Variant report

Variant	rs12812451
Chromosome Location	chr12:104619142-104619143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104617645..104619997-chr12:104678987..104680569,2	K562	blood:
2	chr12:104617675..104620122-chr12:104673280..104676243,2	K562	blood:
3	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257732	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11111937	1.00[ASN][1000 genomes]
rs11111942	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111969	1.00[ASN][1000 genomes]
rs11112015	1.00[ASN][1000 genomes]
rs12809773	1.00[ASN][1000 genomes]
rs12813601	1.00[ASN][1000 genomes]
rs12819539	1.00[ASN][1000 genomes]
rs12826196	1.00[ASN][1000 genomes]
rs12828655	1.00[ASN][1000 genomes]
rs2706272	1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34811234	1.00[ASN][1000 genomes]
rs34863477	1.00[ASN][1000 genomes]
rs35453744	1.00[ASN][1000 genomes]
rs35473944	1.00[ASN][1000 genomes]
rs35653685	1.00[ASN][1000 genomes]
rs35822062	1.00[ASN][1000 genomes]
rs35844634	1.00[ASN][1000 genomes]
rs35945288	1.00[ASN][1000 genomes]
rs4964733	1.00[ASN][1000 genomes]
rs4964778	1.00[ASN][1000 genomes]
rs6539127	1.00[ASN][1000 genomes]
rs66554757	1.00[ASN][1000 genomes]
rs71466293	1.00[ASN][1000 genomes]
rs71466302	1.00[ASN][1000 genomes]
rs7294701	1.00[ASN][1000 genomes]
rs7305137	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311508	0.90[ASW][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313536	0.92[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978310	1.00[ASN][1000 genomes]
rs7979945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
2	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12812451	PML	trans	cerebellum	SCAN
rs12812451	HCFC2	cis	parietal	SCAN
rs12812451	CCDC53	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104614000-104619600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:104614000-104623400	Weak transcription	Right Atrium	heart
3	chr12:104614200-104619800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:104615000-104620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:104615000-104625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104617400-104619400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:104617800-104620200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:104618000-104620200	Weak transcription	HMEC	breast

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