Variant report

Variant	rs12821008
Chromosome Location	chr12:49474605-49474606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49462894..49465042-chr12:49474015..49476697,2	MCF-7	breast:
2	chr12:49473495..49475171-chr12:49478983..49480714,2	MCF-7	breast:
3	chr12:49462069..49464904-chr12:49472018..49475010,2	K562	blood:
4	chr12:49473068..49475650-chr12:49523317..49525672,3	K562	blood:
5	chr12:49473068..49475868-chr12:49523317..49526376,4	K562	blood:
6	chr12:49460491..49475559-chr12:49480736..49489831,23	K562	blood:

Variant related genes	Relation type
ENSG00000258017	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000139549	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10459221	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459232	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1054442	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs10783299	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10783300	0.80[ASN][1000 genomes]
rs10783301	0.89[ASN][1000 genomes]
rs10875908	0.80[ASN][1000 genomes]
rs10875910	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875911	0.80[ASN][1000 genomes]
rs10875912	0.80[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875913	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875914	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875915	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875917	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875918	0.97[ASN][1000 genomes]
rs11168827	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168838	0.94[ASN][1000 genomes]
rs11168839	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168850	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138908	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11614738	0.80[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs12298884	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580349	0.80[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs2117029	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2241726	0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2293445	0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2293446	0.81[ASN][1000 genomes]
rs2304275	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[ASN][1000 genomes]
rs34436857	0.89[ASN][1000 genomes]
rs3741619	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3741622	0.91[JPT][hapmap]
rs3782357	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6580698	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6580699	0.94[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7296288	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7300136	0.97[ASN][1000 genomes]
rs7969091	0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs876333	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	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

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12821008	RHEBL1	cis	parietal	SCAN
rs12821008	RHEBL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49472200-49475800	Enhancers	Fetal Muscle Leg	muscle
2	chr12:49472400-49475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49474400-49475200	Enhancers	Fetal Muscle Trunk	muscle
4	chr12:49474400-49479800	Weak transcription	HSMMtube	muscle
5	chr12:49474400-49481800	Weak transcription	HSMM	muscle

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