Variant report

Variant	rs41323249
Chromosome Location	chr17:17124167-17124168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17123762..17126259-chr17:17137590..17140465,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154803	Chromatin interaction
ENSG00000266498	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11654778	1.00[ASN][1000 genomes]
rs11869409	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951281	1.00[ASN][1000 genomes]
rs34121330	1.00[ASN][1000 genomes]
rs34235236	1.00[ASN][1000 genomes]
rs34518797	0.83[AMR][1000 genomes]
rs34668117	1.00[ASN][1000 genomes]
rs35039203	1.00[ASN][1000 genomes]
rs35554631	1.00[ASN][1000 genomes]
rs3744123	0.85[AFR][1000 genomes]
rs41340844	1.00[ASN][1000 genomes]
rs41400246	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41424546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41525346	1.00[ASN][1000 genomes]
rs55836267	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632718	1.00[ASN][1000 genomes]
rs7224172	1.00[ASN][1000 genomes]
rs8079562	0.83[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41323249	FLCN	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17109400-17131600	Weak transcription	Fetal Heart	heart
2	chr17:17109600-17124200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:17113200-17135200	Strong transcription	Fetal Intestine Small	intestine
4	chr17:17113200-17136600	Strong transcription	Fetal Stomach	stomach
5	chr17:17113400-17131400	Strong transcription	Brain Anterior Caudate	brain
6	chr17:17113400-17131400	Strong transcription	Brain Substantia Nigra	brain
7	chr17:17113400-17134600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr17:17113400-17136200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:17113800-17134600	Strong transcription	Fetal Muscle Leg	muscle
10	chr17:17113800-17137600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:17114000-17131200	Strong transcription	Liver	Liver
12	chr17:17114000-17131200	Strong transcription	Left Ventricle	heart
13	chr17:17114000-17134800	Strong transcription	Fetal Intestine Large	intestine
14	chr17:17114000-17135200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr17:17114000-17136200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:17114000-17136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:17114000-17136400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:17114000-17136400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:17114000-17136400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:17114000-17136400	Strong transcription	Placenta	Placenta
21	chr17:17114000-17136600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr17:17114200-17131600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:17114200-17131600	Strong transcription	Spleen	Spleen
24	chr17:17114200-17136600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:17114400-17131400	Strong transcription	Lung	lung
26	chr17:17114400-17136200	Strong transcription	Primary T cells from cord blood	blood
27	chr17:17114400-17136200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:17114400-17136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:17114400-17136600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:17114600-17134800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr17:17114600-17136000	Strong transcription	Fetal Brain Female	brain
32	chr17:17114600-17136200	Strong transcription	NHLF	lung
33	chr17:17114600-17136400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:17114600-17136400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:17114600-17136400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:17114600-17136400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:17114600-17136400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr17:17114600-17136400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:17114600-17136600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:17114800-17131800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:17114800-17136400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:17114800-17136400	Strong transcription	Osteobl	bone
43	chr17:17115000-17136200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:17115000-17136200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr17:17115200-17139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr17:17115400-17136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:17115600-17130600	Strong transcription	NH-A	brain
48	chr17:17115600-17136400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr17:17115800-17127600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr17:17115800-17131200	Strong transcription	Brain Hippocampus Middle	brain

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