Variant report

Variant	rs10779990
Chromosome Location	chr3:89208581-89208582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:75910543..75911043-chr3:89208197..89208700,2	Hela-S3	cervix:
2	chr3:89207136..89210104-chr3:89214868..89216855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156110	Chromatin interaction
ENSG00000185009	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11128068	0.83[JPT][hapmap]
rs11128069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633482	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12714730	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714731	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317993	0.89[ASN][1000 genomes]
rs34469393	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3923215	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4128782	0.83[JPT][hapmap]
rs62274620	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551392	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7428094	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7428598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7429534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610407	0.83[JPT][hapmap]
rs7619508	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7626554	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639401	0.90[JPT][hapmap]
rs7646011	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9310109	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9835094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868686	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9883199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883603	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005603	chr3:89174152-89223459	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1008916	chr3:89206065-89241915	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10779990	CADM2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89205800-89210200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:89206000-89211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:89207200-89208600	Weak transcription	Fetal Brain Male	brain
4	chr3:89208400-89208600	Enhancers	Fetal Brain Female	brain

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