Variant report

Variant	rs12713377
Chromosome Location	chr2:58472110-58472111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1011314	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1025754	0.81[CHD][hapmap]
rs11125742	0.82[CHB][hapmap]
rs12470316	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs13411119	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs13422644	0.90[AFR][1000 genomes]
rs1439269	0.95[CEU][hapmap];0.94[TSI][hapmap]
rs17049425	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2110664	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732136	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3771216	0.83[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6722988	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6761301	0.80[TSI][hapmap]
rs768298	0.87[CEU][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12713377	FANCL	cis	lymphoblastoid	seeQTL
rs12713377	VRK2	cis	Lymphoblastoid	GTEx
rs12713377	VRK2	cis	multi-tissue	Pritchard
rs12713377	VRK2	cis	lymphoblastoid	seeQTL

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