Variant report

Variant	rs12451366
Chromosome Location	chr17:66828158-66828159
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	chr13:111565306..111566939-chr17:66828153..66829672,2	MCF-7	breast:
2	chr17:66819799..66822410-chr17:66827095..66829795,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10512519	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11655986	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656942	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12601591	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602875	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16973416	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs4147997	0.85[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4148011	0.92[EUR][1000 genomes]
rs56079215	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58601251	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62087820	0.88[EUR][1000 genomes]
rs6501769	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6501788	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215620	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216643	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7217691	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7219718	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8067199	0.98[ASN][1000 genomes]
rs8071366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8071389	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8076099	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs8079580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9913071	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12451366	ABCA8	cis	parietal	SCAN
rs12451366	ABCA8	cis	cerebellum	SCAN
rs12451366	CCDC45	cis	cerebellum	SCAN
rs12451366	PECAM1	cis	cerebellum	SCAN
rs12451366	ACE	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66817600-66828800	Weak transcription	Right Atrium	heart
2	chr17:66826600-66829200	Enhancers	Fetal Lung	lung
3	chr17:66826600-66830000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr17:66826800-66828600	Weak transcription	Ovary	ovary
5	chr17:66826800-66831200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:66827000-66830800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:66827400-66829000	Enhancers	Left Ventricle	heart
8	chr17:66827400-66830200	Enhancers	Adipose Nuclei	Adipose
9	chr17:66827800-66828200	Enhancers	Fetal Muscle Trunk	muscle
10	chr17:66827800-66829200	Enhancers	Fetal Muscle Leg	muscle
11	chr17:66828000-66829000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:66828000-66829200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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