Variant report

Variant	rs4713674
Chromosome Location	chr6:33708169-33708170
allele	A/G
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:33706317..33709748-chr6:33710509..33712632,5	MCF-7	breast:
2	chr6:33677945..33680861-chr6:33707372..33709046,3	K562	blood:
3	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:
4	chr6:33706772..33708979-chr6:33732721..33735158,2	K562	blood:
5	chr6:33701443..33703598-chr6:33706736..33709323,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf125-2	chr6:33707072-33708768	ucscGeneNc_uc010jvd_1

No data

Variant related genes	Relation type
ENSG00000137288	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	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10947430	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10947434	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10947435	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11759396	0.81[JPT][hapmap]
rs1555965	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2147656	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2147657	0.90[AMR][1000 genomes]
rs2229642	0.81[JPT][hapmap]
rs2274458	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2281829	0.90[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296738	0.83[AMR][1000 genomes]
rs2296739	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2296741	0.82[AMR][1000 genomes]
rs2296742	0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs28651968	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2966	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3227	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3818521	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3818523	0.81[JPT][hapmap]
rs3818524	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3818527	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3818530	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711336	0.89[ASW][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs4711338	0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs4711339	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4711340	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4711343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713655	0.87[AMR][1000 genomes]
rs4713658	0.81[JPT][hapmap];0.86[TSI][hapmap]
rs4713659	0.90[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713660	0.83[AMR][1000 genomes]
rs4713661	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713662	0.80[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713665	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713666	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713667	0.80[CHB][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713669	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713670	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]
rs4713671	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[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]
rs4713672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713675	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs509539	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs542441	0.81[JPT][hapmap]
rs560111	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60704560	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs622917	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs626156	0.81[JPT][hapmap]
rs6457739	0.90[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6904816	0.80[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6916949	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6917140	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6919321	1.00[JPT][hapmap]
rs6928010	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6938056	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs749338	0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs749847	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs753890	0.84[AMR][1000 genomes]
rs7739505	0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7759668	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7770465	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs791902	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs791903	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9348924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348925	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366828	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9368773	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9368776	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380375	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9394163	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs942640	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs942641	0.90[JPT][hapmap]
rs942643	0.81[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9469566	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.86[AMR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4713674	ITPR3	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:33690800-33708200	Weak transcription	Gastric	stomach
3	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:33702000-33710000	Genic enhancers	HSMM	muscle
10	chr6:33705200-33709800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:33705400-33709000	Enhancers	Liver	Liver
12	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:33705600-33709200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
14	chr6:33705800-33711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:33706600-33709000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:33706600-33715800	Enhancers	Fetal Intestine Large	intestine
17	chr6:33706800-33709000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:33706800-33709000	Enhancers	Fetal Intestine Small	intestine
19	chr6:33706800-33709200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:33706800-33709200	Enhancers	Pancreas	Pancrea
21	chr6:33706800-33709200	Enhancers	Right Atrium	heart
22	chr6:33706800-33711400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:33707000-33708200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:33707000-33708600	Enhancers	Left Ventricle	heart
25	chr6:33707000-33710200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:33707200-33709800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:33707200-33710000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:33707200-33711400	Enhancers	Fetal Brain Male	brain
29	chr6:33707400-33708400	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr6:33707400-33708400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr6:33707400-33708600	Enhancers	Lung	lung
32	chr6:33707400-33709200	Genic enhancers	Fetal Muscle Leg	muscle
33	chr6:33707400-33714000	Weak transcription	Spleen	Spleen
34	chr6:33707600-33708600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:33707600-33708600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:33707600-33708600	Enhancers	Placenta	Placenta
37	chr6:33707600-33708800	Enhancers	K562	blood
38	chr6:33707600-33709000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr6:33707600-33711000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:33707800-33708200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr6:33707800-33708400	Enhancers	Primary B cells from cord blood	blood
42	chr6:33707800-33708400	Transcr. at gene 5' and 3'	Right Ventricle	heart
43	chr6:33707800-33708600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:33707800-33708600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:33707800-33708600	Enhancers	Brain Cingulate Gyrus	brain
46	chr6:33707800-33709000	Enhancers	Brain Hippocampus Middle	brain
47	chr6:33707800-33709200	Enhancers	Fetal Brain Female	brain
48	chr6:33707800-33710200	Enhancers	Brain Substantia Nigra	brain
49	chr6:33707800-33710600	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr6:33708000-33708200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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