Angular Gyrus	brain
43	chr17:17110400-17115400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:17110400-17115600	Weak transcription	NH-A	brain
45	chr17:17110400-17116000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:17110400-17116200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr17:17110400-17116200	Weak transcription	Colonic Mucosa	Colon
48	chr17:17110400-17116200	Weak transcription	Fetal Thymus	thymus
49	chr17:17110400-17116200	Weak transcription	Ovary	ovary
50	chr17:17110400-17116200	Weak transcription	Rectal Mucosa Donor 31	rectum

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