Variant report

Variant	rs4713667
Chromosome Location	chr6:33680016-33680017
allele	C/G
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	REST	chr6:33678408-33680143	H1-neurons	neurons:	n/a	n/a
2	NRF1	chr6:33678907-33680092	SK-N-SH	brain:	n/a	chr6:33679231-33679240 chr6:33679517-33679526 chr6:33679515-33679529 chr6:33679231-33679245 chr6:33679571-33679582 chr6:33679515-33679526 chr6:33679233-33679242 chr6:33679231-33679242 chr6:33679228-33679242 chr6:33679568-33679582 chr6:33679231-33679242
3	CTCF	chr6:33678674-33680111	SK-N-SH	brain:	n/a	n/a
4	EP300	chr6:33679626-33680058	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:33678969-33680057	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:33678274-33680020	Raji	blood:	n/a	n/a
7	CTCF	chr6:33679314-33680092	A549	lung:	n/a	n/a
8	MTA3	chr6:33678510-33680065	GM12878	blood:	n/a	n/a
9	MXI1	chr6:33678199-33680106	IMR90	lung:	n/a	n/a
10	POU2F2	chr6:33679004-33680088	GM12878	blood:	n/a	chr6:33679806-33679816 chr6:33679789-33679797 chr6:33679806-33679815 chr6:33679800-33679822 chr6:33679788-33679797 chr6:33679268-33679280 chr6:33679807-33679814 chr6:33679803-33679818 chr6:33679787-33679797 chr6:33679787-33679797
11	HCFC1	chr6:33678638-33680112	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr6:33678257-33680089	SK-N-SH	brain:	n/a	n/a
13	RUNX3	chr6:33679272-33680031	GM12878	blood:	n/a	n/a
14	RAD21	chr6:33678850-33680096	HCT-116	colon:	n/a	n/a
15	RAD21	chr6:33678850-33680052	HCT-116	colon:	n/a	n/a
16	POLR2A	chr6:33678439-33680025	HUVEC	blood vessel:	n/a	n/a
17	POU2F2	chr6:33679263-33680030	GM12878	blood:	n/a	chr6:33679806-33679816 chr6:33679789-33679797 chr6:33679806-33679815 chr6:33679800-33679822 chr6:33679788-33679797 chr6:33679268-33679280 chr6:33679807-33679814 chr6:33679803-33679818 chr6:33679787-33679797 chr6:33679787-33679797
18	RAD21	chr6:33678795-33680113	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr6:33677310-33680040	SK-N-MC	brain:	n/a	n/a
20	NFIC	chr6:33678894-33680048	GM12878	blood:	n/a	n/a
21	RAD21	chr6:33679293-33680057	MCF-7	breast:	n/a	n/a
22	POU2F2	chr6:33679189-33680053	GM12891	blood:	n/a	chr6:33679806-33679816 chr6:33679789-33679797 chr6:33679806-33679815 chr6:33679800-33679822 chr6:33679788-33679797 chr6:33679268-33679280 chr6:33679807-33679814 chr6:33679803-33679818 chr6:33679787-33679797 chr6:33679787-33679797
23	SMC3	chr6:33678069-33680180	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33679645..33680333-chr6:34022737..34023251,2	K562	blood:
2	chr6:33264498..33266775-chr6:33678035..33680124,2	MCF-7	breast:
3	chr6:33588748..33590902-chr6:33677628..33680104,3	K562	blood:
4	chr6:33588748..33590595-chr6:33677611..33680104,2	K562	blood:
5	chr6:33679525..33680115-chr6:34122329..34123229,3	MCF-7	breast:
6	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
7	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
8	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
9	chr6:33678014..33680671-chr6:33755515..33757218,2	K562	blood:

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000237441	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000161904	Chromatin interaction
ENSG00000266509	Chromatin interaction
ENSG00000197251	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1014933	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947430	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947434	0.96[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947435	0.90[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11759396	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1555965	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147656	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2229642	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274458	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281829	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296736	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296738	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296739	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296741	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296742	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28651968	0.83[AMR][1000 genomes]
rs2966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818521	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818523	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818524	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818525	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818529	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818530	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711336	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711337	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711338	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711340	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711343	0.90[CHB][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713655	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713658	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713659	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713660	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713663	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4713665	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713666	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713669	0.89[EUR][1000 genomes]
rs4713670	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713671	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713672	0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713674	0.80[CHB][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713675	0.90[CHB][hapmap]
rs509539	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs560111	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60704560	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6457739	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904816	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6916949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928010	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6938056	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749338	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs749847	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753890	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754404	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs764752	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs764754	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7739505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770465	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791902	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs791903	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9348924	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9348925	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9366828	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368773	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368776	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9380375	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394162	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9394163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942640	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469566	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]

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
rs4713667	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33678600-33680200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr6:33679000-33680200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:33679200-33680200	Enhancers	Fetal Heart	heart
4	chr6:33679800-33680200	Enhancers	Primary T cells from cord blood	blood
5	chr6:33679800-33680200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:33679800-33680200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:33679800-33680200	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:33679800-33681800	Weak transcription	Pancreas	Pancrea
9	chr6:33679800-33685000	Weak transcription	Lung	lung
10	chr6:33679800-33685600	Weak transcription	Placenta	Placenta
11	chr6:33680000-33680200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:33680000-33680200	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:33680000-33680200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:33680000-33680200	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:33680000-33680200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:33680000-33680200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:33680000-33680200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr6:33680000-33680200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:33680000-33680200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:33680000-33680200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:33680000-33680200	Enhancers	Liver	Liver
22	chr6:33680000-33680200	Enhancers	Fetal Brain Female	brain
23	chr6:33680000-33680200	Enhancers	Fetal Thymus	thymus
24	chr6:33680000-33680200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:33680000-33680400	Enhancers	Dnd41	blood
26	chr6:33680000-33681200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:33680000-33681600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:33680000-33681600	Weak transcription	HepG2	liver
29	chr6:33680000-33682000	Weak transcription	Fetal Intestine Large	intestine
30	chr6:33680000-33682200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:33680000-33682200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:33680000-33683000	Weak transcription	Stomach Mucosa	stomach
33	chr6:33680000-33683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:33680000-33683800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:33680000-33684000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:33680000-33684000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:33680000-33684000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:33680000-33684000	Weak transcription	Esophagus	oesophagus
39	chr6:33680000-33684000	Weak transcription	Gastric	stomach
40	chr6:33680000-33684000	Weak transcription	Left Ventricle	heart
41	chr6:33680000-33684000	Weak transcription	HMEC	breast
42	chr6:33680000-33684000	Weak transcription	NHEK	skin
43	chr6:33680000-33684200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:33680000-33684200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:33680000-33684200	Weak transcription	Fetal Lung	lung
46	chr6:33680000-33684200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:33680000-33684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:33680000-33684400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:33680000-33684600	Weak transcription	Fetal Brain Male	brain
50	chr6:33680000-33684600	Weak transcription	Fetal Kidney	kidney

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