Variant report

Variant	rs6807632
Chromosome Location	chr3:111395568-111395569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111394548..111396118-chr3:111400082..111401919,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBED2-1	chr3:111394790-111395985	NONHSAT091148
2	lnc-ZBED2-1	chr3:111394790-111395982	NONHSAT091149

Extended variants
information (count: 19 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1355768	1.00[EUR][1000 genomes]
rs1513330	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17202775	0.85[CEU][hapmap]
rs17202782	0.85[CEU][hapmap]
rs1996107	0.98[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2895386	0.87[AMR][1000 genomes]
rs3817260	0.85[CEU][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap]
rs4428148	0.91[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682289	1.00[CEU][hapmap]
rs56172864	0.87[AMR][1000 genomes]
rs56306480	0.87[AMR][1000 genomes]
rs6768092	0.87[AMR][1000 genomes]
rs73852849	0.87[AMR][1000 genomes]
rs7612391	0.85[CEU][hapmap]
rs7637536	0.88[AMR][1000 genomes]
rs7639907	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836430	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6807632	MAGIX	trans	brain	seeQTL
rs6807632	DUSP2	trans	brain	seeQTL
rs6807632	NINL	trans	brain	seeQTL
rs6807632	PENK	trans	brain	seeQTL
rs6807632	SYTL1	trans	brain	seeQTL
rs6807632	EPS8L2	trans	brain	seeQTL
rs6807632	TMEM52	trans	brain	seeQTL
rs6807632	ARC	trans	brain	seeQTL
rs6807632	MC1R	trans	brain	seeQTL
rs6807632	GRM4	trans	brain	seeQTL
rs6807632	COMP	trans	brain	seeQTL
rs6807632	GALNT13	trans	brain	seeQTL
rs6807632	TIMP4	trans	brain	seeQTL
rs6807632	NPAS4	trans	brain	seeQTL
rs6807632	MDGA1	trans	brain	seeQTL
rs6807632	DGKD	trans	brain	seeQTL
rs6807632	ADAMTS5	trans	brain	seeQTL
rs6807632	IGSF9B	trans	brain	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111393600-111395600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:111393600-111395800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:111393600-111396000	Flanking Active TSS	Osteobl	bone
4	chr3:111393600-111396200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr3:111393800-111395600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr3:111393800-111395600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr3:111393800-111395600	Flanking Active TSS	HMEC	breast
8	chr3:111393800-111395800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr3:111393800-111395800	Flanking Active TSS	Fetal Brain Male	brain
10	chr3:111393800-111396200	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr3:111393800-111396200	Flanking Active TSS	HUVEC	blood vessel
12	chr3:111393800-111396400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:111393800-111396600	Flanking Active TSS	NHEK	skin
14	chr3:111393800-111397000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr3:111394000-111395600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr3:111394000-111395600	Flanking Active TSS	Thymus	Thymus
17	chr3:111394000-111395800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr3:111394000-111396400	Flanking Active TSS	Hela-S3	cervix
19	chr3:111394000-111401400	Weak transcription	Aorta	Aorta
20	chr3:111394200-111395600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr3:111394200-111395600	Weak transcription	Gastric	stomach
22	chr3:111394200-111395600	Enhancers	Left Ventricle	heart
23	chr3:111394200-111396000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:111394200-111396000	Enhancers	Spleen	Spleen
25	chr3:111394200-111396200	Weak transcription	Small Intestine	intestine
26	chr3:111394200-111396400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr3:111394200-111396400	Enhancers	Liver	Liver
28	chr3:111394200-111396600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:111394200-111396600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr3:111394200-111396600	Enhancers	Stomach Mucosa	stomach
31	chr3:111394200-111403600	Weak transcription	Pancreas	Pancrea
32	chr3:111394400-111395600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:111394400-111395600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:111394400-111395600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:111394400-111396200	Flanking Active TSS	HepG2	liver
36	chr3:111394400-111396200	Enhancers	HSMM	muscle
37	chr3:111394400-111396600	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:111394400-111396600	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:111394600-111395800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:111394600-111395800	Enhancers	Right Ventricle	heart
41	chr3:111394800-111395600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr3:111394800-111395800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:111394800-111395800	Flanking Active TSS	Fetal Thymus	thymus
44	chr3:111394800-111396000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr3:111394800-111396000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:111394800-111396000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:111394800-111396400	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr3:111394800-111396600	Flanking Active TSS	GM12878-XiMat	blood
49	chr3:111395000-111395600	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr3:111395000-111395800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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