Variant report

Variant	rs4794048
Chromosome Location	chr17:45763073-45763074
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr17:45761066-45765975	A549	lung:	n/a	chr17:45762320-45762329 chr17:45761498-45761507
2	POLR2A	chr17:45762847-45763347	GM12878	blood:	n/a	n/a
3	CTCF	chr17:45763020-45763170	BE2_C	brain:	n/a	n/a
4	POLR2A	chr17:45762826-45763140	K562	blood:	n/a	n/a
5	POLR2A	chr17:45762628-45763266	U87	brain:	n/a	n/a
6	STAT5A	chr17:45762833-45763273	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:45761123-45765686	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:45762941-45763478	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr17:45761016-45766013	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:45762822-45763217	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr17:45760728-45765897	A549	lung:	n/a	n/a
12	POLR2A	chr17:45760907-45765868	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr17:45760984-45765876	U87	brain:	n/a	n/a
14	POLR2A	chr17:45762768-45763716	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:45760971-45763196	HepG2	liver:	n/a	n/a
16	POLR2A	chr17:45760984-45765870	U87	brain:	n/a	n/a
17	POLR2A	chr17:45758952-45766470	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr17:45762873-45763389	GM12891	blood:	n/a	n/a
19	POLR2A	chr17:45762837-45763292	K562	blood:	n/a	n/a
20	PML	chr17:45761117-45763912	GM12878	blood:	n/a	n/a
21	POLR2A	chr17:45762885-45763478	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr17:45761050-45765590	HepG2	liver:	n/a	n/a
23	POLR2A	chr17:45762900-45763131	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr17:45761491-45763433	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr17:45762985-45763336	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr17:45760706-45763765	GM12891	blood:	n/a	n/a
27	POLR2A	chr17:45762828-45763122	HepG2	liver:	n/a	n/a
28	POLR2A	chr17:45762680-45764943	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr17:45761025-45765803	GM12891	blood:	n/a	n/a
30	POLR2A	chr17:45762857-45763174	HCT-116	colon:	n/a	n/a
31	POLR2A	chr17:45760968-45763549	GM12892	blood:	n/a	n/a
32	POLR2A	chr17:45761148-45763557	K562	blood:	n/a	n/a
33	POLR2A	chr17:45760999-45763167	K562	blood:	n/a	n/a
34	POLR2A	chr17:45762532-45763216	HCT-116	colon:	n/a	n/a
35	POLR2A	chr17:45761288-45763317	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:45762748-45763463	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr17:45760244-45765917	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr17:45763006-45763399	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:45760700-45764174	GM12891	blood:	n/a	n/a
40	POLR2A	chr17:45760907-45765675	GM12892	blood:	n/a	n/a
41	POLR2A	chr17:45762821-45763399	MCF-7	breast:	n/a	n/a
42	POLR2A	chr17:45762647-45763478	U87	brain:	n/a	n/a
43	STAT3	chr17:45762960-45763180	MCF10A-Er-Src	breast:	n/a	n/a
44	NFATC1	chr17:45761304-45763295	GM12878	blood:	n/a	n/a
45	POLR2A	chr17:45761166-45766789	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr17:45759834-45765686	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr17:45761164-45763778	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr17:45763048-45763349	K562	blood:	n/a	n/a
49	MTA3	chr17:45761054-45763668	GM12878	blood:	n/a	n/a
50	POLR2A	chr17:45760954-45763530	GM12891	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45761397..45766819-chr17:45768713..45773362,9	K562	blood:
2	chr17:45751990..45755538-chr17:45760652..45765275,4	MCF-7	breast:
3	chr17:45761486..45763110-chr17:45770464..45772427,2	MCF-7	breast:
4	chr17:45758194..45759902-chr17:45762797..45765497,2	K562	blood:
5	chr17:45745574..45748775-chr17:45762933..45765883,3	K562	blood:
6	chr17:45761680..45764235-chr17:45810358..45812226,2	MCF-7	breast:
7	chr17:45762090..45764390-chr17:45820597..45823079,2	K562	blood:
8	chr17:45749021..45751778-chr17:45762179..45764324,3	K562	blood:
9	chr17:45760258..45764544-chr17:45769222..45773538,5	MCF-7	breast:
10	chr17:45759177..45766275-chr17:45767435..45773662,12	K562	blood:
11	chr17:45725427..45729938-chr17:45759883..45763405,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264558	TF binding region
ENSG00000108424	Chromatin interaction
ENSG00000073861	Chromatin interaction
ENSG00000263766	Chromatin interaction
ENSG00000198933	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10853090	0.82[EUR][1000 genomes]
rs11079784	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs11650372	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11656855	0.82[EUR][1000 genomes]
rs11870935	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]
rs11871606	0.92[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs12150231	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12943464	0.96[CEU][hapmap]
rs16942199	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2317826	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]
rs3760370	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs3809868	1.00[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];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4239162	0.92[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4239163	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4264433	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4289035	0.92[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4375701	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4399567	0.87[EUR][1000 genomes]
rs4439799	0.85[CEU][hapmap];0.81[CHD][hapmap]
