Variant report

Variant	rs12579911
Chromosome Location	chr12:57834427-57834428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57827390..57829712-chr12:57833047..57835363,2	MCF-7	breast:
2	chr12:57823623..57830869-chr12:57831560..57839261,11	K562	blood:
3	chr12:57822828..57827240-chr12:57828141..57836129,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258001	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000175189	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap]
rs10747778	1.00[CEU][hapmap]
rs10783818	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10783819	1.00[CEU][hapmap]
rs10876976	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs10876980	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876983	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs11172169	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11172170	1.00[CEU][hapmap]
rs11172190	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172191	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172205	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172211	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172214	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172222	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609986	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12230111	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12296766	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12310220	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12369598	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12423654	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812140	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1284252	0.91[EUR][1000 genomes]
rs1798710	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2063778	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280139	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28504983	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3923885	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs4075325	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4108243	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760236	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4760244	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760305	0.81[EUR][1000 genomes]
rs4760306	0.81[EUR][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4760348	1.00[CEU][hapmap]
rs481196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491750	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs533975	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537482	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs543410	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs560048	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568793	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs575153	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs6581131	1.00[CEU][hapmap]
rs6581134	0.93[GIH][hapmap]
rs6581136	1.00[CEU][hapmap]
rs7132367	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7133939	1.00[CEU][hapmap]
rs7135142	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7298418	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7303070	0.81[EUR][1000 genomes]
rs7307059	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7309659	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7398058	1.00[CEU][hapmap]
rs7486863	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs7977908	1.00[CEU][hapmap]
rs9738004	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12579911	TSPAN31	cis	cerebellum	SCAN
rs12579911	KIF5A	cis	cerebellum	SCAN
rs12579911	KRT81	cis	cerebellum	SCAN
rs12579911	XRCC6BP1	cis	multi-tissue	Pritchard
rs12579911	DKFZP586D0919	cis	multi-tissue	Pritchard
rs12579911	KIAA0748	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57825600-57848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57829400-57843200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57833000-57836200	Weak transcription	Aorta	Aorta
4	chr12:57833400-57843600	Weak transcription	HepG2	liver
5	chr12:57833600-57835000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr12:57833800-57834800	Enhancers	Liver	Liver

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