Variant report

Variant	rs4713660
Chromosome Location	chr6:33670028-33670029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33669978-33671311	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr6:33669940-33670714	SK-N-SH	brain:	n/a	chr6:33670349-33670358
3	CTCF	chr6:33670009-33670674	A549	lung:	n/a	chr6:33670349-33670358
4	POLR2A	chr6:33669974-33670469	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr6:33669667-33670492	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33590320..33593181-chr6:33667665..33670096,2	MCF-7	breast:
2	chr6:33608220..33611008-chr6:33669548..33671759,2	K562	blood:
3	chr6:33606352..33608133-chr6:33668168..33670127,2	K562	blood:
4	chr6:33357291..33360249-chr6:33670006..33672826,2	MCF-7	breast:
5	chr6:33557862..33560664-chr6:33667390..33670226,3	MCF-7	breast:
6	chr6:33665979..33667590-chr6:33668878..33670883,2	K562	blood:
7	chr6:33664567..33666860-chr6:33668703..33672703,6	MCF-7	breast:
8	chr6:33553773..33556336-chr6:33668184..33671160,4	MCF-7	breast:
9	chr6:33420892..33423040-chr6:33668080..33670301,2	MCF-7	breast:

No data

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000266509	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000237649	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1014933	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947430	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10947434	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10947435	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11759396	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1555965	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2147656	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2147657	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2229642	0.88[EUR][1000 genomes]
rs2274458	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281829	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296736	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2296738	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2296739	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296741	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2296742	0.88[EUR][1000 genomes]
rs28651968	0.82[AMR][1000 genomes]
rs2966	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3227	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818521	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818523	0.89[EUR][1000 genomes]
rs3818524	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818525	0.90[EUR][1000 genomes]
rs3818527	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818529	0.90[EUR][1000 genomes]
rs3818530	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711336	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4711337	0.89[EUR][1000 genomes]
rs4711338	0.88[EUR][1000 genomes]
rs4711339	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711340	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711343	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4713655	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713658	0.89[EUR][1000 genomes]
rs4713659	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713661	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713662	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713663	0.84[AFR][1000 genomes]
rs4713665	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713666	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713667	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713669	0.83[EUR][1000 genomes]
rs4713670	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4713671	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4713672	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4713674	0.83[AMR][1000 genomes]
rs60704560	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6457739	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6904816	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6916949	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6917140	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6928010	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938056	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs749338	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs749847	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs753890	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs754404	0.90[EUR][1000 genomes]
rs764752	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs764754	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7739505	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759668	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7770465	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs791903	0.85[EUR][1000 genomes]
rs9348924	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9348925	0.81[AMR][1000 genomes]
rs9366828	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9368773	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368776	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9380375	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394162	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9394163	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942640	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs942641	0.82[EUR][1000 genomes]
rs942643	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469566	0.88[AMR][1000 genomes];0.93[EUR][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
rs4713660	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33661800-33675800	Weak transcription	Ovary	ovary
3	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
4	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
5	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
10	chr6:33665400-33670200	Weak transcription	Fetal Brain Male	brain
11	chr6:33665400-33672200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
13	chr6:33665600-33678200	Weak transcription	NH-A	brain
14	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:33665800-33676600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:33666000-33676200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:33666000-33676600	Weak transcription	Brain Angular Gyrus	brain
18	chr6:33666000-33677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:33666000-33678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:33666200-33677600	Weak transcription	Psoas Muscle	Psoas
21	chr6:33666400-33677800	Weak transcription	Brain Anterior Caudate	brain
22	chr6:33666600-33675800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:33666600-33677800	Weak transcription	Right Atrium	heart
24	chr6:33666600-33678200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:33666600-33678400	Weak transcription	Colonic Mucosa	Colon
26	chr6:33666600-33678400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:33667000-33672000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:33667000-33678400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:33667200-33672000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:33667200-33672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:33667200-33672000	Weak transcription	Gastric	stomach
32	chr6:33667200-33672600	Weak transcription	Lung	lung
33	chr6:33667200-33675200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:33667200-33675400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:33667200-33675800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:33667200-33675800	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:33667200-33676000	Weak transcription	Brain Germinal Matrix	brain
38	chr6:33667200-33676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:33667600-33671000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:33667800-33672000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:33667800-33672400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:33668200-33674800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:33668400-33670400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:33668400-33672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:33668400-33672200	Weak transcription	Thymus	Thymus
46	chr6:33668400-33675000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:33668400-33675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:33668400-33675000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:33668400-33675200	Weak transcription	Liver	Liver
50	chr6:33668400-33677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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