rs4580230	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793842	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs4793978	0.89[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4794001	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4794016	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794047	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794058	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs56226803	0.85[EUR][1000 genomes]
rs62074055	0.82[ASN][1000 genomes]
rs6503796	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs7210738	1.00[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];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7214799	0.83[TSI][hapmap]
rs7219303	0.85[EUR][1000 genomes]
rs7220935	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73315878	0.86[EUR][1000 genomes]
rs8065437	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8065669	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]
rs8072100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8072644	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs8075411	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs8078686	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8078880	0.92[CEU][hapmap]
rs9635762	0.91[CEU][hapmap]
rs9905583	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9905922	0.84[EUR][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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4794048	CDK5RAP3	cis	cerebellum	SCAN
rs4794048	HOXB2	cis	cerebellum	SCAN
rs4794048	NPEPPS	cis	parietal	SCAN
rs4794048	RAB5C	cis	parietal	SCAN
rs4794048	TBKBP1	cis	Nerve Tibial	GTEx
rs4794048	TBKBP1	cis	multi-tissue	Pritchard
rs4794048	TBKBP1	cis	Artery Tibial	GTEx
rs4794048	TBKBP1	cis	lymphoblastoid	seeQTL
rs4794048	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs4794048	C17orf57	cis	parietal	SCAN
rs4794048	SLC25A39	cis	parietal	SCAN
rs4794048	MRPL45P2	cis	lymphoblastoid	seeQTL
rs4794048	DBF4B	cis	cerebellum	SCAN
rs4794048	C17orf57	cis	cerebellum	SCAN
rs4794048	LOC653479	cis	multi-tissue	Pritchard
rs4794048	KLHL11	cis	cerebellum	SCAN
rs4794048	C17orf65	cis	cerebellum	SCAN
rs4794048	VPS25	cis	parietal	SCAN
rs4794048	VPS25	cis	cerebellum	SCAN
rs4794048	TBKBP1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
3	chr17:45730400-45764800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:45730400-45765000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:45731200-45763800	Strong transcription	K562	blood
6	chr17:45733000-45763600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:45733200-45763400	Strong transcription	NHEK	skin
8	chr17:45733200-45765000	Strong transcription	HMEC	breast
9	chr17:45736200-45763600	Strong transcription	Dnd41	blood
10	chr17:45737800-45764200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr17:45738000-45763800	Strong transcription	Liver	Liver
12	chr17:45738400-45763600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr17:45738400-45765600	Strong transcription	Primary T cells from cord blood	blood
14	chr17:45740000-45763400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:45741600-45763600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:45741800-45763400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:45742000-45764800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:45742400-45763800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:45743000-45763200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr17:45743000-45763600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:45743000-45763600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:45743000-45763800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:45743000-45764600	Strong transcription	GM12878-XiMat	blood
24	chr17:45747800-45763800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:45747800-45764400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:45748200-45764400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:45748200-45764400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:45749600-45763200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr17:45751400-45763600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr17:45752600-45765400	Strong transcription	Fetal Thymus	thymus
31	chr17:45753400-45765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:45758200-45770200	Weak transcription	Fetal Heart	heart
33	chr17:45758200-45770600	Weak transcription	Fetal Brain Male	brain
34	chr17:45758400-45763800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:45758400-45767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:45758600-45764200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr17:45759800-45767400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr17:45760000-45764400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:45760000-45765200	Weak transcription	Stomach Mucosa	stomach
40	chr17:45760000-45769400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr17:45760200-45764400	Weak transcription	Brain Angular Gyrus	brain
42	chr17:45760200-45764600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:45760200-45764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:45760200-45769600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:45760200-45769600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:45760200-45770000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr17:45760200-45770000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr17:45760200-45770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr17:45760400-45764600	Weak transcription	Brain Hippocampus Middle	brain
50	chr17:45760400-45765000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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