Variant report

Variant	rs12881435
Chromosome Location	chr14:80260053-80260054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr14:80260052-80260209	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000258637	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11628399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11628403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11628915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586263	0.86[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12586501	1.00[ASN][1000 genomes]
rs12588661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12588956	0.93[ASN][1000 genomes]
rs12589656	0.86[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs12590090	0.93[ASN][1000 genomes]
rs12590550	0.93[ASN][1000 genomes]
rs17174723	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17174897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs17764518	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17764668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17764884	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34549185	0.97[ASN][1000 genomes]
rs34764611	0.83[ASN][1000 genomes]
rs35224540	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35732569	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56122467	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67488951	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7152915	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7155646	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158292	0.86[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs72696796	0.87[ASN][1000 genomes]
rs72698405	1.00[ASN][1000 genomes]
rs8021767	0.86[JPT][hapmap];0.90[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	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1039622	chr14:79908702-80266601	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv902113	chr14:80172094-80929699	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12881435	FOS	cis	parietal	SCAN
rs12881435	POMT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80248000-80262400	Weak transcription	Brain Inferior Temporal Lobe	brain

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