Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165764196..165766988-chr1:165795992..165798651,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

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

rs_ID	r²[population]
rs10800150	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs10800152	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10800159	0.86[EUR][1000 genomes]
rs10918276	0.81[CHB][hapmap]
rs10918281	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs11578163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12021678	0.89[MEX][hapmap]
rs12127304	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12131697	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12723198	0.81[CHB][hapmap]
rs14223	0.81[CHB][hapmap]
rs1913846	0.81[CHB][hapmap]
rs1999992	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153263	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2153264	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2790057	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2814470	0.80[CHB][hapmap]
rs4582768	0.81[TSI][hapmap]
rs4656462	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6426937	0.81[CHB][hapmap]
rs6426940	0.81[CHB][hapmap]
rs6682864	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7411708	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6656194	ALDH9A1	cis	parietal	SCAN
rs6656194	PVRL4	cis	parietal	SCAN
rs6656194	BRP44	cis	parietal	SCAN
rs6656194	VANGL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165764800-165765800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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