Variant report

Variant	rs41337846
Chromosome Location	chr17:17139232-17139233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr17:17138956-17139398	K562	blood:	n/a	n/a
2	POLR2A	chr17:17139171-17140059	K562	blood:	n/a	n/a
3	POLR2A	chr17:17139123-17141667	K562	blood:	n/a	n/a
4	JUN	chr17:17138821-17139335	HepG2	liver:	n/a	chr17:17139285-17139298
5	POLR2A	chr17:17139196-17139625	U87	brain:	n/a	n/a
6	CHD1	chr17:17138651-17141410	IMR90	lung:	n/a	n/a
7	WRNIP1	chr17:17139103-17139281	GM12878	blood:	n/a	n/a
8	JUND	chr17:17138776-17141326	GM12878	blood:	n/a	n/a
9	HCFC1	chr17:17138750-17141455	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr17:17138976-17141234	IMR90	lung:	n/a	n/a
11	NFIC	chr17:17138929-17139591	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr17:17139146-17139280	HUVEC	blood vessel:	n/a	n/a
13	KAP1	chr17:17138909-17140029	U2OS	brain:	n/a	n/a
14	YY1	chr17:17139144-17139323	K562	blood:	n/a	n/a
15	POLR2A	chr17:17138857-17141240	HepG2	liver:	n/a	n/a
16	JUND	chr17:17138904-17139309	HepG2	liver:	n/a	n/a
17	FOXA2	chr17:17139138-17139696	A549	lung:	n/a	chr17:17139395-17139407
18	KAP1	chr17:17138830-17140129	HEK293	kidney:	n/a	n/a
19	POLR2A	chr17:17139003-17139629	U87	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17138742..17142464-chr17:17205516..17208012,3	MCF-7	breast:
2	chr17:17131671..17134526-chr17:17137834..17141080,5	MCF-7	breast:
3	chr17:17138230..17139977-chr17:17206965..17208705,2	K562	blood:
4	chr17:17134971..17137251-chr17:17137733..17141244,3	K562	blood:
5	chr17:17126964..17129201-chr17:17139091..17140803,2	MCF-7	breast:
6	chr17:17135534..17137524-chr17:17138995..17141355,2	MCF-7	breast:
7	chr17:17107449..17109941-chr17:17138935..17142587,4	MCF-7	breast:
8	chr17:17107445..17110008-chr17:17138195..17140495,3	K562	blood:
9	chr17:17137888..17140600-chr17:17205281..17208205,3	MCF-7	breast:
10	chr17:17138850..17142014-chr17:17149192..17152269,3	K562	blood:
11	chr17:17138181..17140588-chr17:17182569..17184810,2	K562	blood:
12	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
13	chr17:17107449..17110459-chr17:17138885..17140924,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPS3-1	chr17:17138747-17139432	ENSG00000266498.1

No data

Variant related genes	Relation type
FLCN	TF binding region
ENSG00000205309	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000179598	Chromatin interaction
ENSG00000141030	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12600635	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601848	0.91[ASN][1000 genomes]
rs12602831	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602871	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961474	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16961493	0.95[ASN][1000 genomes]
rs16961507	0.93[ASN][1000 genomes]
rs2270180	0.91[ASN][1000 genomes]
rs2294155	0.97[ASN][1000 genomes]
rs34518797	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35534166	0.92[ASN][1000 genomes]
rs41283373	0.94[ASN][1000 genomes]
rs41400246	0.84[AMR][1000 genomes]
rs41424546	0.88[AMR][1000 genomes]
rs55689224	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502565	0.96[ASN][1000 genomes]
rs7213351	0.91[ASN][1000 genomes]
rs7219012	0.95[ASN][1000 genomes]
rs7222697	0.91[ASN][1000 genomes]
rs7225789	0.90[ASN][1000 genomes]
rs7226227	0.90[ASN][1000 genomes]
rs8065774	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070995	0.95[ASN][1000 genomes]
rs8075526	0.97[ASN][1000 genomes]
rs8079562	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9890243	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9896078	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	esv1004208	chr17:17136933-17147885	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41337846	FLCN	cis	Artery Tibial	GTEx
rs41337846	NT5M	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17115200-17139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:17135400-17139400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:17138400-17139400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:17138400-17139600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:17138400-17139600	Enhancers	Fetal Heart	heart
6	chr17:17138400-17141400	Active TSS	Fetal Intestine Large	intestine
7	chr17:17138400-17142200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:17138600-17139400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr17:17138600-17139400	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr17:17138600-17139400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr17:17138600-17139400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr17:17138600-17139400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr17:17138600-17139600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr17:17138600-17139600	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr17:17138600-17139600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr17:17138600-17139600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:17138600-17139800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr17:17138600-17139800	Flanking Active TSS	Fetal Brain Female	brain
19	chr17:17138600-17139800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr17:17138600-17139800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr17:17138600-17139800	Flanking Active TSS	NH-A	brain
22	chr17:17138600-17140000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:17138600-17140000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr17:17138600-17140000	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr17:17138600-17140000	Flanking Active TSS	Dnd41	blood
26	chr17:17138600-17140200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr17:17138600-17141600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr17:17138600-17141800	Active TSS	NHDF-Ad	bronchial
29	chr17:17138800-17139400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr17:17138800-17139400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:17138800-17139400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:17138800-17139400	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr17:17138800-17139400	Enhancers	Esophagus	oesophagus
34	chr17:17138800-17139400	Flanking Active TSS	Right Ventricle	heart
35	chr17:17138800-17139400	Enhancers	Small Intestine	intestine
36	chr17:17138800-17139400	Flanking Active TSS	NHLF	lung
37	chr17:17138800-17139600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:17138800-17139600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr17:17138800-17139600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:17138800-17139600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:17138800-17139600	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr17:17138800-17139600	Flanking Active TSS	A549	lung
43	chr17:17138800-17139800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr17:17138800-17139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:17138800-17139800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:17138800-17139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:17138800-17139800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr17:17138800-17139800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr17:17138800-17139800	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr17:17138800-17139800	Flanking Active TSS	Colonic Mucosa	Colon

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