Variant report

Variant	rs8065669
Chromosome Location	chr17:45724996-45724997
allele	A/G
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	SPI1	chr17:45724859-45725385	HL-60	blood:	n/a	chr17:45725110-45725123 chr17:45725112-45725119
2	POLR2A	chr17:45724906-45725490	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:45724243-45725117	HepG2	liver:	n/a	n/a
4	MYC	chr17:45724982-45725410	NB4	blood:	n/a	n/a
5	SPI1	chr17:45724950-45725359	HL-60	blood:	n/a	chr17:45725110-45725123 chr17:45725112-45725119
6	POLR2A	chr17:45724874-45724997	K562	blood:	n/a	n/a
7	POLR2A	chr17:45724864-45725391	HL-60	blood:	n/a	n/a
8	POLR2A	chr17:45724524-45725160	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45724693..45730044-chr17:45766323..45778247,15	K562	blood:

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

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

Extended variants
information (count: 66 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10163469	0.87[EUR][1000 genomes]
rs10853090	0.96[EUR][1000 genomes]
rs11079784	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs11650372	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656855	0.96[EUR][1000 genomes]
rs11870935	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11871606	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs12150231	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12603290	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937560	0.82[EUR][1000 genomes]
rs12943464	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs16942199	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs2317826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760370	0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs3809868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4092460	0.80[EUR][1000 genomes]
rs4239162	0.92[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4239163	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4264433	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4289035	0.92[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4375701	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4399567	0.93[EUR][1000 genomes]
rs4439799	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs4580230	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793842	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4793908	0.90[EUR][1000 genomes]
rs4793913	0.89[EUR][1000 genomes]
rs4793978	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs4794001	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4794016	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794047	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs4794048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794058	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs55633793	0.92[EUR][1000 genomes]
rs56226803	0.95[EUR][1000 genomes]
rs62074014	0.83[ASN][1000 genomes]
rs62074015	0.81[EUR][1000 genomes]
rs6503796	0.83[TSI][hapmap]
rs7207542	0.89[EUR][1000 genomes]
rs7210738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214799	0.83[TSI][hapmap]
rs7219303	0.95[EUR][1000 genomes]
rs7220935	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7223029	0.93[EUR][1000 genomes]
rs73315878	0.93[EUR][1000 genomes]
rs8065437	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8072644	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs8075411	0.92[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs8077106	0.81[EUR][1000 genomes]
rs8078686	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8078880	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8081717	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9635762	0.91[CEU][hapmap]
rs9891111	0.80[EUR][1000 genomes]
rs9905581	0.82[CEU][hapmap]
rs9905583	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9905922	0.94[EUR][1000 genomes]
rs9912311	0.85[CEU][hapmap];0.85[JPT][hapmap]

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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs8065669	VPS25	cis	parietal	SCAN
rs8065669	TBKBP1	cis	Whole Blood	GTEx
rs8065669	SLC25A39	cis	parietal	SCAN
rs8065669	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs8065669	NPEPPS	cis	parietal	SCAN
rs8065669	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs8065669	CDK5RAP3	cis	cerebellum	SCAN
rs8065669	TBKBP1	cis	lymphoblastoid	seeQTL
rs8065669	C17orf65	cis	cerebellum	SCAN
rs8065669	VPS25	cis	cerebellum	SCAN
rs8065669	C17orf57	cis	cerebellum	SCAN
rs8065669	KLHL11	cis	cerebellum	SCAN
rs8065669	TBKBP1	cis	Nerve Tibial	GTEx
rs8065669	MRPL45P2	cis	lymphoblastoid	seeQTL
rs8065669	RAB5C	cis	parietal	SCAN
rs8065669	C17orf57	cis	parietal	SCAN
rs8065669	TBKBP1	cis	Artery Tibial	GTEx
rs8065669	DBF4B	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

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	chr17:45697000-45725800	Weak transcription	Brain Substantia Nigra	brain
4	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
5	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
6	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
7	chr17:45700000-45725600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:45700000-45725800	Weak transcription	Spleen	Spleen
9	chr17:45700400-45725800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:45700600-45725200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr17:45701400-45725600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:45701400-45725800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr17:45701400-45725800	Weak transcription	Left Ventricle	heart
14	chr17:45701400-45726000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:45701800-45725600	Weak transcription	Thymus	Thymus
16	chr17:45702000-45725800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:45702000-45726200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:45702200-45725800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:45702400-45725800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:45702600-45725800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:45702600-45725800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:45702600-45726000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:45702800-45725800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:45702800-45725800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:45702800-45725800	Weak transcription	NHDF-Ad	bronchial
26	chr17:45702800-45726000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:45702800-45726000	Weak transcription	A549	lung
28	chr17:45702800-45726000	Weak transcription	HSMMtube	muscle
29	chr17:45703000-45725600	Weak transcription	Placenta	Placenta
30	chr17:45703600-45725800	Weak transcription	Brain Hippocampus Middle	brain
31	chr17:45704000-45726000	Weak transcription	Osteobl	bone
32	chr17:45704400-45725800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr17:45704600-45726000	Weak transcription	Colon Smooth Muscle	Colon
34	chr17:45705200-45726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:45708000-45725800	Weak transcription	Pancreas	Pancrea
36	chr17:45712000-45726000	Weak transcription	NHEK	skin
37	chr17:45712200-45725800	Weak transcription	HMEC	breast
38	chr17:45712400-45725800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:45712600-45725600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:45714000-45725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr17:45714000-45725200	Weak transcription	Liver	Liver
42	chr17:45714000-45725800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr17:45714000-45725800	Weak transcription	Fetal Intestine Large	intestine
44	chr17:45714400-45725000	Weak transcription	Adipose Nuclei	Adipose
45	chr17:45714400-45725800	Weak transcription	Primary T cells from cord blood	blood
46	chr17:45714800-45726000	Weak transcription	Fetal Intestine Small	intestine
47	chr17:45715400-45725600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:45715400-45725800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:45715400-45725800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:45715600-45725200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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