Variant report

Variant	rs4301023
Chromosome Location	chr3:85057281-85057282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1016305	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1016306	0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1248857	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1248858	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1248859	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1248860	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081745	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1694977	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1872553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872556	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2035561	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2035562	0.95[CHB][hapmap]
rs2326123	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4499618	0.85[CHB][hapmap]
rs4856559	0.80[CHB][hapmap]
rs6549009	0.81[CHB][hapmap]
rs6768455	0.85[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7651996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765461	0.90[CHB][hapmap]
rs9816652	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9831123	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833081	0.85[EUR][1000 genomes]
rs9834688	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836888	0.85[EUR][1000 genomes]
rs9840607	0.84[ASN][1000 genomes]
rs9871198	0.85[CEU][hapmap];0.85[EUR][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	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	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4301023	CADM2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85055200-85057400	Enhancers	HepG2	liver
2	chr3:85055600-85068200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:85055800-85081400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:85056800-85057400	Flanking Active TSS	Liver	Liver
5	chr3:85057000-85058000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:85057000-85058200	Enhancers	A549	lung
7	chr3:85057000-85059400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:85057200-85057400	Enhancers	Brain Hippocampus Middle	brain
9	chr3:85057200-85057400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:85057200-85071400	Weak transcription	Brain Anterior Caudate	brain

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