Variant report

Variant	rs62215040
Chromosome Location	chr21:47087952-47087953
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	chr21:47046713..47049334-chr21:47087367..47089551,2	MCF-7	breast:
2	chr21:47060499..47063225-chr21:47086755..47088271,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1029014	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12151963	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12381207	0.87[ASN][1000 genomes]
rs12483018	0.88[EUR][1000 genomes]
rs12483701	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1467758	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004799	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1964928	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1989537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2150460	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2183595	0.84[ASN][1000 genomes]
rs2183596	0.84[ASN][1000 genomes]
rs2183601	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838973	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838974	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838976	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838978	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838982	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838983	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838985	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838988	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838989	0.88[ASN][1000 genomes]
rs2838990	0.84[ASN][1000 genomes]
rs2838991	0.84[ASN][1000 genomes]
rs2838992	0.84[ASN][1000 genomes]
rs2838993	0.84[ASN][1000 genomes]
rs2838994	0.82[ASN][1000 genomes]
rs2838995	0.82[ASN][1000 genomes]
rs28583990	0.88[ASN][1000 genomes]
rs28625750	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28692915	0.87[EUR][1000 genomes]
rs3367	0.84[ASN][1000 genomes]
rs3920695	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347938	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434082	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818795	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818797	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818798	0.80[ASN][1000 genomes]
rs4819134	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4819144	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55707606	0.82[ASN][1000 genomes]
rs55912508	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55923134	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55957843	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56012600	0.88[ASN][1000 genomes]
rs56213918	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56288252	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300316	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56323347	0.84[ASN][1000 genomes]
rs56378934	0.82[ASN][1000 genomes]
rs57057834	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57282159	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57328058	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57501220	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57990579	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58368336	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58925015	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60604183	0.84[ASN][1000 genomes]
rs60988006	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61100346	0.82[ASN][1000 genomes]
rs61329313	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61540945	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62213277	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215031	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215035	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215047	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215048	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62216072	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62216073	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66552772	0.82[ASN][1000 genomes]
rs67222545	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67565220	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725358	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7279909	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7280055	0.87[ASN][1000 genomes]
rs7280560	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7283803	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7410008	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs744506	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs767137	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133966	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914241	0.84[ASN][1000 genomes]
rs9306139	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637169	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637205	0.82[ASN][1000 genomes]
rs9637206	0.82[ASN][1000 genomes]
rs9647229	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647230	0.84[ASN][1000 genomes]
rs9974491	0.84[ASN][1000 genomes]
rs9975404	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9976200	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976878	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977309	0.82[ASN][1000 genomes]
rs9977908	0.86[ASN][1000 genomes]
rs9978078	0.84[ASN][1000 genomes]
rs9978158	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978740	0.88[ASN][1000 genomes]
rs9978882	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981586	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
7	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62215040	PCBP3	cis	Heart Left Ventricle	GTEx
rs62215040	PCBP3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47086800-47091200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr21:47087000-47088200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr21:47087000-47090600	Weak transcription	Thymus	Thymus
4	chr21:47087200-47090400	Weak transcription	Fetal Thymus	thymus
5	chr21:47087600-47094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links