Variant report

Variant	rs7266451
Chromosome Location	chr20:25084781-25084782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25038683..25041446-chr20:25083785..25085401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005409	1.00[ASN][1000 genomes]
rs12480307	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12480489	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2207632	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2207633	1.00[ASN][1000 genomes]
rs2207635	1.00[ASN][1000 genomes]
rs2207636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387577	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4813546	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4813548	1.00[ASN][1000 genomes]
rs4815366	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4815367	1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs4815368	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55651034	1.00[ASN][1000 genomes]
rs56157240	1.00[ASN][1000 genomes]
rs56369722	1.00[ASN][1000 genomes]
rs58747756	1.00[ASN][1000 genomes]
rs6037014	1.00[ASN][1000 genomes]
rs6050299	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6050300	1.00[ASN][1000 genomes]
rs6050304	1.00[ASN][1000 genomes]
rs6050306	1.00[ASN][1000 genomes]
rs6050308	1.00[ASN][1000 genomes]
rs6076315	0.84[ASW][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6083736	1.00[ASN][1000 genomes]
rs6083737	1.00[ASN][1000 genomes]
rs6083739	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	1.00[ASN][1000 genomes]
rs62215277	1.00[ASN][1000 genomes]
rs62217195	1.00[ASN][1000 genomes]
rs62217196	1.00[ASN][1000 genomes]
rs62217197	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs7344824	1.00[ASN][1000 genomes]
rs743017	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7266451	VSX1	cis	cerebellum	SCAN
rs7266451	NKX2-4	cis	cerebellum	SCAN
rs7266451	PLK1S1	cis	parietal	SCAN
rs7266451	PAX1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25082000-25084800	Weak transcription	Thymus	Thymus
2	chr20:25083800-25085200	Bivalent Enhancer	HepG2	liver

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