Variant report

Variant	rs6763561
Chromosome Location	chr3:119145512-119145513
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119145344..119146916-chr3:119149020..119151478,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11712863	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11713200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049756	0.87[EUR][1000 genomes]
rs2178318	0.89[EUR][1000 genomes]
rs2282171	0.95[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3195852	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35078244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3932422	0.88[EUR][1000 genomes]
rs4687859	0.95[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs4688003	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438532	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6797866	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7613562	0.86[EUR][1000 genomes]
rs7629750	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs9713715	0.89[EUR][1000 genomes]
rs9833154	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9846088	0.95[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs9851177	0.87[EUR][1000 genomes]
rs9855347	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872589	0.90[CEU][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6763561	POGLUT1	cis	Artery Tibial	GTEx
rs6763561	GOLGB1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
2	chr3:119112000-119147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:119133800-119147400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
6	chr3:119134600-119147600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:119134800-119147400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:119135000-119147400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:119135000-119147600	Weak transcription	Fetal Thymus	thymus
10	chr3:119135000-119147800	Weak transcription	Placenta	Placenta
11	chr3:119135000-119148000	Weak transcription	Aorta	Aorta
12	chr3:119135200-119149800	Weak transcription	Gastric	stomach
13	chr3:119135400-119145600	Weak transcription	HUVEC	blood vessel
14	chr3:119135400-119147800	Weak transcription	Ovary	ovary
15	chr3:119135400-119148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
17	chr3:119136800-119145600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:119137400-119147800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:119137800-119146800	Weak transcription	Osteobl	bone
20	chr3:119138000-119148400	Weak transcription	Fetal Stomach	stomach
21	chr3:119138000-119152400	Weak transcription	Lung	lung
22	chr3:119139400-119147000	Weak transcription	Left Ventricle	heart
23	chr3:119142400-119150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119144400-119150400	ZNF genes & repeats	Liver	Liver
25	chr3:119144600-119152000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:119145000-119147800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
27	chr3:119145200-119145600	Weak transcription	NH-A	brain
28	chr3:119145200-119145800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:119145400-119148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:119145400-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links