Variant report

Variant	rs34422348
Chromosome Location	chr15:79020472-79020473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79010822..79012780-chr15:79019538..79021262,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117971	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12324870	0.85[AMR][1000 genomes]
rs12901241	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905273	0.81[AMR][1000 genomes]
rs12906171	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1808065	0.81[EUR][1000 genomes]
rs2005263	0.84[ASN][1000 genomes]
rs2017295	0.84[ASN][1000 genomes]
rs28444683	0.91[AMR][1000 genomes]
rs34067845	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34099810	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34275594	0.83[AMR][1000 genomes]
rs34550457	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34552906	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34653907	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35602248	0.80[AMR][1000 genomes]
rs35701817	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35704045	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35741852	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58526289	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62010555	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62010556	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67775542	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169223	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	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
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34422348	CHRNA5	cis	Muscle Skeletal	GTEx
rs34422348	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79019400-79022000	Enhancers	A549	lung
2	chr15:79019600-79020800	Enhancers	NH-A	brain
3	chr15:79019600-79021400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:79020000-79020800	Enhancers	Fetal Stomach	stomach
5	chr15:79020200-79021200	Enhancers	Stomach Smooth Muscle	stomach
6	chr15:79020200-79021600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:79020200-79021600	Enhancers	Osteobl	bone
8	chr15:79020400-79020600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr15:79020400-79021400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:79020400-79021400	Enhancers	Rectal Smooth Muscle	rectum
11	chr15:79020400-79022000	Enhancers	Colon Smooth Muscle	Colon

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