Variant report

Variant	rs4713670
Chromosome Location	chr6:33699882-33699883
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:33697484..33700204-chr6:33739217..33741356,2	MCF-7	breast:
2	chr6:33699067..33701380-chr6:33760767..33763233,2	MCF-7	breast:
3	chr12:115690369..115693198-chr6:33698849..33701409,2	MCF-7	breast:
4	chr6:33698259..33701003-chr6:33736395..33738930,2	K562	blood:
5	chr6:33697890..33700582-chr6:35133101..35134719,2	MCF-7	breast:
6	chr6:33694998..33697623-chr6:33697893..33701266,3	K562	blood:
7	chr6:33673158..33676456-chr6:33698317..33701048,3	MCF-7	breast:
8	chr6:33697291..33699933-chr6:33725185..33727883,2	MCF-7	breast:
9	chr6:33699163..33701430-chr6:33753710..33757640,3	MCF-7	breast:
10	chr6:33684880..33685463-chr6:33699620..33700206,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1014933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10947430	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10947434	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10947435	1.00[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759396	0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1555965	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2147656	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2147657	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2229642	0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2274458	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2281829	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296736	0.84[EUR][1000 genomes]
rs2296738	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296739	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296741	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296742	0.81[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs28651968	0.87[AMR][1000 genomes]
rs2966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3227	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3818521	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3818523	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs3818524	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3818525	0.86[EUR][1000 genomes]
rs3818527	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3818529	0.86[EUR][1000 genomes]
rs3818530	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711336	1.00[ASW][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4711337	0.85[EUR][1000 genomes]
rs4711338	0.81[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4711339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711340	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711343	0.90[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713655	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4713658	0.81[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4713659	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713660	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4713661	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713662	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713665	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713666	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713667	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713669	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713674	0.90[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713675	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs509539	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs542441	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs560111	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60704560	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs622917	0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs626156	0.81[JPT][hapmap]
rs6457739	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6904816	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6916949	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6917140	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6919321	1.00[JPT][hapmap]
rs6928010	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6938056	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs749338	0.88[ASW][hapmap];0.84[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs749847	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs753890	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs754404	0.86[EUR][1000 genomes]
rs764752	0.85[EUR][1000 genomes]
rs764754	0.85[EUR][1000 genomes]
rs7739505	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7759668	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7770465	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs791902	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs791903	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348924	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348925	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366828	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368773	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368776	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380375	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9394163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs942640	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs942641	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs942643	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9469566	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]
rs9469583	0.90[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4713670	ITPR3	cis	multi-tissue	Pritchard
rs4713670	ITPR3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:33686200-33700200	Weak transcription	Liver	Liver
3	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:33688800-33700000	Strong transcription	HSMM	muscle
5	chr6:33690800-33708200	Weak transcription	Gastric	stomach
6	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
8	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:33692800-33701000	Weak transcription	Fetal Brain Female	brain
10	chr6:33693200-33700800	Strong transcription	Fetal Muscle Leg	muscle
11	chr6:33693400-33701200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:33695000-33702400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:33695200-33700000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33696600-33700400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:33697200-33700400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:33697800-33700000	Enhancers	Placenta	Placenta
20	chr6:33697800-33701000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:33698000-33700000	Enhancers	Pancreas	Pancrea
22	chr6:33698200-33700000	Strong transcription	HSMMtube	muscle
23	chr6:33698200-33700400	Enhancers	Lung	lung
24	chr6:33698200-33700600	Enhancers	Right Atrium	heart
25	chr6:33698200-33700800	Genic enhancers	Brain Substantia Nigra	brain
26	chr6:33698200-33700800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr6:33698200-33701600	Genic enhancers	Left Ventricle	heart
28	chr6:33698200-33702400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:33698400-33703000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:33698400-33703400	Strong transcription	Spleen	Spleen
31	chr6:33698600-33700400	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr6:33698600-33700800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:33698600-33701200	Genic enhancers	Brain Hippocampus Middle	brain
34	chr6:33698800-33700200	Weak transcription	K562	blood
35	chr6:33699200-33700200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:33699400-33700200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr6:33699400-33700400	Enhancers	Esophagus	oesophagus
39	chr6:33699400-33700600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:33699400-33701200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:33699400-33703600	Genic enhancers	Right Ventricle	heart
42	chr6:33699600-33700000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:33699600-33700000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:33699600-33700200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:33699600-33700600	Genic enhancers	Brain Cingulate Gyrus	brain
46	chr6:33699600-33701000	Weak transcription	Psoas Muscle	Psoas
47	chr6:33699600-33701200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:33699800-33700800	Enhancers	HMEC	breast
49	chr6:33699800-33701000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:33699800-33708000	Weak transcription	Fetal Lung	lung

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