Variant report

Variant	rs4794016
Chromosome Location	chr17:45725931-45725932
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45725674-45729177	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:45725668-45726124	K562	blood:	n/a	n/a
3	NR2F2	chr17:45725696-45727482	K562	blood:	n/a	n/a
4	POLR2A	chr17:45725576-45728880	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:45725691-45728518	GM12892	blood:	n/a	n/a
6	MXI1	chr17:45725841-45730440	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr17:45725421-45728496	HepG2	liver:	n/a	n/a
8	POLR2A	chr17:45725931-45728581	GM12892	blood:	n/a	n/a
9	RUNX3	chr17:45725901-45727477	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:45725638-45728972	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr17:45725719-45725948	K562	blood:	n/a	n/a
12	MTA3	chr17:45725853-45726894	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:45725691-45730436	PFSK-1	brain:	n/a	n/a
14	FOXM1	chr17:45725870-45727492	GM12878	blood:	n/a	n/a
15	PML	chr17:45725757-45728556	GM12878	blood:	n/a	n/a
16	ELF1	chr17:45725806-45727464	GM12878	blood:	n/a	chr17:45727229-45727238
17	POLR2A	chr17:45725705-45728918	SK-N-MC	brain:	n/a	n/a
18	POU2F2	chr17:45725917-45727513	GM12878	blood:	n/a	chr17:45727384-45727396 chr17:45727387-45727399 chr17:45726697-45726709
19	POLR2A	chr17:45725834-45726033	HUVEC	blood vessel:	n/a	n/a
20	MTA3	chr17:45725581-45728872	GM12878	blood:	n/a	n/a
21	POLR2A	chr17:45725692-45729440	GM12892	blood:	n/a	n/a
22	POLR2A	chr17:45725588-45728999	PANC-1	pancreas:	n/a	n/a
23	NFIC	chr17:45725902-45727472	GM12878	blood:	n/a	chr17:45726658-45726686

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45725427..45729938-chr17:45759883..45763405,4	K562	blood:
2	chr17:45725747..45727611-chr17:45884252..45887189,2	MCF-7	breast:
3	chr17:45725675..45729413-chr17:45768882..45774493,5	K562	blood:
4	chr17:45568465..45570063-chr17:45725230..45727294,2	K562	blood:
5	chr17:45725833..45728916-chr17:45770004..45772680,3	MCF-7	breast:
6	chr17:45724693..45730044-chr17:45766323..45778247,15	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC040934.1-3	chr17:45724887-45727274	NONHSAT054322

No data

Variant related genes	Relation type
KPNB1	TF binding region
ENSG00000264558	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000228782	Chromatin interaction
ENSG00000006025	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10163469	0.87[EUR][1000 genomes]
rs10853090	0.96[EUR][1000 genomes]
rs11079784	0.94[EUR][1000 genomes]
rs11650372	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11656855	0.96[EUR][1000 genomes]
rs11870935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871606	0.96[EUR][1000 genomes]
rs12150231	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603290	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12937560	0.82[EUR][1000 genomes]
rs12943464	0.92[EUR][1000 genomes]
rs2317826	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3760370	0.93[EUR][1000 genomes]
rs3809868	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4092460	0.80[EUR][1000 genomes]
rs4239162	0.92[EUR][1000 genomes]
rs4239163	0.92[EUR][1000 genomes]
rs4264433	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4289035	0.95[EUR][1000 genomes]
rs4375701	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4399567	0.93[EUR][1000 genomes]
rs4580230	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4793842	0.88[EUR][1000 genomes]
rs4793908	0.90[EUR][1000 genomes]
rs4793913	0.89[EUR][1000 genomes]
rs4793978	0.94[EUR][1000 genomes]
rs4794001	0.96[EUR][1000 genomes]
rs4794047	0.87[ASN][1000 genomes]
rs4794048	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55633793	0.92[EUR][1000 genomes]
rs56226803	0.95[EUR][1000 genomes]
rs62074014	0.82[ASN][1000 genomes]
rs62074015	0.81[EUR][1000 genomes]
rs7207542	0.89[EUR][1000 genomes]
rs7210738	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7219303	0.95[EUR][1000 genomes]
rs7220935	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7223029	0.93[EUR][1000 genomes]
rs73315878	0.93[EUR][1000 genomes]
rs8065437	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8065669	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8072100	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8075411	0.91[EUR][1000 genomes]
rs8077106	0.81[EUR][1000 genomes]
rs8078686	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078880	0.91[EUR][1000 genomes]
rs8081717	0.81[EUR][1000 genomes]
rs9891111	0.80[EUR][1000 genomes]
rs9905583	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9905922	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4794016	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4794016	TBKBP1	cis	Nerve Tibial	GTEx
rs4794016	TBKBP1	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45696600-45726000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr17:45696800-45726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
4	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
5	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
6	chr17:45701400-45726000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:45702000-45726200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:45702600-45726000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:45702800-45726000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:45702800-45726000	Weak transcription	A549	lung
11	chr17:45702800-45726000	Weak transcription	HSMMtube	muscle
12	chr17:45704000-45726000	Weak transcription	Osteobl	bone
13	chr17:45704600-45726000	Weak transcription	Colon Smooth Muscle	Colon
14	chr17:45705200-45726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:45712000-45726000	Weak transcription	NHEK	skin
16	chr17:45714800-45726000	Weak transcription	Fetal Intestine Small	intestine
17	chr17:45715800-45726000	Weak transcription	Fetal Stomach	stomach
18	chr17:45717400-45726000	Weak transcription	Psoas Muscle	Psoas
19	chr17:45718800-45726000	Weak transcription	NHLF	lung
20	chr17:45719000-45726000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:45719600-45726000	Weak transcription	Fetal Brain Male	brain
22	chr17:45720600-45726000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:45724000-45726200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:45724200-45726800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr17:45724400-45726800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr17:45724600-45726000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr17:45724600-45726200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:45724800-45726000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr17:45724800-45726000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:45724800-45726000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr17:45724800-45726000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr17:45724800-45726000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr17:45724800-45726000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:45724800-45726000	Enhancers	Fetal Muscle Trunk	muscle
35	chr17:45724800-45726200	Enhancers	Primary hematopoietic stem cells	blood
36	chr17:45724800-45726200	Enhancers	Fetal Thymus	thymus
37	chr17:45725000-45726200	Enhancers	Adipose Nuclei	Adipose
38	chr17:45725200-45726000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:45725200-45726000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr17:45725200-45726000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr17:45725200-45726200	Enhancers	Liver	Liver
42	chr17:45725200-45726600	Flanking Active TSS	GM12878-XiMat	blood
43	chr17:45725400-45726000	Enhancers	Primary B cells from cord blood	blood
44	chr17:45725400-45726000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:45725600-45726000	Enhancers	Fetal Muscle Leg	muscle
46	chr17:45725600-45726000	Enhancers	Thymus	Thymus
47	chr17:45725600-45726200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr17:45725600-45726200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:45725600-45726200	Enhancers	Placenta	Placenta
50	chr17:45725600-45726200	Enhancers	Skeletal Muscle Female	skeletal muscle

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