Variant report

Variant	rs2013383
Chromosome Location	chr17:45791123-45791124
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45773167..45774951-chr17:45788821..45791623,2	K562	blood:
2	chr17:45784401..45787875-chr17:45788488..45791249,4	MCF-7	breast:
3	chr17:45790758..45793292-chr17:45796969..45798828,2	K562	blood:
4	chr17:45790485..45792888-chr17:48942013..48944583,2	MCF-7	breast:
5	chr17:45790830..45793042-chr17:45810606..45812831,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141232	Chromatin interaction
ENSG00000073861	Chromatin interaction
ENSG00000229980	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11079783	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs11868838	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1808192	0.90[GIH][hapmap];0.81[AMR][1000 genomes]
rs1962307	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs3760371	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4267364	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4497739	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs4794052	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794053	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62074054	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503804	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6503807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7214799	0.81[CEU][hapmap]
rs7222225	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs8070463	0.80[GIH][hapmap]
rs8075566	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9913503	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908571	chr17:45765249-45821510	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2013383	C17orf57	cis	cerebellum	SCAN
rs2013383	CDK5RAP3	cis	cerebellum	SCAN
rs2013383	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2013383	TBKBP1	cis	Artery Aorta	GTEx
rs2013383	KRT17	cis	cerebellum	SCAN
rs2013383	TBKBP1	cis	Thyroid	GTEx
rs2013383	TBKBP1	cis	multi-tissue	Pritchard
rs2013383	TBKBP1	cis	Nerve Tibial	GTEx
rs2013383	TBKBP1	cis	Whole Blood	GTEx
rs2013383	TBKBP1	cis	Esophagus Mucosa	GTEx
rs2013383	TBKBP1	cis	lung	GTEx
rs2013383	HOXB6	cis	cerebellum	SCAN
rs2013383	MRPL45P2	cis	lymphoblastoid	seeQTL
rs2013383	RAB5C	cis	parietal	SCAN
rs2013383	TBKBP1	cis	lymphoblastoid	seeQTL
rs2013383	KRTAP9-3	cis	cerebellum	SCAN
rs2013383	TBKBP1	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45785000-45791600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:45785400-45791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:45785400-45791200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:45785800-45792000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:45786400-45791800	Weak transcription	Esophagus	oesophagus
6	chr17:45787000-45791200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:45787200-45792000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:45787400-45792000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:45788200-45795200	Weak transcription	Pancreas	Pancrea
10	chr17:45788200-45799800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr17:45788400-45798000	Enhancers	Primary B cells from peripheral blood	blood
12	chr17:45788600-45792800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr17:45788600-45793800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr17:45788800-45791600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:45788800-45795800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:45789200-45791600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:45789200-45791600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:45789200-45793600	Enhancers	Primary B cells from cord blood	blood
19	chr17:45789200-45794800	Weak transcription	Thymus	Thymus
20	chr17:45789200-45795000	Weak transcription	Brain Angular Gyrus	brain
21	chr17:45789400-45791200	Weak transcription	Fetal Brain Female	brain
22	chr17:45789400-45791800	Weak transcription	Right Ventricle	heart
23	chr17:45789400-45795800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr17:45789400-45798400	Weak transcription	Gastric	stomach
25	chr17:45789600-45791800	Enhancers	GM12878-XiMat	blood
26	chr17:45789800-45795600	Weak transcription	Primary T cells from cord blood	blood
27	chr17:45790000-45791200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:45790000-45791600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:45790000-45793400	Weak transcription	Fetal Thymus	thymus
30	chr17:45790000-45799800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr17:45790000-45810400	Weak transcription	Right Atrium	heart
32	chr17:45790200-45792400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr17:45790600-45791200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:45790600-45795000	Enhancers	Spleen	Spleen
35	chr17:45790800-45791400	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr17:45790800-45793400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr17:45791000-45791600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:45791000-45792000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:45791000-45792400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:45791000-45793400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:45791000-45795400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links