Variant report

Variant	rs11168439
Chromosome Location	chr12:48572568-48572569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48569957..48573539-chr12:48589775..48593231,3	K562	blood:
2	chr12:48570309..48573490-chr12:48574476..48577438,4	MCF-7	breast:
3	chr12:48572524..48575406-chr2:20550361..20552479,2	MCF-7	breast:
4	chr12:48570659..48574858-chr12:48591622..48593711,4	K562	blood:
5	chr12:48570737..48572645-chr12:48574965..48576517,2	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000177875	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1049392	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10875752	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10875754	0.92[ASN][1000 genomes]
rs10875759	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875761	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875765	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10875766	0.86[ASN][1000 genomes]
rs11168412	0.81[ASN][1000 genomes]
rs11168424	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168434	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11168435	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11168438	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11168442	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168443	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168444	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168445	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168446	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168447	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168448	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168453	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168454	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12228924	0.81[ASN][1000 genomes]
rs12425679	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2171643	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2286020	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56097189	0.98[ASN][1000 genomes]
rs57430775	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58540891	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58556309	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59537300	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580658	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66507954	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132898	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133274	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136243	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136782	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7136788	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302354	0.81[ASN][1000 genomes]
rs73104071	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73105950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73304926	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962390	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962569	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8181670	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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
rs11168439	C12orf68	cis	Esophagus Mucosa	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48570000-48573200	Weak transcription	Fetal Kidney	kidney
2	chr12:48570200-48575200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:48570600-48575000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:48571200-48576200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48571400-48573000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:48571400-48576000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48572400-48572600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links