Variant report

Variant	rs2691093
Chromosome Location	chr3:81885274-81885275
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	chr3:81885124..81886646-chr3:81889084..81891267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242009	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1155277	0.96[CEU][hapmap]
rs11711331	0.89[GIH][hapmap]
rs12495343	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635671	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073613	0.82[CHD][hapmap]
rs13091492	0.82[ASN][1000 genomes]
rs1375086	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs1404297	0.89[EUR][1000 genomes]
rs1464791	0.82[ASN][1000 genomes]
rs1829967	0.88[EUR][1000 genomes]
rs1973800	0.90[EUR][1000 genomes]
rs1973801	0.90[EUR][1000 genomes]
rs1997002	0.90[EUR][1000 genomes]
rs2244294	0.90[EUR][1000 genomes]
rs2252530	0.88[EUR][1000 genomes]
rs2594547	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs2594549	0.96[CEU][hapmap]
rs2594551	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs2594553	0.96[CEU][hapmap]
rs2594558	0.84[EUR][1000 genomes]
rs2594562	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[EUR][1000 genomes]
rs2680245	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[EUR][1000 genomes]
rs2680246	0.83[EUR][1000 genomes]
rs2680257	0.96[CEU][hapmap]
rs2680260	0.89[EUR][1000 genomes]
rs2680274	0.89[EUR][1000 genomes]
rs2680277	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2680280	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2691077	0.90[EUR][1000 genomes]
rs2691078	0.90[EUR][1000 genomes]
rs2691079	0.90[EUR][1000 genomes]
rs2691080	0.90[EUR][1000 genomes]
rs2691083	0.90[EUR][1000 genomes]
rs2691084	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2691085	0.82[EUR][1000 genomes]
rs2691089	0.90[EUR][1000 genomes]
rs2873054	0.86[ASN][1000 genomes]
rs3755713	0.82[GIH][hapmap]
rs3772882	0.84[GIH][hapmap]
rs3772883	0.84[GIH][hapmap]
rs3772899	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3772902	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3821548	0.89[GIH][hapmap]
rs3849570	0.89[GIH][hapmap]
rs4411908	0.84[GIH][hapmap]
rs6765917	0.86[ASN][1000 genomes]
rs6803932	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[EUR][1000 genomes]
rs7611902	0.90[EUR][1000 genomes]
rs7620240	0.86[GIH][hapmap]
rs7641973	0.81[ASN][1000 genomes]
rs950904	0.90[EUR][1000 genomes]
rs9810377	0.86[EUR][1000 genomes]
rs9818090	0.92[CEU][hapmap]
rs9822266	0.90[EUR][1000 genomes]
rs9832088	0.89[EUR][1000 genomes]
rs9841087	0.85[ASN][1000 genomes]
rs9860204	0.90[EUR][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	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2691093	GRIN1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81883400-81886600	Weak transcription	Dnd41	blood
2	chr3:81885200-81889000	Enhancers	HUES48 Cell Line	embryonic stem cell

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