Variant report

Variant	rs7429717
Chromosome Location	chr3:68093710-68093711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1345174	0.91[CEU][hapmap];0.92[JPT][hapmap]
rs1349005	0.81[CEU][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1374837	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs1447755	0.81[EUR][1000 genomes]
rs4572789	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs4856812	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs4856813	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs6548935	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs6792324	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs6792729	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6793147	0.83[EUR][1000 genomes]
rs6800897	0.86[GIH][hapmap];0.93[MEX][hapmap]
rs6808653	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7431177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs9812127	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs9818541	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs9857691	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs9874728	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs9881594	0.91[CEU][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1010231	chr3:67894825-68117879	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv999747	chr3:68066423-68188180	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv536584	chr3:68066423-68188180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2752014	chr3:68091879-68416989	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7429717	LRIG1	cis	cerebellum	SCAN
rs7429717	MAGI1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links