Variant report

Variant	rs10779987
Chromosome Location	chr3:81970856-81970857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CADM2-7	chr3:81970822-81970884	XLOC_002719

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10779986	0.89[EUR][1000 genomes]
rs11127746	0.86[EUR][1000 genomes]
rs11705789	0.89[EUR][1000 genomes]
rs13068700	0.87[EUR][1000 genomes]
rs1851918	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1851926	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1851928	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35779564	0.85[EUR][1000 genomes]
rs4440144	0.84[ASN][1000 genomes]
rs4479620	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4605572	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4618242	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6548779	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6548784	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6766011	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778265	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785385	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6797240	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809792	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809793	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9817070	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9870954	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877408	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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
2	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
rs10779987	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81965200-81971400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:81970000-81971000	Enhancers	Ovary	ovary
3	chr3:81970000-81972400	Enhancers	Fetal Stomach	stomach
4	chr3:81970200-81971000	Enhancers	Fetal Heart	heart
5	chr3:81970400-81972200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:81970600-81971000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:81970800-81971200	Enhancers	Fetal Muscle Leg	muscle

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