Variant report

Variant	rs11079783
Chromosome Location	chr17:45686016-45686017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45679584..45682875-chr17:45684553..45688203,6	K562	blood:
2	chr17:45681295..45682836-chr17:45684602..45686967,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141279	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10163469	0.92[AFR][1000 genomes]
rs11079784	0.81[CEU][hapmap];0.88[LWK][hapmap];0.81[TSI][hapmap]
rs11656056	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11656855	0.87[AFR][1000 genomes]
rs11656856	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871606	0.80[LWK][hapmap];0.81[TSI][hapmap]
rs12936468	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1912486	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs1912487	0.85[CEU][hapmap]
rs1962307	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013383	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs34200664	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736438	0.89[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap]
rs3760370	0.86[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];0.88[AFR][1000 genomes]
rs3760371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826536	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs4239162	0.81[TSI][hapmap]
rs4267364	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4289035	0.80[ASW][hapmap];0.81[TSI][hapmap]
rs4497739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4793836	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4793842	0.86[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap]
rs4793908	0.88[AFR][1000 genomes]
rs4793913	0.84[AFR][1000 genomes]
rs4793978	0.86[LWK][hapmap];0.81[TSI][hapmap]
rs4794001	0.81[TSI][hapmap]
rs4794047	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs4794052	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4794053	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4794058	0.86[ASW][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap]
rs62074016	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6503796	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs6503804	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6503807	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6505048	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505049	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6505062	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7207542	0.89[AFR][1000 genomes]
rs7213086	0.83[EUR][1000 genomes]
rs7214799	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7222225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072644	0.86[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap]
rs8075411	0.86[ASW][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes]
rs8075566	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs8078309	0.89[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs9891111	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9893901	0.85[TSI][hapmap]
rs9905581	0.92[CEU][hapmap]
rs9912311	0.85[CEU][hapmap]
rs9913503	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs9915919	0.85[CEU][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	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
4	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	nsv471403	chr17:45608444-45700642	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv482203	chr17:45608444-45700642	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11079783	HOXB6	cis	cerebellum	SCAN
rs11079783	TBKBP1	cis	Whole Blood	GTEx
rs11079783	VPS25	cis	cerebellum	SCAN
rs11079783	TBKBP1	cis	Nerve Tibial	GTEx
rs11079783	LOC653479	cis	multi-tissue	Pritchard
rs11079783	KRTAP9-3	cis	cerebellum	SCAN
rs11079783	KLHL11	cis	cerebellum	SCAN
rs11079783	TBKBP1	cis	lymphoblastoid	seeQTL
rs11079783	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11079783	MRPL45P2	cis	lymphoblastoid	seeQTL
rs11079783	TBKBP1	cis	Artery Aorta	GTEx
rs11079783	C17orf57	cis	cerebellum	SCAN
rs11079783	TBKBP1	cis	Artery Tibial	GTEx
rs11079783	TBKBP1	cis	multi-tissue	Pritchard
rs11079783	CDK5RAP3	cis	cerebellum	SCAN
rs11079783	TBKBP1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45657200-45688200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:45659200-45698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:45662600-45689800	Weak transcription	Psoas Muscle	Psoas
4	chr17:45663800-45702800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:45664800-45695000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:45665600-45686200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:45665600-45698200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:45666000-45694200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:45666200-45688200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:45666800-45687200	Strong transcription	Placenta	Placenta
11	chr17:45666800-45693600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:45667200-45687400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:45667200-45698600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:45667400-45687400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr17:45667400-45687800	Strong transcription	Liver	Liver
16	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr17:45668200-45688400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:45668200-45699000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:45669200-45687000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:45669200-45687200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:45670000-45703000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:45670200-45689000	Weak transcription	Stomach Mucosa	stomach
23	chr17:45670200-45698600	Weak transcription	Fetal Heart	heart
24	chr17:45670400-45686600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:45670400-45698200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:45670600-45687200	Strong transcription	Fetal Intestine Large	intestine
27	chr17:45672400-45688000	Strong transcription	Dnd41	blood
28	chr17:45672400-45704200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr17:45672600-45687600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr17:45672600-45688400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:45672600-45691000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:45672600-45703000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:45672800-45687800	Strong transcription	Fetal Thymus	thymus
34	chr17:45673000-45687200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr17:45673200-45687200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:45673400-45687400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr17:45673400-45687800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:45679000-45696000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:45679200-45695800	Weak transcription	Small Intestine	intestine
40	chr17:45679600-45691800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:45679600-45695600	Weak transcription	Fetal Brain Male	brain
42	chr17:45679800-45695800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr17:45681600-45689000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:45682000-45687400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:45682200-45699000	Strong transcription	Fetal Muscle Leg	muscle
46	chr17:45682200-45699200	Weak transcription	Right Atrium	heart
47	chr17:45682400-45686200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr17:45682400-45687000	Strong transcription	NHLF	lung
49	chr17:45682600-45687000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:45682600-45689200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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