Variant report

Variant	rs4794052
Chromosome Location	chr17:45769236-45769237
allele	C/T
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	MXI1	chr17:45768997-45773036	SK-N-SH	brain:	n/a	chr17:45771274-45771283 chr17:45771276-45771285
2	JUND	chr17:45769216-45770072	SK-N-SH	brain:	n/a	chr17:45769650-45769660 chr17:45769696-45769705 chr17:45769650-45769660 chr17:45769694-45769705 chr17:45769696-45769704 chr17:45769651-45769659 chr17:45769650-45769660 chr17:45769696-45769703 chr17:45769694-45769706 chr17:45769695-45769705 chr17:45769650-45769660 chr17:45769695-45769704
3	PAX5	chr17:45768941-45769273	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45725675..45729413-chr17:45768882..45774493,5	K562	blood:
2	chr17:45749788..45752546-chr17:45768460..45770094,2	K562	blood:
3	chr17:45767069..45769525-chr17:45771131..45772683,2	K562	blood:
4	chr17:45759280..45761453-chr17:45769227..45771829,2	MCF-7	breast:
5	chr17:45724693..45730044-chr17:45766323..45778247,15	K562	blood:
6	chr17:45768574..45772572-chr17:48939145..48944059,6	MCF-7	breast:
7	chr17:45748954..45758231-chr17:45766475..45774270,24	MCF-7	breast:
8	chr17:45759177..45766275-chr17:45767435..45773662,12	K562	blood:
9	chr17:45768051..45770034-chr17:48948476..48950883,2	MCF-7	breast:
10	chr17:45769138..45771658-chr17:46124750..46126805,2	MCF-7	breast:

Variant related genes	Relation type
TBKBP1	TF binding region
ENSG00000264558	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000263766	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11079783	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs11868838	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1808192	0.90[GIH][hapmap]
rs1962307	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2013383	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760371	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4267364	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497739	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs4794053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56131210	0.81[EUR][1000 genomes]
rs62074054	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6503804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503807	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214799	0.81[CEU][hapmap]
rs7222225	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs8070463	0.80[GIH][hapmap];0.81[TSI][hapmap]
rs8075566	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078309	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913503	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv908571	chr17:45765249-45821510	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4794052	TBKBP1	cis	Nerve Tibial	GTEx
rs4794052	MRPL45P2	cis	lymphoblastoid	seeQTL
rs4794052	TBKBP1	cis	Artery Aorta	GTEx
rs4794052	TBKBP1	cis	Thyroid	GTEx
rs4794052	TBKBP1	cis	Whole Blood	GTEx
rs4794052	RAB5C	cis	parietal	SCAN
rs4794052	KRTAP9-3	cis	cerebellum	SCAN
rs4794052	C17orf57	cis	parietal	SCAN
rs4794052	TBKBP1	cis	lung	GTEx
rs4794052	HOXB6	cis	cerebellum	SCAN
rs4794052	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4794052	TBKBP1	cis	Artery Tibial	GTEx
rs4794052	TBKBP1	cis	Esophagus Mucosa	GTEx
rs4794052	KRT17	cis	cerebellum	SCAN
rs4794052	TBKBP1	cis	lymphoblastoid	seeQTL
rs4794052	C17orf57	cis	cerebellum	SCAN
rs4794052	CDK5RAP3	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45758200-45770200	Weak transcription	Fetal Heart	heart
2	chr17:45758200-45770600	Weak transcription	Fetal Brain Male	brain
3	chr17:45760000-45769400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:45760200-45769600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:45760200-45769600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:45760200-45770000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:45760200-45770000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr17:45760200-45770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:45760400-45769800	Weak transcription	Right Ventricle	heart
10	chr17:45760400-45770000	Weak transcription	Colonic Mucosa	Colon
11	chr17:45760400-45770000	Weak transcription	Pancreas	Pancrea
12	chr17:45760400-45770200	Weak transcription	Colon Smooth Muscle	Colon
13	chr17:45760400-45770400	Weak transcription	Gastric	stomach
14	chr17:45760400-45770400	Weak transcription	Hela-S3	cervix
15	chr17:45761200-45770000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:45761600-45769800	Weak transcription	Esophagus	oesophagus
17	chr17:45762000-45769400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr17:45762200-45770200	Weak transcription	Small Intestine	intestine
19	chr17:45762200-45770400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:45762400-45769600	Weak transcription	Lung	lung
21	chr17:45762400-45769800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:45762400-45770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr17:45762600-45770000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:45762600-45770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:45762600-45770400	Weak transcription	Left Ventricle	heart
26	chr17:45762600-45770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:45762600-45770600	Weak transcription	Aorta	Aorta
28	chr17:45762800-45769600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr17:45762800-45770000	Weak transcription	Fetal Stomach	stomach
30	chr17:45763200-45770200	Weak transcription	Fetal Intestine Large	intestine
31	chr17:45763400-45770000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:45763400-45770400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:45763400-45770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:45763600-45769400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr17:45763600-45770400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:45763800-45769600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr17:45763800-45770200	Weak transcription	Liver	Liver
38	chr17:45764200-45769800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr17:45764400-45769600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr17:45764400-45769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:45764600-45769400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:45764600-45769800	Weak transcription	Right Atrium	heart
43	chr17:45764800-45769400	Weak transcription	Primary B cells from cord blood	blood
44	chr17:45764800-45769600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:45764800-45770600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr17:45765000-45769800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:45765000-45769800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:45765000-45770600	Weak transcription	HMEC	breast
49	chr17:45765200-45769600	Weak transcription	HUVEC	blood vessel
50	chr17:45765200-45770600	Weak transcription	Muscle Satellite Cultured Cells	--

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