Variant report

Variant	rs4247120
Chromosome Location	chr17:16919203-16919204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16917707..16920531-chr17:16944662..16947361,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11078374	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11871902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2090018	1.00[ASN][1000 genomes]
rs2271520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2349646	1.00[ASN][1000 genomes]
rs28461224	1.00[ASN][1000 genomes]
rs4247118	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	1.00[ASN][1000 genomes]
rs4514740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985696	1.00[ASN][1000 genomes]
rs4985701	1.00[ASN][1000 genomes]
rs4985702	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985717	1.00[ASN][1000 genomes]
rs4985740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985746	1.00[ASN][1000 genomes]
rs4985778	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6502563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7206981	1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208929	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208973	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7217091	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	1.00[ASN][1000 genomes]
rs8064550	1.00[ASN][1000 genomes]
rs8072184	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8073842	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9893911	1.00[ASN][1000 genomes]
rs9898995	1.00[ASN][1000 genomes]
rs9908767	1.00[ASN][1000 genomes]
rs9914671	1.00[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	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2761948	chr17:16868561-16920568	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv962271	chr17:16912264-16922846	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4247120	FLCN	cis	cerebellum	SCAN
rs4247120	LOC162632	cis	parietal	SCAN
rs4247120	TRPV2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16903200-16921000	Weak transcription	Lung	lung
2	chr17:16905800-16920000	Weak transcription	Fetal Intestine Large	intestine
3	chr17:16906800-16923400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:16913600-16921000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:16915000-16923600	Weak transcription	HSMMtube	muscle
6	chr17:16915200-16920000	Weak transcription	Fetal Intestine Small	intestine
7	chr17:16917400-16919400	Enhancers	NHEK	skin
8	chr17:16917400-16920200	Enhancers	HMEC	breast
9	chr17:16917400-16922000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr17:16917400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:16917400-16926200	Enhancers	Stomach Mucosa	stomach
12	chr17:16918000-16922000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr17:16918000-16922000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:16918000-16926200	Enhancers	Placenta	Placenta
15	chr17:16918200-16922000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:16918400-16920200	Enhancers	A549	lung
17	chr17:16918400-16920600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:16918400-16922000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr17:16918400-16922000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:16918600-16919400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:16918600-16919400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr17:16918600-16921400	Weak transcription	HUVEC	blood vessel
23	chr17:16918600-16921800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:16918600-16921800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr17:16918600-16924200	Weak transcription	Osteobl	bone
26	chr17:16918800-16920600	Enhancers	Primary B cells from peripheral blood	blood
27	chr17:16918800-16923200	Weak transcription	HSMM	muscle
28	chr17:16918800-16924200	Enhancers	Hela-S3	cervix
29	chr17:16918800-16924200	Weak transcription	K562	blood
30	chr17:16918800-16930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:16919000-16919400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:16919000-16920200	Weak transcription	Fetal Thymus	thymus
33	chr17:16919000-16920200	Weak transcription	Gastric	stomach
34	chr17:16919000-16920600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr17:16919000-16920800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr17:16919000-16921000	Weak transcription	Esophagus	oesophagus
37	chr17:16919000-16921000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr17:16919000-16921200	Weak transcription	Spleen	Spleen
39	chr17:16919000-16921400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:16919000-16921600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr17:16919000-16922800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr17:16919000-16924200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:16919200-16920200	Weak transcription	Pancreas	Pancrea
44	chr17:16919200-16920200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr17:16919200-16920400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:16919200-16921200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr17:16919200-16921200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr17:16919200-16923600	Weak transcription	Brain Anterior Caudate	brain
49	chr17:16919200-16924200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr17:16919200-16924200	Weak transcription	Small Intestine	intestine

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