Variant report

Variant	rs12052316
Chromosome Location	chr2:98846093-98846094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10170356	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124071	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11124075	0.81[EUR][1000 genomes]
rs12712252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1466156	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17429187	0.91[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes]
rs2122752	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2122755	0.85[CEU][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs4281956	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851915	0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56149802	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6543413	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711478	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6714220	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72819905	0.80[EUR][1000 genomes]
rs7579916	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7590288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7603439	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv582513	chr2:98829237-98869914	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv582514	chr2:98835962-98869914	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12052316	CNNM4	cis	cerebellum	SCAN

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

No data

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

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