Variant report

Variant	rs581235
Chromosome Location	chr6:117649988-117649989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17079053	0.99[EUR][1000 genomes]
rs17632578	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1894674	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2243385	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2243386	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2301485	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2301486	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3756891	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3798379	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs473006	0.99[EUR][1000 genomes]
rs489576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493451	0.82[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs493548	0.99[EUR][1000 genomes]
rs497186	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs498251	0.99[EUR][1000 genomes]
rs499199	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs499338	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs499599	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs501109	0.93[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs506557	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs508278	0.83[ASW][hapmap];0.82[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs518987	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs528633	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs530066	0.82[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs530713	0.99[EUR][1000 genomes]
rs541866	0.98[EUR][1000 genomes]
rs543230	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs543706	0.99[EUR][1000 genomes]
rs545537	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546631	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs549557	0.92[EUR][1000 genomes]
rs552183	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs568514	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573886	0.94[EUR][1000 genomes]
rs574664	0.99[EUR][1000 genomes]
rs575006	0.99[EUR][1000 genomes]
rs580099	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs584647	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs592757	0.99[EUR][1000 genomes]
rs61077141	0.95[EUR][1000 genomes]
rs680920	0.95[EUR][1000 genomes]
rs687218	0.99[EUR][1000 genomes]
rs73566821	0.96[EUR][1000 genomes]
rs9481702	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9489127	0.89[EUR][1000 genomes]
rs9489135	0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs581235	GOPC	cis	cerebellum	SCAN
rs581235	MFSD3	trans	parietal	SCAN
rs581235	FAM26D	cis	parietal	SCAN
rs581235	PAOX	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117644200-117676000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:117649000-117650000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:117649000-117650000	Enhancers	HSMMtube	muscle
4	chr6:117649000-117650400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:117649200-117650200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr6:117649200-117650400	Strong transcription	HSMM	muscle
7	chr6:117649600-117650000	Enhancers	Adipose Nuclei	Adipose
8	chr6:117649800-117650000	Enhancers	Psoas Muscle	Psoas
9	chr6:117649800-117650200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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