Variant report

Variant	rs12813453
Chromosome Location	chr12:67328297-67328298
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	chr12:67326854..67328503-chr12:67662512..67664147,2	MCF-7	breast:
2	chr12:67322533..67324494-chr12:67328156..67330477,2	K562	blood:

Variant related genes	Relation type
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10506512	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176491	0.81[EUR][1000 genomes]
rs12809312	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12809578	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810010	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12810857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810930	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811330	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811382	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12812455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815385	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815995	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12818812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12818966	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12819213	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12820561	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12820755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12820762	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12820990	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820993	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12821155	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12821257	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12821510	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12821539	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12821983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825803	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12829393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12830426	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12832716	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1316645	0.82[CEU][hapmap];0.80[GIH][hapmap]
rs17182971	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17780496	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35928413	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4913514	0.81[EUR][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	nsv1053250	chr12:67067995-67381411	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1044939	chr12:67207260-67377982	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1036984	chr12:67273098-67427543	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1054433	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541523	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12813453	C12orf66	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67323800-67330400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:67327800-67328800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:67328000-67328400	Enhancers	Rectal Smooth Muscle	rectum
4	chr12:67328200-67328800	Enhancers	Placenta	Placenta
5	chr12:67328200-67329200	Enhancers	Colon Smooth Muscle	Colon

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