Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76528266..76531083-chr1:76533694..76535257,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10493580	0.81[EUR][1000 genomes]
rs11162070	0.82[EUR][1000 genomes]
rs11162073	0.82[EUR][1000 genomes]
rs11162079	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1144343	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1144346	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1146663	0.92[ASN][1000 genomes]
rs11805321	0.83[EUR][1000 genomes]
rs12038667	0.81[EUR][1000 genomes]
rs12039427	0.84[EUR][1000 genomes]
rs12040748	0.83[EUR][1000 genomes]
rs1251576	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1251806	0.82[ASN][1000 genomes]
rs12568806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1763465	0.84[ASN][1000 genomes]
rs291075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146895	0.87[EUR][1000 genomes]
rs4146896	0.87[EUR][1000 genomes]
rs4949690	0.83[EUR][1000 genomes]
rs58483436	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6703146	0.81[EUR][1000 genomes]
rs6704184	0.82[EUR][1000 genomes]
rs699829	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs699830	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517793	0.83[EUR][1000 genomes]
rs7517974	0.83[EUR][1000 genomes]
rs7529565	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv947186	chr1:76512447-76530843	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1477	chr1:76515963-76534339	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv521786	chr1:76525783-76535434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1417407	MSH4	cis	parietal	SCAN
rs1417407	ACADM	cis	cerebellum	SCAN
rs1417407	MSH4	cis	cerebellum	SCAN
rs1417407	LRRIQ3	cis	cerebellum	SCAN
rs1417407	RABGGTB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76521800-76531000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76526200-76531000	Weak transcription	A549	lung
3	chr1:76529800-76531600	Enhancers	Placenta Amnion	Placenta Amnion

Quick Search: