Variant report

Variant	rs12228446
Chromosome Location	chr12:62834376-62834377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10877892	0.82[JPT][hapmap]
rs11174439	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs11174456	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs11174491	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs11174502	0.84[ASN][1000 genomes]
rs11174503	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs11174515	0.89[ASN][1000 genomes]
rs11174526	1.00[JPT][hapmap]
rs11174531	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11174549	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11174554	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11174561	0.86[ASW][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11559995	0.89[ASN][1000 genomes]
rs12161814	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4405369	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7302781	0.89[ASN][1000 genomes]
rs74095806	0.89[ASN][1000 genomes]
rs7953138	0.82[JPT][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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899157	chr12:62783967-62843620	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12228446	SHMT2	cis	parietal	SCAN
rs12228446	KIF5A	cis	parietal	SCAN
rs12228446	LRP1	cis	parietal	SCAN
rs12228446	ARHGEF25	cis	cerebellum	SCAN
rs12228446	R3HDM2	cis	cerebellum	SCAN
rs12228446	AGAP2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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

what's new

Quick links