Variant report

Variant	rs4504146
Chromosome Location	chr3:134020548-134020549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134020501..134024033-chr3:134091484..134094450,3	MCF-7	breast:
2	chr3:134020415..134022058-chr3:134026557..134028767,2	MCF-7	breast:
3	chr3:134019644..134021494-chr3:134068815..134070339,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEP63-4	chr3:134019881-134020649	refGeneNc_1711_NR_002811

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13094988	0.88[ASN][1000 genomes]
rs1344687	0.83[ASN][1000 genomes]
rs2270733	0.83[ASN][1000 genomes]
rs34426406	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34591691	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34596580	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34688449	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34913236	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35160848	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35369871	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4131649	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4131651	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4234420	0.83[ASN][1000 genomes]
rs4437113	0.83[ASN][1000 genomes]
rs4449291	0.83[ASN][1000 genomes]
rs4470481	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4510358	0.83[ASN][1000 genomes]
rs4533618	0.85[ASN][1000 genomes]
rs4558731	0.83[ASN][1000 genomes]
rs4574266	0.83[ASN][1000 genomes]
rs4682661	0.83[ASN][1000 genomes]
rs6774600	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71331752	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431754	0.83[ASN][1000 genomes]
rs7614238	0.83[ASN][1000 genomes]
rs7621320	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7641605	0.83[ASN][1000 genomes]
rs7644134	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7652144	0.83[ASN][1000 genomes]
rs9289466	0.83[ASN][1000 genomes]
rs9289467	0.83[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
rs4504146	RP11-375I20.6	cis	Thyroid	GTEx
rs4504146	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4504146	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs4504146	RP11-375I20.6	cis	Nerve Tibial	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	chr3:134020000-134020800	Enhancers	Adipose Nuclei	Adipose
7	chr3:134020200-134020600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr3:134020400-134020600	Enhancers	Left Ventricle	heart

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