Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84528524..84531344-chr1:84538975..84541375,2	MCF-7	breast:
2	chr1:84530745..84533538-chr1:84541261..84543799,3	K562	blood:

Variant related genes	Relation type
ENSG00000271576	Chromatin interaction
ENSG00000142875	Chromatin interaction

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10493750	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11163897	0.85[JPT][hapmap]
rs11163898	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11163900	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12070547	0.98[ASN][1000 genomes]
rs12119275	0.84[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12132002	0.86[GIH][hapmap]
rs12132032	0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12404263	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12405120	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12724598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12746741	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17099118	0.91[TSI][hapmap]
rs34495740	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35452337	0.96[ASN][1000 genomes]
rs3903924	0.82[ASN][1000 genomes]
rs3915908	0.82[ASN][1000 genomes]
rs6669045	0.88[ASN][1000 genomes]
rs6674038	0.85[JPT][hapmap]
rs6703653	0.84[JPT][hapmap]
rs67276144	0.98[ASN][1000 genomes]
rs72711192	0.88[ASN][1000 genomes]
rs7520283	0.84[JPT][hapmap]
rs953197	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs957828	0.85[JPT][hapmap]

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	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3861699	MCOLN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84528400-84532600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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