Variant report

Variant	rs1416297
Chromosome Location	chr6:145269757-145269758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1111810	0.84[ASN][1000 genomes]
rs11752326	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200093	0.85[EUR][1000 genomes]
rs13213543	0.81[EUR][1000 genomes]
rs13216473	1.00[CEU][hapmap]
rs13216871	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1338704	1.00[CEU][hapmap]
rs1338705	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1572675	0.85[EUR][1000 genomes]
rs17074550	0.81[EUR][1000 genomes]
rs1832481	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2050719	0.80[EUR][1000 genomes]
rs2185145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211068	0.99[EUR][1000 genomes]
rs6570662	0.94[AMR][1000 genomes]
rs6570663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932709	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7742978	0.96[EUR][1000 genomes]
rs7753021	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7768827	0.80[EUR][1000 genomes]
rs7769009	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7773947	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322009	0.84[EUR][1000 genomes]
rs9373436	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9373439	0.85[EUR][1000 genomes]
rs9373440	0.97[EUR][1000 genomes]
rs9376878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376879	0.84[ASN][1000 genomes]
rs9386093	0.84[ASN][1000 genomes]
rs9390263	0.81[EUR][1000 genomes]
rs9390264	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9390269	0.85[EUR][1000 genomes]
rs9399523	0.85[EUR][1000 genomes]
rs9399524	0.85[EUR][1000 genomes]
rs9399525	0.85[EUR][1000 genomes]
rs9403636	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9403640	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403644	0.81[ASN][1000 genomes]
rs9403645	0.81[EUR][1000 genomes]
rs9403651	0.99[EUR][1000 genomes]
rs9403652	0.85[EUR][1000 genomes]
rs9403653	0.84[EUR][1000 genomes]
rs9497135	0.94[AMR][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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886742	chr6:145269757-145376903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1416297	PLAGL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145268800-145269800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:145269600-145269800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links