Variant report

Variant	rs6503796
Chromosome Location	chr17:45765249-45765250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 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	chr17:45758194..45759902-chr17:45762797..45765497,2	K562	blood:
4	chr17:45745574..45748775-chr17:45762933..45765883,3	K562	blood:
5	chr17:45756251..45758927-chr17:45764749..45766522,2	MCF-7	breast:
6	chr17:45752325..45755092-chr17:45763938..45765718,2	K562	blood:
7	chr17:45726655..45728758-chr17:45764709..45766556,3	K562	blood:
8	chr17:45765002..45766681-chr17:59500785..59503339,2	MCF-7	breast:
9	chr17:45728622..45731157-chr17:45764804..45766776,2	MCF-7	breast:
10	chr17:45759177..45766275-chr17:45767435..45773662,12	K562	blood:
11	chr17:45763121..45767993-chr17:48940261..48944774,6	MCF-7	breast:
12	chr17:45763614..45766168-chr17:49023284..49025624,2	MCF-7	breast:
13	chr17:45751990..45754304-chr17:45764467..45767340,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141232	Chromatin interaction
ENSG00000263766	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000108424	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10163469	0.85[ASN][1000 genomes]
rs10853090	0.86[ASN][1000 genomes]
rs11079783	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs11079784	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs11656855	0.86[ASN][1000 genomes]
rs11870935	0.83[TSI][hapmap]
rs11871606	0.93[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs12936468	0.84[ASN][1000 genomes]
rs12943464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1962307	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs2317826	0.83[TSI][hapmap]
rs3760370	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs3760371	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs3809868	0.83[TSI][hapmap]
rs4239162	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4239163	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4289035	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs4399567	0.90[ASN][1000 genomes]
rs4497739	0.84[CEU][hapmap]
rs4793842	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs4793908	0.84[ASN][1000 genomes]
rs4793913	0.84[ASN][1000 genomes]
rs4793978	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs4794001	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs4794047	0.84[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs4794048	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4794058	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs55633793	0.86[ASN][1000 genomes]
rs56226803	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62074015	0.81[ASN][1000 genomes]
rs6505049	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7207542	0.84[ASN][1000 genomes]
rs7210738	0.83[TSI][hapmap]
rs7213086	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7214799	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7219303	0.89[ASN][1000 genomes]
rs7222225	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs7223029	0.86[ASN][1000 genomes]
rs73315878	0.88[ASN][1000 genomes]
rs8065669	0.83[TSI][hapmap]
rs8070463	0.84[CHD][hapmap]
rs8072644	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs8075411	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs8078880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9635762	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9891111	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9905922	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6503796	TBKBP1	cis	Artery Aorta	GTEx
rs6503796	TBKBP1	cis	Artery Tibial	GTEx
rs6503796	C17orf57	cis	cerebellum	SCAN
rs6503796	TBKBP1	cis	lymphoblastoid	seeQTL
rs6503796	CDK5RAP3	cis	cerebellum	SCAN
rs6503796	HOXB6	cis	cerebellum	SCAN
rs6503796	KRTAP9-3	cis	cerebellum	SCAN
rs6503796	MRPL45P2	cis	Muscle Skeletal	GTEx
rs6503796	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs6503796	MRPL45P2	cis	lymphoblastoid	seeQTL
rs6503796	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6503796	TBKBP1	cis	lung	GTEx
rs6503796	KLHL11	cis	cerebellum	SCAN
rs6503796	TBKBP1	cis	Nerve Tibial	GTEx
rs6503796	C17orf57	cis	parietal	SCAN
rs6503796	TBKBP1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 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	chr17:45738400-45765600	Strong transcription	Primary T cells from cord blood	blood
3	chr17:45752600-45765400	Strong transcription	Fetal Thymus	thymus
4	chr17:45758200-45770200	Weak transcription	Fetal Heart	heart
5	chr17:45758200-45770600	Weak transcription	Fetal Brain Male	brain
6	chr17:45758400-45767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:45759800-45767400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr17:45760000-45769400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:45760200-45769600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr17:45760200-45769600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:45760200-45770000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:45760200-45770000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr17:45760200-45770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:45760400-45766800	Weak transcription	Fetal Intestine Small	intestine
15	chr17:45760400-45768800	Weak transcription	Fetal Kidney	kidney
16	chr17:45760400-45769800	Weak transcription	Right Ventricle	heart
17	chr17:45760400-45770000	Weak transcription	Colonic Mucosa	Colon
18	chr17:45760400-45770000	Weak transcription	Pancreas	Pancrea
19	chr17:45760400-45770200	Weak transcription	Colon Smooth Muscle	Colon
20	chr17:45760400-45770400	Weak transcription	Gastric	stomach
21	chr17:45760400-45770400	Weak transcription	Hela-S3	cervix
22	chr17:45761000-45765400	Strong transcription	Fetal Brain Female	brain
23	chr17:45761200-45770000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr17:45761600-45765600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr17:45761600-45765800	Strong transcription	Brain Germinal Matrix	brain
26	chr17:45761600-45769800	Weak transcription	Esophagus	oesophagus
27	chr17:45762000-45769400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr17:45762200-45765600	Enhancers	NHLF	lung
29	chr17:45762200-45770200	Weak transcription	Small Intestine	intestine
30	chr17:45762200-45770400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:45762400-45769600	Weak transcription	Lung	lung
32	chr17:45762400-45769800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:45762400-45770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr17:45762600-45769000	Weak transcription	Thymus	Thymus
35	chr17:45762600-45770000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr17:45762600-45770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr17:45762600-45770400	Weak transcription	Left Ventricle	heart
38	chr17:45762600-45770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr17:45762600-45770600	Weak transcription	Aorta	Aorta
40	chr17:45762800-45765400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr17:45762800-45765800	Genic enhancers	A549	lung
42	chr17:45762800-45766000	Enhancers	HepG2	liver
43	chr17:45762800-45769600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr17:45762800-45770000	Weak transcription	Fetal Stomach	stomach
45	chr17:45763200-45765600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr17:45763200-45765600	Enhancers	NHDF-Ad	bronchial
47	chr17:45763200-45770200	Weak transcription	Fetal Intestine Large	intestine
48	chr17:45763400-45768000	Weak transcription	NHEK	skin
49	chr17:45763400-45770000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:45763400-45770400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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