Variant report

Variant	rs6580658
Chromosome Location	chr12:48582232-48582233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48575723..48577470-chr12:48580708..48582766,2	K562	blood:
2	chr12:48581131..48583094-chr12:48584524..48586500,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177875	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1049392	0.89[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs10747529	0.81[JPT][hapmap]
rs10875733	0.80[JPT][hapmap]
rs10875739	0.80[JPT][hapmap]
rs10875752	0.88[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10875754	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10875759	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875761	0.89[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875765	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875766	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168353	0.80[JPT][hapmap]
rs11168354	0.82[JPT][hapmap]
rs11168358	0.82[JPT][hapmap]
rs11168363	0.80[JPT][hapmap]
rs11168364	0.80[JPT][hapmap]
rs11168373	0.81[JPT][hapmap]
rs11168404	0.80[JPT][hapmap]
rs11168417	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs11168424	0.89[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs11168434	0.89[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11168435	0.88[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11168438	0.89[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs11168439	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168442	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168443	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168444	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168445	0.80[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168446	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168447	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168448	0.88[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168453	0.89[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168454	0.89[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422355	0.82[JPT][hapmap]
rs12425679	0.86[AMR][1000 genomes]
rs17122567	0.80[JPT][hapmap]
rs2171643	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2286020	0.89[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes]
rs2408954	0.82[JPT][hapmap]
rs3825403	0.80[JPT][hapmap]
rs4258439	0.81[JPT][hapmap]
rs56097189	0.96[ASN][1000 genomes]
rs57430775	0.83[AMR][1000 genomes]
rs58540891	0.86[AMR][1000 genomes]
rs58556309	0.86[AMR][1000 genomes]
rs59537300	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66507954	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132898	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7133274	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136243	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136782	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136788	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299704	0.80[JPT][hapmap]
rs7302354	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7303677	0.80[JPT][hapmap]
rs73104071	0.86[AMR][1000 genomes]
rs73105950	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73304926	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484942	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs765260	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7962390	0.89[CHB][hapmap];0.80[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962569	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181670	0.89[CHB][hapmap];0.80[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs886589	0.81[CHB][hapmap];0.80[JPT][hapmap]

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
rs6580658	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	chr12:48580400-48582400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:48580400-48583000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:48580400-48583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:48580400-48583400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:48580400-48583800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48580400-48585600	Weak transcription	Esophagus	oesophagus
9	chr12:48582000-48582400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48582000-48584000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:48582200-48583400	Enhancers	Osteobl	bone

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