Variant report

Variant	rs56356751
Chromosome Location	chr17:45557025-45557026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11079774	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11079775	0.85[ASN][1000 genomes]
rs12449647	0.86[EUR][1000 genomes]
rs12451409	0.86[EUR][1000 genomes]
rs12452315	0.84[ASN][1000 genomes]
rs12452796	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12944103	0.83[EUR][1000 genomes]
rs1912482	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1912483	0.82[EUR][1000 genomes]
rs1912487	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2085755	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136751	0.84[EUR][1000 genomes]
rs2175290	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28458768	0.86[EUR][1000 genomes]
rs28507314	0.87[EUR][1000 genomes]
rs34537623	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35016056	0.82[EUR][1000 genomes]
rs3883319	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4338849	0.87[ASN][1000 genomes]
rs4968317	0.81[EUR][1000 genomes]
rs4968319	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56952963	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58512566	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59231671	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62076540	0.88[EUR][1000 genomes]
rs62076542	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67688344	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7208530	0.85[EUR][1000 genomes]
rs7214410	0.82[EUR][1000 genomes]
rs8076778	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8079744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9889709	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9890782	0.81[EUR][1000 genomes]
rs9892497	0.86[EUR][1000 genomes]
rs9892686	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9893901	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9894179	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9894905	0.84[ASN][1000 genomes]
rs9895274	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9895746	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9897492	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9900360	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9900366	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9902574	0.84[EUR][1000 genomes]
rs9905581	0.86[EUR][1000 genomes]
rs9907159	0.86[EUR][1000 genomes]
rs9908016	0.86[EUR][1000 genomes]
rs9908393	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9912101	0.86[EUR][1000 genomes]
rs9912311	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9912592	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9914653	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9915919	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv908569	chr17:45537395-45603094	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv1808961	chr17:45542951-45664746	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv9566	chr17:45550586-45559287	Strong transcription Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
19	nsv960119	chr17:45551104-45560111	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases
20	esv33689	chr17:45551959-45664575	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv471513	chr17:45552080-45671439	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56356751	TBKBP1	cis	Artery Tibial	GTEx
rs56356751	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs56356751	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56356751	MRPL45P2	cis	Muscle Skeletal	GTEx
rs56356751	TBKBP1	cis	Nerve Tibial	GTEx
rs56356751	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs56356751	TBKBP1	cis	Artery Aorta	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45518000-45568800	Weak transcription	K562	blood
2	chr17:45518600-45569200	Weak transcription	Brain Anterior Caudate	brain
3	chr17:45519400-45569400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr17:45526400-45568800	Weak transcription	Brain Angular Gyrus	brain
5	chr17:45526600-45568800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:45527000-45568800	Weak transcription	Colon Smooth Muscle	Colon
7	chr17:45527800-45568800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:45529800-45558200	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:45530200-45568800	Weak transcription	A549	lung
10	chr17:45531200-45560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:45531400-45568800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr17:45531600-45569200	Weak transcription	Primary T cells from cord blood	blood
13	chr17:45534800-45569400	Weak transcription	Esophagus	oesophagus
14	chr17:45537800-45569000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:45538200-45569000	Weak transcription	Brain Substantia Nigra	brain
16	chr17:45539800-45569400	Weak transcription	Brain Germinal Matrix	brain
17	chr17:45540400-45569600	Weak transcription	Small Intestine	intestine
18	chr17:45540600-45568800	Weak transcription	Right Ventricle	heart
19	chr17:45541200-45559000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:45541800-45568800	Weak transcription	NHEK	skin
21	chr17:45542800-45558000	Weak transcription	Primary B cells from cord blood	blood
22	chr17:45543600-45568800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:45543600-45568800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr17:45543800-45568800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:45544000-45569600	Weak transcription	Spleen	Spleen
26	chr17:45544400-45559600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr17:45544400-45568800	Weak transcription	NH-A	brain
28	chr17:45544400-45569000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr17:45544600-45559400	Strong transcription	Fetal Stomach	stomach
30	chr17:45545000-45569000	Weak transcription	HSMMtube	muscle
31	chr17:45545400-45559200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:45545800-45568800	Weak transcription	HSMM	muscle
33	chr17:45545800-45569200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:45546000-45558200	Weak transcription	Aorta	Aorta
35	chr17:45546200-45568800	Weak transcription	Hela-S3	cervix
36	chr17:45547000-45557200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:45547200-45568800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:45548400-45562200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:45548400-45568800	Weak transcription	Pancreas	Pancrea
40	chr17:45548800-45559000	Strong transcription	Fetal Intestine Small	intestine
41	chr17:45548800-45568800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr17:45548800-45569000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:45549000-45568800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:45550400-45569000	Weak transcription	Colonic Mucosa	Colon
45	chr17:45550600-45557800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr17:45550800-45559000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:45550800-45568800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:45550800-45568800	Weak transcription	HMEC	breast
49	chr17:45551000-45568800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:45551000-45568800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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