Variant report

Variant	rs6938056
Chromosome Location	chr6:33669577-33669578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:33669500-33669650	HPF	lung:	n/a	n/a
2	POLR2A	chr6:33669576-33669589	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:33669540-33669690	HEK293	kidney:	n/a	n/a
4	POLR2A	chr6:33669429-33669611	K562	blood:	n/a	n/a
5	POLR2A	chr6:33669374-33669808	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:33669246-33669735	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:33669074-33669812	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:33669245-33669764	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr6:33669558-33669655	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:33669332-33669928	SK-N-MC	brain:	n/a	n/a

No data

(count:11 , 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	chr6:33661102..33664232-chr6:33667999..33669816,4	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	chr6:33667241..33669923-chr6:33710850..33712681,2	K562	blood:
9	chr6:33556676..33558804-chr6:33667221..33669587,2	K562	blood:
10	chr6:33553773..33556336-chr6:33668184..33671160,4	MCF-7	breast:
11	chr6:33420892..33423040-chr6:33668080..33670301,2	MCF-7	breast:

No data

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000266509	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	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947430	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10947434	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947435	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11759396	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1555965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2147656	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2147657	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229642	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2274458	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281829	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296736	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296738	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296739	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296741	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296742	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28651968	0.82[AMR][1000 genomes]
rs2966	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3818523	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818524	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818525	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818529	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818530	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711336	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711337	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711338	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711340	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711343	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713655	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4713658	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713659	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713660	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713661	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713662	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713663	0.90[AFR][1000 genomes]
rs4713665	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713666	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713667	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713669	0.88[EUR][1000 genomes]
rs4713670	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713671	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713672	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713674	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs509539	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs560111	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60704560	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6457739	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6904816	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6916949	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928010	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs749338	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs749847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753890	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs754404	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs764752	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs764754	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7739505	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770465	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs791902	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs791903	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9348924	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9348925	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9366828	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368773	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368776	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9380375	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394162	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9394163	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942640	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942641	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs942643	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469566	0.94[AMR][1000 genomes];0.98[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
rs6938056	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	chr6:33662800-33669600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
5	chr6:33663600-33669600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
7	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
12	chr6:33665400-33669600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr6:33665400-33669800	Strong transcription	NHLF	lung
14	chr6:33665400-33670200	Weak transcription	Fetal Brain Male	brain
15	chr6:33665400-33672200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
17	chr6:33665600-33669600	Strong transcription	Hela-S3	cervix
18	chr6:33665600-33678200	Weak transcription	NH-A	brain
19	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:33665800-33676600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:33666000-33669600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr6:33666000-33676200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:33666000-33676600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:33666000-33677800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:33666000-33678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:33666200-33677600	Weak transcription	Psoas Muscle	Psoas
27	chr6:33666400-33677800	Weak transcription	Brain Anterior Caudate	brain
28	chr6:33666600-33669800	Strong transcription	Fetal Stomach	stomach
29	chr6:33666600-33675800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:33666600-33677800	Weak transcription	Right Atrium	heart
31	chr6:33666600-33678200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:33666600-33678400	Weak transcription	Colonic Mucosa	Colon
33	chr6:33666600-33678400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:33667000-33672000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:33667000-33678400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:33667200-33669600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:33667200-33672000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:33667200-33672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:33667200-33672000	Weak transcription	Gastric	stomach
40	chr6:33667200-33672600	Weak transcription	Lung	lung
41	chr6:33667200-33675200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:33667200-33675400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:33667200-33675800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:33667200-33675800	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:33667200-33676000	Weak transcription	Brain Germinal Matrix	brain
46	chr6:33667200-33676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:33667400-33669600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:33667600-33671000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:33667800-33670000	Weak transcription	HSMMtube	muscle
50	chr6:33667800-33672000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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