Variant report

Variant	rs9469566
Chromosome Location	chr6:33667605-33667606
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:33667560-33667710	HAc	cerebellar:	n/a	n/a
2	EBF1	chr6:33667602-33667997	GM12878	blood:	n/a	chr6:33667801-33667811 chr6:33667800-33667811 chr6:33667802-33667811 chr6:33667669-33667679
3	CTCF	chr6:33667480-33667630	HEEpiC	esophagus:	n/a	n/a
4	EBF1	chr6:33667603-33667882	GM12878	blood:	n/a	chr6:33667801-33667811 chr6:33667800-33667811 chr6:33667802-33667811 chr6:33667669-33667679
5	RUNX3	chr6:33667573-33667954	GM12878	blood:	n/a	chr6:33667787-33667802

No.	Distal block	Cell Line	Cell type
1	chr6:33243707..33246364-chr6:33666916..33668671,2	MCF-7	breast:
2	chr6:33557862..33560664-chr6:33667390..33670226,3	MCF-7	breast:
3	chr6:33557322..33558111-chr6:33667371..33668903,6	MCF-7	breast:
4	chr6:33667241..33669923-chr6:33710850..33712681,2	K562	blood:
5	chr6:33556676..33558804-chr6:33667221..33669587,2	K562	blood:
6	chr6:33667395..33669385-chr6:33670170..33673083,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269490	TF binding region
UQCC2	TF binding region
ENSG00000235863	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1014933	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947435	0.81[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[AMR][1000 genomes]
rs11759396	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1555965	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2147656	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2147657	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2229642	0.94[EUR][1000 genomes]
rs2274458	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281829	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296736	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296738	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2296739	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296741	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2296742	0.81[CHD][hapmap];0.94[EUR][1000 genomes]
rs28651968	0.83[AMR][1000 genomes]
rs2966	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3227	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818523	0.82[CEU][hapmap];0.95[EUR][1000 genomes]
rs3818524	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818525	0.94[EUR][1000 genomes]
rs3818527	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818529	0.94[EUR][1000 genomes]
rs3818530	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711336	0.80[ASW][hapmap];0.81[CEU][hapmap];0.81[CHD][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711337	0.93[EUR][1000 genomes]
rs4711338	0.81[CHD][hapmap];0.94[EUR][1000 genomes]
rs4711339	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711340	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711343	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713655	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713658	0.82[CEU][hapmap];0.81[CHD][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4713659	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713660	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713661	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713662	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713665	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713666	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4713667	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713669	0.88[EUR][1000 genomes]
rs4713670	0.81[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713671	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713672	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713674	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713675	1.00[CHB][hapmap]
rs509539	0.81[EUR][1000 genomes]
rs560111	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs60704560	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6457739	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916949	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6917140	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6928010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6938056	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs749338	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs749847	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs753890	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs754404	0.94[EUR][1000 genomes]
rs764752	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs764754	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7739505	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759668	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7770465	0.96[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs791902	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs791903	0.88[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs9348924	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9348925	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9366828	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368773	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368776	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9380375	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394162	0.81[EUR][1000 genomes]
rs9394163	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942640	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942641	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs942643	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9469566	ITPR3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:33660200-33667800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:33660200-33669400	Strong transcription	HepG2	liver
11	chr6:33661400-33669200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:33661600-33668600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:33661600-33668800	Genic enhancers	NHEK	skin
14	chr6:33661800-33675800	Weak transcription	Ovary	ovary
15	chr6:33662800-33669600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:33663000-33668000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:33663000-33669000	Strong transcription	K562	blood
18	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
19	chr6:33663200-33668200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:33663600-33668400	Strong transcription	Liver	Liver
21	chr6:33663600-33669600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:33663800-33668600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
24	chr6:33664200-33668000	Strong transcription	Fetal Intestine Small	intestine
25	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:33664800-33668400	Strong transcription	Fetal Intestine Large	intestine
27	chr6:33664800-33669400	Strong transcription	Placenta	Placenta
28	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:33665000-33668400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:33665000-33668600	Enhancers	Primary B cells from cord blood	blood
31	chr6:33665000-33668800	Genic enhancers	GM12878-XiMat	blood
32	chr6:33665200-33668800	Genic enhancers	Primary T cells from cord blood	blood
33	chr6:33665200-33668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:33665200-33669000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
37	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
38	chr6:33665400-33668000	Strong transcription	A549	lung
39	chr6:33665400-33668000	Strong transcription	NHDF-Ad	bronchial
40	chr6:33665400-33668200	Strong transcription	HSMM	muscle
41	chr6:33665400-33668400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:33665400-33669400	Strong transcription	Osteobl	bone
43	chr6:33665400-33669600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr6:33665400-33669800	Strong transcription	NHLF	lung
45	chr6:33665400-33670200	Weak transcription	Fetal Brain Male	brain
46	chr6:33665400-33672200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
48	chr6:33665600-33668000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:33665600-33669600	Strong transcription	Hela-S3	cervix
50	chr6:33665600-33678200	Weak transcription	NH-A	brain

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