Variant report

Variant	rs3818524
Chromosome Location	chr6:33660695-33660696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33587314..33592159-chr6:33656861..33661736,6	K562	blood:
2	chr6:33659672..33661992-chr6:33673865..33675730,2	MCF-7	breast:
3	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1014933	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10947430	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947434	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947435	0.83[AMR][1000 genomes]
rs11759396	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1555965	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2147656	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2147657	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2229642	0.91[EUR][1000 genomes]
rs2274458	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2281829	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296736	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296738	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296739	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2296741	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296742	0.91[EUR][1000 genomes]
rs2966	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3227	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3818521	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818523	0.92[EUR][1000 genomes]
rs3818525	0.91[EUR][1000 genomes]
rs3818527	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3818529	0.91[EUR][1000 genomes]
rs3818530	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711336	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4711337	0.90[EUR][1000 genomes]
rs4711338	0.91[EUR][1000 genomes]
rs4711339	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4711340	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711343	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4713655	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713658	0.92[EUR][1000 genomes]
rs4713659	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713660	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713661	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713662	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713663	0.85[AFR][1000 genomes]
rs4713665	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713666	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713667	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713669	0.86[EUR][1000 genomes]
rs4713670	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713671	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713672	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4713674	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60704560	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6457739	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6904816	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916949	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6917140	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6928010	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938056	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs749338	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs749847	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs753890	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs754404	0.91[EUR][1000 genomes]
rs764752	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs764754	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7739505	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7759668	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7770465	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs791903	0.85[EUR][1000 genomes]
rs9348924	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9348925	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9366828	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368773	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368776	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9380375	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9394163	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942640	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942641	0.82[EUR][1000 genomes]
rs942643	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9469566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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
rs3818524	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
2	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:33621400-33672600	Strong transcription	Dnd41	blood
5	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:33630400-33660800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr6:33631800-33661200	Weak transcription	Liver	Liver
10	chr6:33636800-33661400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:33637400-33661600	Strong transcription	Esophagus	oesophagus
12	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:33641200-33661600	Strong transcription	NHEK	skin
15	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:33641800-33661800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:33644000-33662000	Weak transcription	Fetal Kidney	kidney
18	chr6:33649800-33661400	Strong transcription	Pancreas	Pancrea
19	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:33652000-33661800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:33653600-33661800	Strong transcription	Hela-S3	cervix
24	chr6:33654000-33660800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:33654600-33661600	Weak transcription	Fetal Brain Female	brain
26	chr6:33654800-33661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:33654800-33662600	Weak transcription	Small Intestine	intestine
28	chr6:33655000-33663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
30	chr6:33656400-33661600	Strong transcription	A549	lung
31	chr6:33656400-33662600	Weak transcription	Brain Substantia Nigra	brain
32	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
33	chr6:33657000-33660800	Weak transcription	Fetal Brain Male	brain
34	chr6:33657000-33661400	Weak transcription	Ovary	ovary
35	chr6:33658000-33663400	Genic enhancers	Right Ventricle	heart
36	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr6:33658200-33660800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
39	chr6:33658400-33661000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:33658400-33661800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr6:33658600-33663400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:33658800-33662600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:33659000-33660800	Genic enhancers	HSMM	muscle
45	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr6:33659200-33661400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:33659200-33661800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr6:33659200-33665200	Genic enhancers	HMEC	breast
49	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
50	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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