Variant report

Variant	rs4953853
Chromosome Location	chr2:110385397-110385398
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110371654..110373301-chr2:110384115..110386947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1036317	0.84[EUR][1000 genomes]
rs1036318	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10496432	0.87[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1811388	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28441405	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28445980	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570680	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28612440	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28719680	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3213866	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34111852	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34311530	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34441132	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34517320	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34821058	0.87[ASW][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35120088	0.83[AMR][1000 genomes]
rs35223862	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35392016	0.83[AMR][1000 genomes]
rs35550721	0.85[EUR][1000 genomes]
rs35955221	0.83[AMR][1000 genomes]
rs4482487	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953729	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953730	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4953788	0.82[ASW][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953847	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55794045	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56265736	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56794190	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58031484	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6594050	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594053	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594054	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709945	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6719215	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6725792	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6737736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6751785	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6760577	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824788	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824796	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824802	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72826816	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72826817	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs753492	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7565483	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7577865	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs892462	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9330317	0.83[AMR][1000 genomes]
rs9330321	0.83[AMR][1000 genomes]
rs9752531	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9798179	0.83[AMR][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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4953853	ACOXL	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110377200-110387400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:110381800-110387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:110385200-110387400	Weak transcription	HepG2	liver

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