Variant report

Variant	rs7296288
Chromosome Location	chr12:49479968-49479969
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49478072..49490419-chr12:49518907..49527034,52	K562	blood:
2	chr12:49477289..49493962-chr12:49512467..49528127,64	K562	blood:
3	chr12:49479128..49483320-chr12:49657445..49660768,5	K562	blood:
4	chr12:49473495..49475171-chr12:49478983..49480714,2	MCF-7	breast:
5	chr12:49479532..49482702-chr12:49503014..49506133,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123416	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10459221	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10459232	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1054442	0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs10783299	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10783301	0.85[ASN][1000 genomes]
rs10875910	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10875912	0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875913	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875914	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs10875915	0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875917	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10875918	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11168827	1.00[JPT][hapmap]
rs11168838	0.89[ASN][1000 genomes]
rs11168839	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs11168850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1138908	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11614738	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12298884	0.97[ASN][1000 genomes]
rs12580349	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12821008	0.91[ASN][1000 genomes]
rs2117029	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2241726	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293445	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2304275	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34436857	0.86[ASN][1000 genomes]
rs3741619	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3741622	0.91[JPT][hapmap]
rs3782357	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs6580698	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580699	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300136	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7969091	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs876333	0.81[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7296288	DDN	cis	Muscle Skeletal	GTEx
rs7296288	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs7296288	RHEBL1	cis	parietal	SCAN
rs7296288	RHEBL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49474400-49481800	Weak transcription	HSMM	muscle
2	chr12:49476200-49481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49478400-49480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:49479800-49480200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:49479800-49480200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:49479800-49480400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:49479800-49480400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:49479800-49480400	Enhancers	HSMMtube	muscle

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