Variant report

No.	Distal block	Cell Line	Cell type
1	chr15:78720134..78723465-chr15:78728938..78732082,4	MCF-7	breast:
2	chr15:78722992..78724695-chr15:78731841..78733511,2	K562	blood:
3	chr15:78722314..78725378-chr15:78725474..78727729,3	MCF-7	breast:
4	chr15:78722350..78724464-chr15:78728456..78730722,3	K562	blood:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10519198	0.93[EUR][1000 genomes]
rs11072762	0.89[EUR][1000 genomes]
rs11072765	0.93[EUR][1000 genomes]
rs11639224	0.93[EUR][1000 genomes]
rs12899131	0.93[EUR][1000 genomes]
rs12909921	0.93[EUR][1000 genomes]
rs12910090	0.94[EUR][1000 genomes]
rs1847529	0.94[EUR][1000 genomes]
rs2036529	0.83[ASN][1000 genomes]
rs2036532	0.93[EUR][1000 genomes]
rs2568497	0.82[ASN][1000 genomes]
rs2568498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568499	0.82[ASN][1000 genomes]
rs2568500	0.94[EUR][1000 genomes]
rs2656055	0.82[ASN][1000 genomes]
rs2869032	0.81[ASN][1000 genomes]
rs4390557	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4436747	0.85[EUR][1000 genomes]
rs8041628	0.94[EUR][1000 genomes]
rs954144	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2656058	CHRNA5	cis	Nerve Tibial	GTEx
rs2656058	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs2656058	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs2656058	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2656058	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs2656058	CHRNA5	cis	Esophagus Mucosa	GTEx
rs2656058	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs2656058	CHRNA5	cis	Heart Left Ventricle	GTEx
rs2656058	CHRNA5	cis	Muscle Skeletal	GTEx
rs2656058	RP11-650L12.2	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78716400-78726200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:78720800-78726400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr15:78720800-78728400	Weak transcription	K562	blood
5	chr15:78721000-78726600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:78722200-78726200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:78722400-78724400	Weak transcription	Liver	Liver
8	chr15:78723400-78723600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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