Variant report

Variant	rs2317826
Chromosome Location	chr17:45730899-45730900
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	POLR2A	chr17:45730890-45731263	K562	blood:	n/a	n/a
2	POLR2A	chr17:45730841-45731330	GM12892	blood:	n/a	n/a
3	MAFK	chr17:45730850-45731152	HepG2	liver:	n/a	chr17:45730988-45731002 chr17:45730989-45731000 chr17:45730989-45731000
4	POLR2A	chr17:45730676-45731371	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr17:45730664-45731387	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:45729030-45736507	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr17:45730719-45731358	SK-N-MC	brain:	n/a	n/a
8	MAFF	chr17:45730882-45731157	HepG2	liver:	n/a	chr17:45730984-45731002
9	POLR2A	chr17:45730703-45731406	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr17:45730841-45731417	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:45730752-45731432	U87	brain:	n/a	n/a
12	POLR2A	chr17:45730708-45731353	HepG2	liver:	n/a	n/a
13	MAFK	chr17:45730828-45731159	HepG2	liver:	n/a	chr17:45730988-45731002 chr17:45730989-45731000 chr17:45730989-45731000

No.	Distal block	Cell Line	Cell type
1	chr17:45729511..45731867-chr17:45908734..45910627,2	MCF-7	breast:
2	chr17:45730053..45732033-chr17:45770907..45773039,2	K562	blood:
3	chr17:45726598..45732836-chr17:45743871..45749720,11	K562	blood:
4	chr17:45728622..45731157-chr17:45764804..45766776,2	MCF-7	breast:
5	chr17:45729521..45732354-chr17:45842842..45844447,2	MCF-7	breast:
6	chr17:45730303..45731847-chr17:45769244..45772062,2	K562	blood:

Variant related genes	Relation type
ENSG00000263766	TF binding region
KPNB1	TF binding region
ENSG00000141294	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000159111	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:58)

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	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656855	0.95[EUR][1000 genomes]
rs11870935	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]
rs11871606	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12150231	0.93[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	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs16942199	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs3760370	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs3809868	0.94[ASW][hapmap];1.00[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];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4239162	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4239163	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs4264433	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4289035	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs4375701	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4399567	0.94[EUR][1000 genomes]
rs4439799	0.85[CEU][hapmap]
rs4580230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793842	0.88[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4793908	0.89[EUR][1000 genomes]
rs4793913	0.88[EUR][1000 genomes]
rs4793978	0.89[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4794001	0.92[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4794016	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794047	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs4794048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794058	0.92[CEU][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	0.94[ASW][hapmap];1.00[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];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214799	0.83[TSI][hapmap]
rs7219303	0.96[EUR][1000 genomes]
rs7220935	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7223029	0.92[EUR][1000 genomes]
rs7223246	0.84[ASW][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs73315878	0.94[EUR][1000 genomes]
rs8065437	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065669	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]
rs8072100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072644	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs8075411	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs8077106	0.80[EUR][1000 genomes]
rs8078686	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078880	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs8081717	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9635762	0.91[CEU][hapmap]
rs9905581	0.82[CEU][hapmap]
rs9905583	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905922	0.95[EUR][1000 genomes]
rs9912311	0.85[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2317826	RAB5C	cis	parietal	SCAN
rs2317826	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs2317826	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs2317826	SLC25A39	cis	parietal	SCAN
rs2317826	DBF4B	cis	cerebellum	SCAN
rs2317826	NPEPPS	cis	parietal	SCAN
rs2317826	C17orf57	cis	parietal	SCAN
rs2317826	KLHL11	cis	cerebellum	SCAN
rs2317826	VPS25	cis	cerebellum	SCAN
rs2317826	TBKBP1	cis	lymphoblastoid	seeQTL
rs2317826	MRPL45P2	cis	lymphoblastoid	seeQTL
rs2317826	TBKBP1	cis	Nerve Tibial	GTEx
rs2317826	C17orf57	cis	cerebellum	SCAN
rs2317826	C17orf65	cis	cerebellum	SCAN
rs2317826	TBKBP1	cis	Artery Tibial	GTEx
rs2317826	VPS25	cis	parietal	SCAN
rs2317826	CDK5RAP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728200-45731400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr17:45728400-45731000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:45728400-45731400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
4	chr17:45728400-45732200	Weak transcription	Pancreas	Pancrea
5	chr17:45728600-45731200	Transcr. at gene 5' and 3'	Hela-S3	cervix
6	chr17:45728600-45731400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr17:45728600-45731400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
8	chr17:45728600-45732600	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr17:45728600-45732800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:45728600-45734000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:45728600-45735200	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr17:45728800-45731000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:45728800-45731000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:45728800-45731400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:45728800-45732000	Weak transcription	Right Atrium	heart
16	chr17:45728800-45732200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:45728800-45732200	Weak transcription	Gastric	stomach
18	chr17:45728800-45732600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr17:45728800-45732800	Genic enhancers	Primary T cells from cord blood	blood
20	chr17:45728800-45732800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr17:45728800-45732800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr17:45728800-45733600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:45728800-45742400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:45728800-45744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:45728800-45762800	Strong transcription	Fetal Stomach	stomach
26	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr17:45729000-45731000	Weak transcription	Brain Angular Gyrus	brain
28	chr17:45729000-45731200	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr17:45729000-45732800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr17:45729000-45733000	Genic enhancers	Osteobl	bone
31	chr17:45729000-45733200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:45729000-45743400	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr17:45729200-45731200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:45729200-45732200	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr17:45729200-45732200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr17:45729200-45733000	Genic enhancers	HepG2	liver
37	chr17:45729200-45733200	Genic enhancers	NHEK	skin
38	chr17:45729200-45734000	Genic enhancers	Liver	Liver
39	chr17:45729200-45736600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr17:45729200-45736800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr17:45729200-45760400	Strong transcription	Fetal Muscle Leg	muscle
42	chr17:45729200-45760600	Strong transcription	Fetal Brain Female	brain
43	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
44	chr17:45729400-45731000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:45729400-45731000	Weak transcription	Fetal Heart	heart
46	chr17:45729400-45731000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr17:45729400-45731000	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr17:45729400-45731200	Strong transcription	Brain Hippocampus Middle	brain
49	chr17:45729400-45731600	Strong transcription	Fetal Intestine Large	intestine
50	chr17:45729400-45732000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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