Variant report

Variant	rs11904581
Chromosome Location	chr2:67858049-67858050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10184721	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10187948	0.85[AMR][1000 genomes]
rs10189868	0.85[AMR][1000 genomes]
rs10189870	0.85[AMR][1000 genomes]
rs10204519	0.94[AMR][1000 genomes]
rs11883783	0.85[AMR][1000 genomes]
rs11898758	0.82[AMR][1000 genomes]
rs11900117	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11904407	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13398669	0.82[AMR][1000 genomes]
rs13398896	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13422158	0.82[AMR][1000 genomes]
rs2861699	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs60347662	0.82[AMR][1000 genomes]
rs6546323	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs6749548	0.82[AMR][1000 genomes]
rs6757264	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6760771	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6761524	0.82[AMR][1000 genomes]
rs72899995	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72901828	0.82[AMR][1000 genomes]
rs72901866	0.82[AMR][1000 genomes]
rs7559840	0.85[AMR][1000 genomes]
rs7567910	0.82[AMR][1000 genomes]
rs7568300	1.00[AMR][1000 genomes]
rs7569221	0.85[AMR][1000 genomes]
rs7569836	0.85[AMR][1000 genomes]
rs7570412	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7573396	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7579880	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582772	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7583557	0.85[AMR][1000 genomes]
rs7589963	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7594754	0.82[AMR][1000 genomes]
rs7604451	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11904581	GAP43	trans	lymphoblastoid	seeQTL
rs11904581	PITPNC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67854600-67860000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:67854600-67860200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:67857200-67858800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:67857400-67858600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:67857800-67859400	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links