Variant report

Variant	rs8011716
Chromosome Location	chr14:80757649-80757650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NRXN3-3	chr14:80757306-80757664	ncRnaDb_ncrna_FR101408_1

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10131076	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10133463	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10140980	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10144099	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10146631	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10149251	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10150064	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10150190	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10483947	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11159454	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851891	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388378	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17110449	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17110492	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17110521	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1884071	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1907526	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955625	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160354	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160355	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs224969	0.81[AMR][1000 genomes]
rs2267872	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2267873	0.86[TSI][hapmap]
rs2273173	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295138	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28607034	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28883971	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55859799	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884286	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56033314	0.89[EUR][1000 genomes]
rs61989398	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6574551	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7140952	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs7141617	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7145153	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7145584	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7146189	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154177	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7154898	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159642	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7159995	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7160310	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7350729	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8003183	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8009555	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9652301	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9972105	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9972275	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[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	nsv902113	chr14:80172094-80929699	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv902115	chr14:80700351-80844239	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1371	chr14:80719478-80761504	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8011716	NRXN3	cis	parietal	SCAN
rs8011716	KIAA1737	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80757600-80757800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links