Variant report

Variant	rs3853545
Chromosome Location	chr17:17184033-17184034
allele	G/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	GABPA	chr17:17183697-17185174	A549	lung:	n/a	n/a
2	USF1	chr17:17183916-17184803	ECC-1	luminal epithelium:	n/a	chr17:17184207-17184223
3	SP2	chr17:17183824-17184571	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:17183806-17184937	GM12892	blood:	n/a	n/a
5	CHD2	chr17:17183906-17185110	K562	blood:	n/a	chr17:17184198-17184208
6	NFIC	chr17:17183764-17184272	GM12878	blood:	n/a	chr17:17184070-17184098
7	ATF1	chr17:17183975-17184885	K562	blood:	n/a	n/a
8	FOS	chr17:17183913-17184299	K562	blood:	n/a	n/a
9	HA-E2F1	chr17:17183649-17184940	MCF-7	breast:	n/a	chr17:17184536-17184547
10	POLR2A	chr17:17183803-17185007	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr17:17183904-17184940	GM12878	blood:	n/a	chr17:17184216-17184232
12	TBP	chr17:17183919-17184991	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr17:17183800-17185157	A549	lung:	n/a	n/a
14	POLR2A	chr17:17183862-17185070	GM12878	blood:	n/a	n/a
15	CTCF	chr17:17183837-17184241	H1-hESC	embryonic stem cell:	n/a	chr17:17184018-17184031 chr17:17184177-17184190
16	JUND	chr17:17183933-17184913	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAFK	chr17:17183880-17184234	HepG2	liver:	n/a	chr17:17184034-17184049 chr17:17184034-17184050
18	MAX	chr17:17183891-17184785	Hela-S3	cervix:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
19	SIN3AK20	chr17:17184015-17184881	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr17:17183872-17184867	Hela-S3	cervix:	n/a	n/a
21	ETS1	chr17:17183804-17184966	A549	lung:	n/a	chr17:17184133-17184149 chr17:17184611-17184620 chr17:17184197-17184208 chr17:17184609-17184619
22	CTCF	chr17:17183960-17184110	BJ	skin:	n/a	chr17:17184018-17184031
23	POLR2A	chr17:17183759-17184247	U87	brain:	n/a	n/a
24	GABPA	chr17:17183738-17184757	K562	blood:	n/a	n/a
25	E2F6	chr17:17183997-17184739	K562	blood:	n/a	chr17:17184537-17184548
26	POLR2A	chr17:17183720-17185169	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr17:17183837-17184868	K562	blood:	n/a	n/a
28	POLR2A	chr17:17183805-17184951	GM19099	blood:	n/a	n/a
29	MAFF	chr17:17183952-17184180	K562	blood:	n/a	chr17:17184033-17184051
30	PBX3	chr17:17183817-17185002	SK-N-SH	brain:	n/a	n/a
31	HEY1	chr17:17183806-17184795	HepG2	liver:	n/a	n/a
32	HDAC2	chr17:17183864-17184188	MCF-7	breast:	n/a	n/a
33	YY1	chr17:17183832-17184725	HepG2	liver:	n/a	chr17:17184570-17184579 chr17:17184568-17184579
34	ZEB1	chr17:17184024-17184637	GM12878	blood:	n/a	n/a
35	MYC	chr17:17183917-17184085	MCF10A-Er-Src	breast:	n/a	n/a
36	IRF1	chr17:17183932-17184974	K562	blood:	n/a	chr17:17184144-17184158
37	GABPA	chr17:17183877-17184883	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr17:17183803-17185095	NB4	blood:	n/a	n/a
39	MAX	chr17:17183764-17184965	ECC-1	luminal epithelium:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
40	SP1	chr17:17183810-17184830	H1-hESC	embryonic stem cell:	n/a	chr17:17184195-17184209 chr17:17184561-17184573 chr17:17184198-17184210 chr17:17184198-17184210 chr17:17184199-17184208
41	CHD2	chr17:17183856-17184978	GM12878	blood:	n/a	chr17:17184198-17184208
42	TCF12	chr17:17183700-17185248	A549	lung:	n/a	n/a
43	MAFK	chr17:17183931-17185006	Hela-S3	cervix:	n/a	chr17:17184034-17184049 chr17:17184034-17184050
44	TCF7L2	chr17:17184017-17184633	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr17:17183723-17185127	U87	brain:	n/a	n/a
46	POLR2A	chr17:17183833-17184946	K562	blood:	n/a	n/a
47	FOXA1	chr17:17183935-17184163	T-47D	breast:	n/a	n/a
48	POLR2A	chr17:17183744-17185036	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr17:17183845-17184880	K562	blood:	n/a	n/a
50	USF1	chr17:17183984-17184220	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17177648..17180936-chr17:17181197..17184729,6	MCF-7	breast:
2	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
3	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
4	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
5	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
6	chr17:17138181..17140588-chr17:17182569..17184810,2	K562	blood:
7	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
8	chr17:17108079..17111792-chr17:17180254..17184300,4	K562	blood:
9	chr17:17109460..17111792-chr17:17182647..17184300,2	K562	blood:
10	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:
11	chr14:60558608..60559155-chr17:17184009..17184723,2	Hela-S3	cervix:
12	chr17:17173847..17176636-chr17:17182577..17185189,4	MCF-7	breast:

