Variant report

Variant	rs4672066
Chromosome Location	chr2:55956223-55956224
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	chr2:55952706..55954305-chr2:55954375..55956858,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10180127	0.87[ASN][1000 genomes]
rs10207466	0.92[ASN][1000 genomes]
rs10496050	0.82[JPT][hapmap]
rs1084522	0.90[JPT][hapmap]
rs1084525	0.90[JPT][hapmap]
rs1346792	0.94[ASN][1000 genomes]
rs1346793	0.94[ASN][1000 genomes]
rs1579497	0.92[ASN][1000 genomes]
rs1975487	0.81[JPT][hapmap]
rs2586950	0.90[JPT][hapmap]
rs2627765	0.82[JPT][hapmap]
rs2627775	0.90[JPT][hapmap]
rs2627776	0.90[JPT][hapmap]
rs2868428	0.82[ASN][1000 genomes]
rs35504023	0.82[JPT][hapmap]
rs4671257	0.85[ASN][1000 genomes]
rs6545506	0.81[JPT][hapmap]
rs6717410	0.94[ASN][1000 genomes]
rs6728604	0.92[ASN][1000 genomes]
rs706548	0.90[JPT][hapmap]
rs7557041	0.92[ASN][1000 genomes]
rs7589673	0.82[ASN][1000 genomes]
rs782584	0.90[JPT][hapmap]
rs782586	0.90[JPT][hapmap]
rs782588	0.90[JPT][hapmap]
rs782590	0.90[JPT][hapmap]
rs782595	0.90[JPT][hapmap]
rs782602	0.90[JPT][hapmap]
rs782606	1.00[JPT][hapmap]
rs782607	0.81[ASN][1000 genomes]
rs782629	0.81[JPT][hapmap]
rs782632	0.82[JPT][hapmap]
rs782652	0.90[JPT][hapmap]
rs9677174	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672066	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55949200-55963200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:55955400-55957000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:55955600-55956800	Enhancers	Adipose Nuclei	Adipose
4	chr2:55955800-55956800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:55955800-55960000	Weak transcription	Fetal Stomach	stomach

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