Variant report

Variant	rs56226803
Chromosome Location	chr17:45742233-45742234
allele	A/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	POLR2A	chr17:45742197-45742641	K562	blood:	n/a	n/a
2	POLR2A	chr17:45741828-45742805	HepG2	liver:	n/a	n/a
3	BCL3	chr17:45741340-45742522	A549	lung:	n/a	n/a
4	CTCF	chr17:45741054-45742623	SK-N-SH	brain:	n/a	chr17:45741874-45741890 chr17:45741875-45741896 chr17:45741873-45741891
5	POLR2A	chr17:45741266-45742246	HL-60	blood:	n/a	n/a
6	POLR2A	chr17:45742179-45743272	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:45742156-45743260	GM12878	blood:	n/a	n/a
8	CTCF	chr17:45741164-45743551	A549	lung:	n/a	chr17:45741874-45741890 chr17:45741875-45741896 chr17:45741873-45741891
9	POLR2A	chr17:45741530-45742864	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr17:45741170-45742308	SK-N-SH	brain:	n/a	chr17:45741877-45741890 chr17:45741874-45741893
11	POLR2A	chr17:45741175-45743629	A549	lung:	n/a	n/a
12	POLR2A	chr17:45742156-45743626	PFSK-1	brain:	n/a	n/a
13	CTCF	chr17:45741550-45742251	HCT-116	colon:	n/a	chr17:45741874-45741890 chr17:45741875-45741896 chr17:45741873-45741891
14	POLR2A	chr17:45740451-45743175	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr17:45741171-45743478	K562	blood:	n/a	n/a
16	SMC3	chr17:45741368-45742578	SK-N-SH	brain:	n/a	chr17:45741875-45741889
17	CTCF	chr17:45741638-45742239	HCT-116	colon:	n/a	chr17:45741874-45741890 chr17:45741875-45741896 chr17:45741873-45741891
18	POLR2A	chr17:45741429-45742365	HepG2	liver:	n/a	n/a
19	RAD21	chr17:45741531-45742338	HCT-116	colon:	n/a	chr17:45741877-45741890 chr17:45741874-45741893
20	POLR2A	chr17:45741092-45742435	GM12892	blood:	n/a	n/a
21	POLR2A	chr17:45741434-45742337	HepG2	liver:	n/a	n/a
22	POLR2A	chr17:45741158-45742514	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45739359..45743830-chr17:45751715..45754078,4	K562	blood:
2	chr17:45725155..45731513-chr17:45739091..45743405,6	MCF-7	breast:
3	chr17:45740425..45743047-chr17:45769342..45771775,2	K562	blood:
4	chr17:45738206..45745873-chr17:45748268..45754078,8	K562	blood:
5	chr17:45741427..45742405-chr17:45867146..45867910,3	MCF-7	breast:
6	chr17:45741724..45742280-chr17:45819394..45820344,2	K562	blood:
7	chr17:45741494..45743868-chr17:45744087..45748162,5	K562	blood:

Variant related genes	Relation type
KPNB1	TF binding region
ENSG00000263766	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000108424	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10163469	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853090	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11079782	0.88[ASN][1000 genomes]
rs11079784	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1138193	0.88[ASN][1000 genomes]
rs11650372	0.94[EUR][1000 genomes]
rs11656855	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870935	0.96[EUR][1000 genomes]
rs11871606	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150231	0.94[EUR][1000 genomes]
rs12936468	0.95[ASN][1000 genomes]
rs12937560	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12943464	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317826	0.96[EUR][1000 genomes]
rs35919601	0.87[ASN][1000 genomes]
rs3760370	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809868	0.95[EUR][1000 genomes]
rs3865314	0.88[ASN][1000 genomes]
rs4092460	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4239162	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4239163	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4264433	0.90[EUR][1000 genomes]
rs4289035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375701	0.92[EUR][1000 genomes]
rs4399567	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4580230	0.96[EUR][1000 genomes]
rs4793836	0.90[ASN][1000 genomes]
rs4793842	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4793908	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793913	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793978	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794001	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794016	0.95[EUR][1000 genomes]
rs4794048	0.85[EUR][1000 genomes]
rs55633793	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62074015	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6503796	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6505049	0.94[ASN][1000 genomes]
rs7207542	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7210738	0.94[EUR][1000 genomes]
rs7213086	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214799	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7219303	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220935	0.92[EUR][1000 genomes]
rs7223029	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73315878	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065437	0.94[EUR][1000 genomes]
rs8065669	0.95[EUR][1000 genomes]
rs8072100	0.87[EUR][1000 genomes]
rs8072644	0.87[ASN][1000 genomes]
rs8075411	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8078686	0.87[EUR][1000 genomes]
rs8078880	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8082284	0.83[ASN][1000 genomes]
rs9635762	0.82[ASN][1000 genomes]
rs9635763	0.85[ASN][1000 genomes]
rs9891111	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9905583	0.97[EUR][1000 genomes]
rs9905922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

SNP	Gene	Cis/trans	Tissue	Source
rs56226803	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs56226803	TBKBP1	cis	Whole Blood	GTEx
rs56226803	TBKBP1	cis	Nerve Tibial	GTEx
rs56226803	TBKBP1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728800-45742400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr17:45728800-45744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:45728800-45762800	Strong transcription	Fetal Stomach	stomach
4	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr17:45729000-45743400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr17:45729200-45760400	Strong transcription	Fetal Muscle Leg	muscle
7	chr17:45729200-45760600	Strong transcription	Fetal Brain Female	brain
8	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
9	chr17:45729600-45762600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:45729800-45752000	Strong transcription	Left Ventricle	heart
11	chr17:45729800-45761600	Strong transcription	HSMM	muscle
12	chr17:45730400-45764800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:45730400-45765000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:45730800-45760600	Strong transcription	Lung	lung
15	chr17:45731000-45757600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:45731200-45762200	Strong transcription	Fetal Lung	lung
17	chr17:45731200-45763800	Strong transcription	K562	blood
18	chr17:45731400-45744600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:45731400-45762000	Strong transcription	NH-A	brain
20	chr17:45732400-45743600	Strong transcription	NHDF-Ad	bronchial
21	chr17:45732400-45753400	Weak transcription	Right Atrium	heart
22	chr17:45732400-45762600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:45732600-45743400	Strong transcription	NHLF	lung
24	chr17:45732600-45748400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr17:45732600-45760200	Strong transcription	Brain Germinal Matrix	brain
26	chr17:45732600-45760400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:45732600-45762000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:45732600-45762200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:45732800-45742600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:45732800-45750600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:45732800-45753200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:45732800-45760200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:45732800-45760600	Strong transcription	Fetal Intestine Large	intestine
34	chr17:45732800-45762200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:45732800-45762200	Strong transcription	Adipose Nuclei	Adipose
36	chr17:45732800-45762600	Strong transcription	Brain Anterior Caudate	brain
37	chr17:45733000-45742800	Strong transcription	A549	lung
38	chr17:45733000-45745600	Strong transcription	Osteobl	bone
39	chr17:45733000-45759200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:45733000-45759400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr17:45733000-45761600	Strong transcription	HepG2	liver
42	chr17:45733000-45763600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:45733200-45742600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:45733200-45743000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:45733200-45743600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:45733200-45760200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr17:45733200-45760400	Strong transcription	Hela-S3	cervix
48	chr17:45733200-45762400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:45733200-45763400	Strong transcription	NHEK	skin
50	chr17:45733200-45765000	Strong transcription	HMEC	breast

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