Variant report

Variant	rs1613416
Chromosome Location	chr17:17133121-17133122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17133076-17133278	K562	blood:	n/a	n/a
2	CTCF	chr17:17133100-17133250	WERI-Rb-1	eye:	n/a	chr17:17133142-17133151

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17131671..17134526-chr17:17137834..17141080,5	MCF-7	breast:
2	chr17:17132573..17135085-chr17:17184051..17185920,2	K562	blood:

Variant related genes	Relation type
FLCN	TF binding region
ENSG00000266498	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000154803	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1029829	0.90[ASN][1000 genomes]
rs1029830	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1029832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10459910	0.83[ASN][1000 genomes]
rs11652745	0.93[ASN][1000 genomes]
rs12325679	0.96[ASN][1000 genomes]
rs12450037	0.93[ASN][1000 genomes]
rs12452947	0.90[ASN][1000 genomes]
rs12935953	0.92[ASN][1000 genomes]
rs12937908	0.92[ASN][1000 genomes]
rs12947291	0.95[ASN][1000 genomes]
rs1624963	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1708618	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1708619	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1708620	0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1708623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708626	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708629	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736200	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1736201	0.82[ASN][1000 genomes]
rs1736202	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1736203	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1736206	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1736207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1736210	0.94[ASN][1000 genomes]
rs1736213	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736215	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736219	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3182911	0.86[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3853545	0.90[ASN][1000 genomes]
rs4985705	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4985752	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4985759	0.92[ASN][1000 genomes]
rs4985761	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs62066064	0.93[ASN][1000 genomes]
rs7208065	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]
rs7219248	0.92[ASN][1000 genomes]
rs7220275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8065832	1.00[ASW][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs8070574	0.92[ASN][1000 genomes]
rs8072402	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8072869	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8080386	1.00[MEX][hapmap]
rs9890657	0.95[ASN][1000 genomes]
rs9894884	0.95[ASN][1000 genomes]
rs9901894	0.96[ASN][1000 genomes]
rs9903294	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9907107	0.91[ASN][1000 genomes]
rs9908150	0.85[CEU][hapmap]
rs9908205	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1613416	FLCN	cis	Skin Sun Exposed Lower leg	GTEx
rs1613416	COPS3	cis	Whole Blood	GTEx
rs1613416	FLCN	cis	Heart Left Ventricle	GTEx
rs1613416	FLCN	cis	lymphoblastoid	seeQTL
rs1613416	FLCN	cis	Esophagus Muscularis	GTEx
rs1613416	FLCN	cis	Nerve Tibial	GTEx
rs1613416	FLCN	cis	Adipose Subcutaneous	GTEx
rs1613416	FLCN	cis	Esophagus Mucosa	GTEx
rs1613416	FLCN	cis	Thyroid	GTEx
rs1613416	RASD1	cis	parietal	SCAN
rs1613416	FLCN	cis	cerebellum	SCAN
rs1613416	PLD6	cis	cerebellum	SCAN
rs1613416	RAI1	cis	cerebellum	SCAN
rs1613416	FLCN	cis	Stomach	GTEx
rs1613416	FLCN	cis	Artery Tibial	GTEx
rs1613416	FLCN	cis	lung	GTEx
rs1613416	FLCN	cis	parietal	SCAN
rs1613416	FLCN	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17113200-17135200	Strong transcription	Fetal Intestine Small	intestine
2	chr17:17113200-17136600	Strong transcription	Fetal Stomach	stomach
3	chr17:17113400-17134600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:17113400-17136200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:17113800-17134600	Strong transcription	Fetal Muscle Leg	muscle
6	chr17:17113800-17137600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:17114000-17134800	Strong transcription	Fetal Intestine Large	intestine
8	chr17:17114000-17135200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr17:17114000-17136200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:17114000-17136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:17114000-17136400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:17114000-17136400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:17114000-17136400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:17114000-17136400	Strong transcription	Placenta	Placenta
15	chr17:17114000-17136600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:17114200-17136600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:17114400-17136200	Strong transcription	Primary T cells from cord blood	blood
18	chr17:17114400-17136200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:17114400-17136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:17114400-17136600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:17114600-17134800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr17:17114600-17136000	Strong transcription	Fetal Brain Female	brain
23	chr17:17114600-17136200	Strong transcription	NHLF	lung
24	chr17:17114600-17136400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:17114600-17136400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:17114600-17136400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:17114600-17136400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:17114600-17136400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr17:17114600-17136400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr17:17114600-17136600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:17114800-17136400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:17114800-17136400	Strong transcription	Osteobl	bone
33	chr17:17115000-17136200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:17115000-17136200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:17115200-17139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:17115400-17136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:17115600-17136400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:17115800-17136000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr17:17116000-17133800	Strong transcription	Esophagus	oesophagus
40	chr17:17116000-17135400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr17:17116000-17135800	Strong transcription	Thymus	Thymus
42	chr17:17116000-17136000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr17:17116000-17136000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr17:17116000-17136000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr17:17116000-17136200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr17:17116000-17136200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:17116000-17136200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr17:17116000-17136400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr17:17116000-17136400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:17116000-17136400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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