Variant report

Variant	rs2387577
Chromosome Location	chr20:25048940-25048941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25048502..25051261-chr20:25062095..25064063,2	MCF-7	breast:
2	chr20:24972253..24980445-chr20:25044479..25049663,13	MCF-7	breast:
3	chr20:25043693..25045702-chr20:25047001..25049231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100987	Chromatin interaction
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1005409	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2144372	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2207632	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	1.00[ASN][1000 genomes]
rs2207636	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4813546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815364	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs4815366	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4815368	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	1.00[ASN][1000 genomes]
rs58747756	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037013	1.00[JPT][hapmap]
rs6037014	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6083734	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	1.00[ASN][1000 genomes]
rs6083737	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6115024	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115037	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304082	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	1.00[ASN][1000 genomes]
rs62217195	1.00[ASN][1000 genomes]
rs62217196	1.00[ASN][1000 genomes]
rs62217197	1.00[ASN][1000 genomes]
rs62217199	1.00[ASN][1000 genomes]
rs7263632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7266451	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7344824	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs743018	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3345945	chr20:25046552-25049850	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3361205	chr20:25046552-25049950	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2387577	ACSS1	cis	cerebellum	SCAN
rs2387577	VSX1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25046400-25057200	Weak transcription	Brain Substantia Nigra	brain
2	chr20:25046600-25052000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:25046800-25057400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:25046800-25058200	Weak transcription	Right Atrium	heart
5	chr20:25048600-25051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:25048600-25056800	Weak transcription	Gastric	stomach
7	chr20:25048800-25049200	Weak transcription	Fetal Kidney	kidney
8	chr20:25048800-25053000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:25048800-25057200	Weak transcription	Pancreas	Pancrea

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