Variant report

Variant	rs12464134
Chromosome Location	chr2:99540101-99540102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12712037	0.83[CHB][hapmap]
rs12712040	0.82[ASN][1000 genomes]
rs12990579	0.83[CHB][hapmap]
rs13006398	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13024838	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17758170	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1878589	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs6542841	0.89[CHB][hapmap]
rs6741166	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6757098	0.89[CHB][hapmap]
rs6760065	0.89[CHB][hapmap]
rs7423519	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.83[MKK][hapmap];0.89[ASN][1000 genomes]
rs7565819	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7588441	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs883773	0.89[CHB][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12464134	TSGA10	cis	cerebellum	SCAN
rs12464134	CNGA3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99532400-99542800	Weak transcription	Pancreas	Pancrea
2	chr2:99538000-99550800	Weak transcription	Gastric	stomach
3	chr2:99538400-99542600	Weak transcription	NHEK	skin
4	chr2:99538400-99551400	Weak transcription	Esophagus	oesophagus
5	chr2:99539800-99540600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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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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