Variant report

Variant	rs4516626
Chromosome Location	chr3:85152987-85152988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11127876	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs11713170	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12714616	1.00[CHB][hapmap]
rs12714617	1.00[CHB][hapmap]
rs13061527	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13064817	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13066623	1.00[CHB][hapmap]
rs13074075	0.88[AMR][1000 genomes]
rs13078384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13078494	0.85[AMR][1000 genomes]
rs13095644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097560	0.85[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2101344	1.00[CHB][hapmap]
rs2171143	1.00[CHB][hapmap]
rs2220244	0.85[MEX][hapmap]
rs2326225	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs34201102	0.85[AMR][1000 genomes]
rs4635723	0.85[AMR][1000 genomes]
rs66500121	0.85[AMR][1000 genomes]
rs6775752	0.85[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs6790864	0.86[MEX][hapmap]
rs6791035	0.85[AMR][1000 genomes]
rs6791363	1.00[CHB][hapmap]
rs6808586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7623714	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7628129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7630382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9284802	0.84[AMR][1000 genomes]
rs9309967	1.00[CHB][hapmap]
rs9309969	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs9647393	1.00[CHB][hapmap]
rs9814600	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9814835	0.86[MEX][hapmap]
rs9815258	1.00[CHB][hapmap]
rs9818659	1.00[CHB][hapmap]
rs9819278	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821807	1.00[CHB][hapmap]
rs9823454	1.00[CHB][hapmap]
rs9828496	1.00[CHB][hapmap]
rs9831374	0.80[ASN][1000 genomes]
rs9835904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9838091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839194	0.85[AMR][1000 genomes]
rs9846802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860513	1.00[CHB][hapmap]
rs9873321	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9875381	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9878472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9881257	1.00[CHB][hapmap]
rs9883252	0.85[CEU][hapmap];0.85[AMR][1000 genomes]

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	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877093	chr3:85101501-85194054	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590897	chr3:85122624-85187085	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877094	chr3:85124697-85253981	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4516626	CADM2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85151600-85153000	Enhancers	Fetal Intestine Small	intestine
2	chr3:85151600-85161200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:85152600-85153000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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