Variant report

Variant	rs58512566
Chromosome Location	chr17:45523858-45523859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11079774	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079775	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12449647	0.83[EUR][1000 genomes]
rs12451409	0.83[EUR][1000 genomes]
rs12452315	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12452796	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453233	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1912482	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1912483	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912487	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2085755	0.95[ASN][1000 genomes]
rs2136751	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2175290	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317631	0.88[ASN][1000 genomes]
rs28458768	0.83[EUR][1000 genomes]
rs28507314	0.84[EUR][1000 genomes]
rs34537623	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35016056	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3883319	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4338849	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968317	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4968319	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968320	0.87[ASN][1000 genomes]
rs56356751	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56952963	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62076461	0.88[ASN][1000 genomes]
rs62076542	0.85[ASN][1000 genomes]
rs6504872	0.88[ASN][1000 genomes]
rs67688344	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7206971	0.86[ASN][1000 genomes]
rs7208530	0.82[EUR][1000 genomes]
rs7214410	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9889709	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9890782	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9892497	0.83[EUR][1000 genomes]
rs9892686	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893901	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9894905	0.94[ASN][1000 genomes]
rs9895274	0.95[ASN][1000 genomes]
rs9895746	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9897492	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9900360	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9900366	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9902574	0.81[EUR][1000 genomes]
rs9905581	0.83[EUR][1000 genomes]
rs9907159	0.83[EUR][1000 genomes]
rs9908016	0.83[EUR][1000 genomes]
rs9908393	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9912101	0.83[EUR][1000 genomes]
rs9912311	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9914653	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9915919	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv470590	chr17:45419138-45547077	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv457821	chr17:45419139-45547078	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv575462	chr17:45419139-45547078	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv908566	chr17:45465735-45569714	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv1806110	chr17:45477544-45673592	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv908568	chr17:45506682-45590420	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv833468	chr17:45511563-45683164	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv1793478	chr17:45518444-45671051	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
18	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs58512566	TBKBP1	cis	Nerve Tibial	GTEx
rs58512566	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs58512566	TBKBP1	cis	Artery Tibial	GTEx
rs58512566	MRPL45P2	cis	Muscle Skeletal	GTEx
rs58512566	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs58512566	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs58512566	TBKBP1	cis	Artery Aorta	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45501400-45554200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:45501400-45554400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr17:45501600-45555400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:45501600-45556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:45501800-45533400	Weak transcription	Gastric	stomach
6	chr17:45501800-45547400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr17:45501800-45550200	Weak transcription	Ovary	ovary
8	chr17:45502200-45548000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:45502800-45548600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:45503200-45545400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:45505200-45550200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr17:45507200-45555000	Weak transcription	Fetal Thymus	thymus
13	chr17:45507600-45554200	Weak transcription	Left Ventricle	heart
14	chr17:45509400-45527800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:45509600-45527800	Weak transcription	Fetal Stomach	stomach
16	chr17:45512200-45530400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr17:45512200-45530800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:45512200-45550200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:45513000-45544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:45513400-45545400	Weak transcription	Liver	Liver
21	chr17:45514000-45530200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:45515400-45551600	Weak transcription	Fetal Intestine Large	intestine
23	chr17:45515600-45554200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr17:45515800-45531800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:45516000-45556400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr17:45516200-45531800	Weak transcription	Esophagus	oesophagus
27	chr17:45516800-45553200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:45517000-45550600	Weak transcription	Adipose Nuclei	Adipose
29	chr17:45517200-45547600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr17:45517400-45547400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:45517600-45530200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:45517600-45550200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr17:45518000-45568800	Weak transcription	K562	blood
34	chr17:45518200-45554200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:45518400-45545800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:45518400-45550200	Weak transcription	Lung	lung
37	chr17:45518600-45569200	Weak transcription	Brain Anterior Caudate	brain
38	chr17:45518800-45530200	Weak transcription	Fetal Muscle Leg	muscle
39	chr17:45519000-45545400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:45519000-45551600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr17:45519400-45569400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr17:45519600-45550200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:45519800-45555000	Weak transcription	Thymus	Thymus
44	chr17:45520000-45542400	Weak transcription	Fetal Lung	lung
45	chr17:45520000-45550600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:45520200-45530600	Weak transcription	Primary T cells from cord blood	blood
47	chr17:45520200-45549200	Weak transcription	HepG2	liver
48	chr17:45520400-45526000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr17:45520800-45534000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr17:45521000-45530600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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