Variant report

Variant	rs1551213
Chromosome Location	chr3:85304062-85304063
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11127878	0.90[CHB][hapmap];0.91[YRI][hapmap]
rs11715683	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs12374196	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490643	0.94[CHB][hapmap];0.89[YRI][hapmap]
rs12630455	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs12632038	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12637719	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[YRI][hapmap]
rs12638015	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13062591	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs13085411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13087094	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13089143	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097955	0.86[ASN][1000 genomes]
rs1470797	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17022526	0.94[CHB][hapmap];0.89[YRI][hapmap]
rs2326225	0.86[TSI][hapmap]
rs4411894	0.83[EUR][1000 genomes]
rs4635720	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4856562	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7622240	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7622775	0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[YRI][hapmap]
rs768324	0.90[CHB][hapmap];0.91[YRI][hapmap]
rs9309973	0.86[CHB][hapmap]
rs9811546	1.00[LWK][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap]
rs9817509	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9845394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848082	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9852851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9872078	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873321	0.82[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv877096	chr3:85163167-85366517	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv460747	chr3:85163167-85391672	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590899	chr3:85163167-85391672	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1001124	chr3:85167047-85309046	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv877098	chr3:85177173-85361645	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv470716	chr3:85194054-85316648	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv877099	chr3:85200179-85304062	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv590903	chr3:85200742-85316648	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv999255	chr3:85222822-85323285	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv536617	chr3:85222822-85323285	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv877100	chr3:85234199-85336559	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1006718	chr3:85243599-85323285	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1012601	chr3:85246185-85426996	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv536618	chr3:85246185-85426996	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1551213	CADM2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85288400-85307600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85303000-85308200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:85303600-85304600	Enhancers	Brain Angular Gyrus	brain
4	chr3:85303600-85305400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:85303800-85304400	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:85304000-85304200	Enhancers	Brain Substantia Nigra	brain

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