Variant related genes	Relation type
COPS3	TF binding region
ENSG00000154803	Chromatin interaction
ENSG00000126773	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000205309	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1029829	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029830	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029832	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652745	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12325679	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12450037	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452947	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935953	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12937908	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12947291	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1613416	0.90[ASN][1000 genomes]
rs1624963	0.86[ASN][1000 genomes]
rs1708618	0.92[ASN][1000 genomes]
rs1708619	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1708620	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1708623	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1708626	0.93[ASN][1000 genomes]
rs1708627	0.93[ASN][1000 genomes]
rs1708629	0.93[ASN][1000 genomes]
rs1736200	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736201	0.80[ASN][1000 genomes]
rs1736202	0.94[ASN][1000 genomes]
rs1736203	0.94[ASN][1000 genomes]
rs1736206	0.92[ASN][1000 genomes]
rs1736207	0.92[ASN][1000 genomes]
rs1736210	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1736213	0.92[ASN][1000 genomes]
rs1736214	0.92[ASN][1000 genomes]
rs1736215	0.90[ASN][1000 genomes]
rs1736219	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3182911	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985759	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985761	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066064	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7219248	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7220275	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065832	0.85[EUR][1000 genomes]
rs8070574	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8072402	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072869	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9890657	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9894884	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9901894	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9903294	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9907107	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv9499	chr17:17181611-17187670	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3853545	FLCN	cis	Nerve Tibial	GTEx
rs3853545	FLCN	cis	Adipose Subcutaneous	GTEx
rs3853545	FLCN	cis	Esophagus Mucosa	GTEx
rs3853545	FLCN	cis	Thyroid	GTEx
rs3853545	COPS3	cis	Whole Blood	GTEx
rs3853545	FLCN	cis	Heart Left Ventricle	GTEx
rs3853545	FLCN	cis	Artery Aorta	GTEx
rs3853545	FLCN	cis	lung	GTEx
rs3853545	FLCN	cis	Artery Tibial	GTEx
rs3853545	FLCN	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17182800-17185000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr17:17182800-17185000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:17183000-17184200	Active TSS	Right Atrium	heart
4	chr17:17183000-17184800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr17:17183000-17185200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:17183200-17184800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:17183200-17184800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:17183200-17184800	Active TSS	K562	blood
9	chr17:17183200-17185000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr17:17183200-17185000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr17:17183200-17185000	Active TSS	NHDF-Ad	bronchial
12	chr17:17183200-17185200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr17:17183200-17185200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:17183200-17185200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:17183200-17185200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:17183200-17185400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:17183200-17185400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr17:17183200-17185400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr17:17183400-17184200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:17183400-17184400	Active TSS	HepG2	liver
21	chr17:17183400-17184600	Weak transcription	Fetal Heart	heart
22	chr17:17183400-17184600	Active TSS	Small Intestine	intestine
23	chr17:17183400-17184600	Active TSS	HSMM	muscle
24	chr17:17183400-17184800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:17183400-17184800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:17183400-17184800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:17183400-17184800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:17183400-17184800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:17183400-17184800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr17:17183400-17184800	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr17:17183400-17184800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:17183400-17184800	Active TSS	Brain Hippocampus Middle	brain
33	chr17:17183400-17184800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr17:17183400-17184800	Active TSS	Brain Substantia Nigra	brain
35	chr17:17183400-17184800	Active TSS	Colon Smooth Muscle	Colon
36	chr17:17183400-17184800	Active TSS	Fetal Lung	lung
37	chr17:17183400-17184800	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr17:17183400-17184800	Active TSS	Rectal Smooth Muscle	rectum
39	chr17:17183400-17184800	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr17:17183400-17184800	Active TSS	A549	lung
41	chr17:17183400-17184800	Active TSS	Dnd41	blood
42	chr17:17183400-17184800	Active TSS	GM12878-XiMat	blood
43	chr17:17183400-17184800	Active TSS	Hela-S3	cervix
44	chr17:17183400-17184800	Active TSS	HMEC	breast
45	chr17:17183400-17184800	Active TSS	HSMMtube	muscle
46	chr17:17183400-17184800	Active TSS	NH-A	brain
47	chr17:17183400-17184800	Active TSS	NHEK	skin
48	chr17:17183400-17184800	Active TSS	NHLF	lung
49	chr17:17183400-17185000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:17183400-17185000	Active TSS	Duodenum Mucosa	Duodenum

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