Variant report

Variant	rs11168442
Chromosome Location	chr12:48583037-48583038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48582939..48585251-chr12:48585602..48588583,3	K562	blood:
2	chr12:48479571..48480121-chr12:48582809..48583469,2	K562	blood:
3	chr12:48356916..48357462-chr12:48583008..48583508,2	K562	blood:
4	chr12:48582333..48583154-chr12:48590725..48591457,2	K562	blood:
5	chr12:48582939..48584871-chr12:48586838..48589561,2	K562	blood:
6	chr12:48581131..48583094-chr12:48584524..48586500,2	MCF-7	breast:
7	chr12:48583004..48587511-chr12:48589337..48593893,5	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1049392	0.85[AMR][1000 genomes]
rs10875752	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10875754	0.85[ASN][1000 genomes]
rs10875759	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875765	0.99[ASN][1000 genomes]
rs10875766	0.91[ASN][1000 genomes]
rs11168424	0.85[AMR][1000 genomes]
rs11168434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168435	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168438	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11168439	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168443	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168445	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168448	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168454	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425679	0.88[AMR][1000 genomes]
rs2171643	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2286020	0.88[AMR][1000 genomes]
rs56097189	0.95[ASN][1000 genomes]
rs57430775	0.86[AMR][1000 genomes]
rs58540891	0.88[AMR][1000 genomes]
rs58556309	0.88[AMR][1000 genomes]
rs59537300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580658	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66507954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132898	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7133274	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136243	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136782	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136788	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73104071	0.88[AMR][1000 genomes]
rs73105950	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73304926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484942	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181670	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168442	C12orf68	cis	Esophagus Mucosa	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:48580200-48583200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48580400-48583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:48580400-48583400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:48580400-48583800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48580400-48585600	Weak transcription	Esophagus	oesophagus
7	chr12:48582000-48584000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:48582200-48583400	Enhancers	Osteobl	bone
9	chr12:48582400-48583200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48582400-48583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:48583000-48590200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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