Variant report

Variant	rs1962307
Chromosome Location	chr17:45707871-45707872
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	chr17:45707513..45710355-chr17:45712521..45715412,3	K562	blood:
2	chr17:45695070..45697639-chr17:45706118..45708659,3	K562	blood:

Variant related genes	Relation type
ENSG00000263766	Chromatin interaction
ENSG00000141279	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079783	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]
rs11079784	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs11656056	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11656856	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871606	0.81[TSI][hapmap]
rs12936468	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1912486	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs2013383	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs34200664	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3760370	0.81[TSI][hapmap]
rs3760371	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239162	0.81[TSI][hapmap]
rs4267364	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4289035	0.86[ASW][hapmap];0.93[LWK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes]
rs4497739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4793842	0.81[TSI][hapmap]
rs4793978	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	0.81[TSI][hapmap]
rs62074016	0.83[AMR][1000 genomes];0.83[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	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505049	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6505062	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213086	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7214799	0.85[ASW][hapmap];0.92[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7222225	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072644	0.81[TSI][hapmap]
rs8075411	0.81[TSI][hapmap]
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	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9905581	0.92[CEU][hapmap]
rs9912311	0.85[CEU][hapmap]
rs9913503	0.85[CEU][hapmap];0.80[TSI][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
rs1962307	KLHL11	cis	cerebellum	SCAN
rs1962307	TBKBP1	cis	lymphoblastoid	seeQTL
rs1962307	KRTAP9-3	cis	cerebellum	SCAN
rs1962307	MRPL45P2	cis	lymphoblastoid	seeQTL
rs1962307	LOC653479	cis	multi-tissue	Pritchard
rs1962307	TBKBP1	cis	Artery Tibial	GTEx
rs1962307	CDK5RAP3	cis	cerebellum	SCAN
rs1962307	VPS25	cis	cerebellum	SCAN
rs1962307	TBKBP1	cis	Artery Aorta	GTEx
rs1962307	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1962307	TBKBP1	cis	multi-tissue	Pritchard
rs1962307	C17orf57	cis	cerebellum	SCAN
rs1962307	TBKBP1	cis	lung	GTEx
rs1962307	TBKBP1	cis	Nerve Tibial	GTEx
rs1962307	HOXB6	cis	cerebellum	SCAN
rs1962307	TBKBP1	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:45691800-45716600	Weak transcription	Right Ventricle	heart
3	chr17:45692800-45714600	Weak transcription	Aorta	Aorta
4	chr17:45696600-45709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:45696600-45713600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:45696600-45726000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:45696800-45726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:45697000-45725800	Weak transcription	Brain Substantia Nigra	brain
9	chr17:45697200-45713400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:45697200-45713600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:45697200-45726000	Weak transcription	Brain Angular Gyrus	brain
12	chr17:45698000-45716000	Weak transcription	Psoas Muscle	Psoas
13	chr17:45698600-45714400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:45699400-45726000	Weak transcription	Brain Anterior Caudate	brain
15	chr17:45699400-45726200	Weak transcription	Fetal Kidney	kidney
16	chr17:45699600-45713800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:45699800-45712600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:45699800-45713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:45699800-45717600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:45700000-45710000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:45700000-45714000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:45700000-45725600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:45700000-45725800	Weak transcription	Spleen	Spleen
24	chr17:45700200-45708000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:45700200-45713000	Weak transcription	Brain Germinal Matrix	brain
26	chr17:45700400-45725800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:45700600-45725200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:45701200-45711600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr17:45701200-45713000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr17:45701400-45711000	Weak transcription	HMEC	breast
31	chr17:45701400-45711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:45701400-45711200	Weak transcription	Primary B cells from cord blood	blood
33	chr17:45701400-45711200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:45701400-45711200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:45701400-45713200	Weak transcription	HUVEC	blood vessel
36	chr17:45701400-45718800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:45701400-45724800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:45701400-45725600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:45701400-45725800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr17:45701400-45725800	Weak transcription	Left Ventricle	heart
41	chr17:45701400-45726000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:45701600-45711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:45701600-45713400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr17:45701600-45714400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:45701800-45723800	Weak transcription	Lung	lung
46	chr17:45701800-45725600	Weak transcription	Thymus	Thymus
47	chr17:45702000-45711400	Weak transcription	Fetal Intestine Large	intestine
48	chr17:45702000-45712800	Weak transcription	Fetal Intestine Small	intestine
49	chr17:45702000-45725800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:45702000-45726200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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