Variant report

Variant	rs12685971
Chromosome Location	chr9:110462320-110462321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10117620	0.93[EUR][1000 genomes]
rs10123702	0.93[EUR][1000 genomes]
rs10123747	0.93[EUR][1000 genomes]
rs12351388	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12684877	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60514260	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60640360	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1808541	chr9:110444938-110488612	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv427850	chr9:110456613-110632324	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv428221	chr9:110456613-110632324	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12685971	SMC2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110456400-110463000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:110456600-110463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:110456800-110463000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:110457400-110463000	Weak transcription	Fetal Lung	lung
5	chr9:110461000-110463000	Weak transcription	Gastric	stomach
6	chr9:110461400-110462400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:110461400-110462800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr9:110461600-110462800	Weak transcription	Brain Germinal Matrix	brain
9	chr9:110462000-110465400	Weak transcription	Stomach Mucosa	stomach

Quick Search:

Input of quick search could be:

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

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