Variant report

Variant	rs11870935
Chromosome Location	chr17:45732605-45732606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45732422-45732786	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:45731881-45732818	U87	brain:	n/a	n/a
3	POLR2A	chr17:45732067-45732728	K562	blood:	n/a	n/a
4	POLR2A	chr17:45732382-45732762	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:45732351-45732660	MCF-7	breast:	n/a	n/a
6	POLR2A	chr17:45732001-45732747	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:45731960-45733448	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:45732054-45733391	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:45732346-45732683	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr17:45732027-45732716	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:45732267-45733389	PANC-1	pancreas:	n/a	n/a
12	MAFK	chr17:45732456-45732744	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:45731953-45732653	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr17:45732099-45733279	HepG2	liver:	n/a	n/a
15	POLR2A	chr17:45732002-45732881	GM12891	blood:	n/a	n/a
16	HEY1	chr17:45732071-45732630	K562	blood:	n/a	n/a
17	POLR2A	chr17:45731918-45733334	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:45732064-45732770	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr17:45729030-45736507	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr17:45732384-45732674	GM12891	blood:	n/a	n/a
21	POLR2A	chr17:45731983-45733362	GM12892	blood:	n/a	n/a
22	POLR2A	chr17:45731537-45734456	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr17:45732368-45732696	HCT-116	colon:	n/a	n/a
24	POLR2A	chr17:45731875-45733393	U87	brain:	n/a	n/a
25	POLR2A	chr17:45732173-45733382	HepG2	liver:	n/a	n/a
26	POLR2A	chr17:45732193-45733275	K562	blood:	n/a	n/a
27	POLR2A	chr17:45731645-45733127	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr17:45732139-45732622	K562	blood:	n/a	n/a
29	MAFK	chr17:45732421-45732655	HepG2	liver:	n/a	n/a
30	POLR2A	chr17:45732045-45734273	HepG2	liver:	n/a	n/a
31	POLR2A	chr17:45732344-45732645	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr17:45732108-45732643	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45726598..45732836-chr17:45743871..45749720,11	K562	blood:
2	chr17:45731399..45733307-chr17:45733395..45735702,2	MCF-7	breast:
3	chr17:45731312..45732928-chr17:45751109..45752660,2	K562	blood:

No data

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

Extended variants
information (count: 63 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10163469	0.86[EUR][1000 genomes]
rs10853090	0.95[EUR][1000 genomes]
rs11079784	0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11650372	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656855	0.95[EUR][1000 genomes]
rs11871606	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12150231	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603290	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12937560	0.82[EUR][1000 genomes]
rs12943464	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs16942199	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2317826	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760370	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs3809868	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4239162	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4239163	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs4264433	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4289035	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs4375701	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4399567	0.94[EUR][1000 genomes]
rs4439799	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs4580230	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793842	0.84[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4793908	0.89[EUR][1000 genomes]
rs4793913	0.88[EUR][1000 genomes]
rs4793978	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4794001	0.89[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4794016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794047	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs4794048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794058	0.89[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs55633793	0.91[EUR][1000 genomes]
rs56226803	0.96[EUR][1000 genomes]
rs62074014	0.82[ASN][1000 genomes]
rs62074015	0.80[EUR][1000 genomes]
rs6503796	0.83[TSI][hapmap]
rs7207542	0.88[EUR][1000 genomes]
rs7210738	1.00[ASW][hapmap];0.96[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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214799	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs7219303	0.96[EUR][1000 genomes]
rs7220935	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7223029	0.92[EUR][1000 genomes]
rs73315878	0.94[EUR][1000 genomes]
rs8065437	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065669	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]
rs8072100	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072644	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap]
rs8075411	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs8077106	0.80[EUR][1000 genomes]
rs8078686	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078880	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs8081717	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9635762	0.87[CEU][hapmap]
rs9905583	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905922	0.95[EUR][1000 genomes]
rs9912311	0.82[CEU][hapmap];0.84[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11870935	NPEPPS	cis	parietal	SCAN
rs11870935	TBKBP1	cis	Artery Tibial	GTEx
rs11870935	TBKBP1	cis	Nerve Tibial	GTEx
rs11870935	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs11870935	VPS25	cis	parietal	SCAN
rs11870935	C17orf57	cis	cerebellum	SCAN
rs11870935	RAB5C	cis	parietal	SCAN
rs11870935	SLC25A39	cis	parietal	SCAN
rs11870935	KLHL11	cis	cerebellum	SCAN
rs11870935	MRPL45P2	cis	lymphoblastoid	seeQTL
rs11870935	HEXIM2	cis	parietal	SCAN
rs11870935	CDK5RAP3	cis	cerebellum	SCAN
rs11870935	HOXB2	cis	cerebellum	SCAN
rs11870935	VPS25	cis	cerebellum	SCAN
rs11870935	DBF4B	cis	cerebellum	SCAN
rs11870935	C17orf57	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728600-45732800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:45728600-45734000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:45728600-45735200	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr17:45728800-45732800	Genic enhancers	Primary T cells from cord blood	blood
5	chr17:45728800-45732800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr17:45728800-45732800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr17:45728800-45733600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:45728800-45742400	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr17:45728800-45744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:45728800-45762800	Strong transcription	Fetal Stomach	stomach
11	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:45729000-45732800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
13	chr17:45729000-45733000	Genic enhancers	Osteobl	bone
14	chr17:45729000-45733200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr17:45729000-45743400	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr17:45729200-45733000	Genic enhancers	HepG2	liver
17	chr17:45729200-45733200	Genic enhancers	NHEK	skin
18	chr17:45729200-45734000	Genic enhancers	Liver	Liver
19	chr17:45729200-45736600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr17:45729200-45736800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr17:45729200-45760400	Strong transcription	Fetal Muscle Leg	muscle
22	chr17:45729200-45760600	Strong transcription	Fetal Brain Female	brain
23	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
24	chr17:45729400-45732800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:45729400-45733200	Genic enhancers	HMEC	breast
26	chr17:45729400-45736400	Strong transcription	Colonic Mucosa	Colon
27	chr17:45729400-45737400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr17:45729400-45741800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr17:45729600-45736600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:45729600-45737000	Strong transcription	Thymus	Thymus
31	chr17:45729600-45742200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:45729600-45762600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:45729800-45733000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:45729800-45733200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr17:45729800-45752000	Strong transcription	Left Ventricle	heart
36	chr17:45729800-45761600	Strong transcription	HSMM	muscle
37	chr17:45730000-45733200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr17:45730000-45733200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr17:45730000-45733800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr17:45730000-45736200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr17:45730000-45736600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr17:45730000-45739600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:45730000-45740000	Strong transcription	Aorta	Aorta
44	chr17:45730000-45741000	Strong transcription	HSMMtube	muscle
45	chr17:45730000-45741600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr17:45730200-45733200	Strong transcription	Fetal Brain Male	brain
47	chr17:45730200-45736200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr17:45730200-45736200	Strong transcription	Fetal Thymus	thymus
49	chr17:45730200-45741400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:45730400-45734000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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