Variant report

Variant	rs34596580
Chromosome Location	chr3:134024941-134024942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
3	chr3:134023446..134026056-chr3:134203882..134206260,2	K562	blood:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000214289	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13094988	0.83[ASN][1000 genomes]
rs1344687	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270733	0.97[ASN][1000 genomes]
rs34426406	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34591691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688449	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913236	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160848	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35369871	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234420	0.97[ASN][1000 genomes]
rs4270476	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4437113	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449291	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4470481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504146	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4510358	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4533618	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4558731	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4574266	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682661	0.97[ASN][1000 genomes]
rs4682663	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71331752	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431754	0.97[ASN][1000 genomes]
rs7614238	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621320	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641605	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644134	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7652144	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289466	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289467	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863226	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34596580	RP11-375I20.6	cis	Thyroid	GTEx
rs34596580	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs34596580	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs34596580	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134015800-134026800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:134018400-134026800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:134018600-134026800	Weak transcription	A549	lung
4	chr3:134018600-134027000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:134019000-134026800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:134020600-134026800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:134022400-134027000	Weak transcription	Fetal Lung	lung
8	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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