Variant report

Variant	rs6768455
Chromosome Location	chr3:85040649-85040650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12714616	0.81[TSI][hapmap]
rs13075873	0.89[EUR][1000 genomes]
rs1872553	0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs2200472	0.96[CHD][hapmap]
rs36032153	0.84[EUR][1000 genomes]
rs4301023	0.85[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4856554	0.92[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7645633	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7651996	0.85[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs9816652	0.84[EUR][1000 genomes]
rs9831123	0.80[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs9833081	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834688	0.86[EUR][1000 genomes]
rs9836888	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849305	0.81[EUR][1000 genomes]
rs9860513	0.81[CEU][hapmap]
rs9870384	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9871198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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	nsv1000793	chr3:85020452-85051839	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	esv3380589	chr3:85037562-85040860	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6768455	CADM2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85034200-85042600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:85034200-85048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:85035200-85041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:85035600-85052800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:85037400-85042400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:85037800-85041000	Weak transcription	Fetal Lung	lung
7	chr3:85037800-85042400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:85040000-85043400	Enhancers	Brain Angular Gyrus	brain
9	chr3:85040200-85041200	Enhancers	Adipose Nuclei	Adipose
10	chr3:85040200-85041200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:85040200-85041400	Enhancers	Brain Hippocampus Middle	brain
12	chr3:85040200-85041400	Enhancers	Brain Substantia Nigra	brain
13	chr3:85040400-85041200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:85040400-85041400	Enhancers	Brain Anterior Caudate	brain
15	chr3:85040400-85041400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:85040600-85041000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:85040600-85043000	Enhancers	HUES48 Cell Line	embryonic stem cell

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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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