Variant report

Variant	rs12325679
Chromosome Location	chr17:17154605-17154606
allele	A/G
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	chr17:17154455-17154866	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
COPS3	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1029829	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1029830	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1029832	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10459910	0.83[ASN][1000 genomes]
rs11652745	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450037	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452947	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12935953	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12937908	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12947291	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613416	0.96[ASN][1000 genomes]
rs1624963	0.92[ASN][1000 genomes]
rs1708618	0.98[ASN][1000 genomes]
rs1708619	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1708620	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1708623	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708626	0.99[ASN][1000 genomes]
rs1708627	0.99[ASN][1000 genomes]
rs1708629	0.99[ASN][1000 genomes]
rs1736200	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736201	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1736202	1.00[ASN][1000 genomes]
rs1736203	1.00[ASN][1000 genomes]
rs1736206	0.98[ASN][1000 genomes]
rs1736207	0.98[ASN][1000 genomes]
rs1736210	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736213	0.98[ASN][1000 genomes]
rs1736214	0.98[ASN][1000 genomes]
rs1736215	0.96[ASN][1000 genomes]
rs1736219	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2458529	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3182911	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3853545	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985759	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985761	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066064	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219248	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7220275	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065832	0.87[EUR][1000 genomes]
rs8070574	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8072402	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072869	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9890657	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894884	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901894	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903294	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907107	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12325679	FLCN	cis	Esophagus Muscularis	GTEx
rs12325679	FLCN	cis	Heart Left Ventricle	GTEx
rs12325679	FLCN	cis	lung	GTEx
rs12325679	FLCN	cis	Artery Aorta	GTEx
rs12325679	FLCN	cis	Artery Tibial	GTEx
rs12325679	FLCN	cis	Adipose Subcutaneous	GTEx
rs12325679	COPS3	cis	Whole Blood	GTEx
rs12325679	FLCN	cis	Nerve Tibial	GTEx
rs12325679	FLCN	cis	Esophagus Mucosa	GTEx
rs12325679	FLCN	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17141600-17161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:17141800-17155600	Weak transcription	Psoas Muscle	Psoas
3	chr17:17141800-17156600	Weak transcription	Fetal Heart	heart
4	chr17:17141800-17162200	Weak transcription	Stomach Mucosa	stomach
5	chr17:17146000-17171000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:17148400-17160000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:17148600-17159000	Strong transcription	Brain Hippocampus Middle	brain
8	chr17:17148600-17161200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr17:17148600-17167400	Strong transcription	Fetal Intestine Small	intestine
10	chr17:17148600-17172000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr17:17148600-17178800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:17148600-17179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:17148600-17179600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr17:17148600-17180000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:17148800-17178400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:17148800-17178400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:17148800-17179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:17148800-17179600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:17148800-17179600	Strong transcription	Fetal Muscle Leg	muscle
20	chr17:17148800-17179800	Strong transcription	Fetal Stomach	stomach
21	chr17:17148800-17180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:17148800-17180400	Strong transcription	Fetal Thymus	thymus
23	chr17:17149000-17154800	Strong transcription	A549	lung
24	chr17:17149000-17155400	Strong transcription	Liver	Liver
25	chr17:17149000-17156600	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr17:17149000-17156800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr17:17149000-17156800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:17149000-17165200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr17:17149000-17165600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:17149000-17165600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:17149000-17165600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:17149000-17165800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:17149000-17165800	Strong transcription	Fetal Brain Female	brain
34	chr17:17149000-17166000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:17149000-17174800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:17149000-17174800	Strong transcription	Adipose Nuclei	Adipose
37	chr17:17149000-17174800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr17:17149000-17178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr17:17149000-17178800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr17:17149000-17179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:17149000-17179400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:17149000-17180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:17149000-17181200	Strong transcription	Dnd41	blood
44	chr17:17149200-17157600	Strong transcription	Brain Substantia Nigra	brain
45	chr17:17149200-17157800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:17149200-17157800	Strong transcription	NHEK	skin
47	chr17:17149200-17159400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr17:17149200-17160400	Strong transcription	Lung	lung
49	chr17:17149200-17164000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:17149200-17164000	Strong transcription	Rectal Smooth Muscle	rectum

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