Variant report

Variant	rs12329855
Chromosome Location	chr21:47204727-47204728
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	chr21:47204063..47206978-chr21:47208624..47210264,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12329841	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12482648	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12482853	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2094888	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2183595	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2183596	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838989	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838990	0.80[ASN][1000 genomes]
rs2838991	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838992	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838993	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838994	0.81[EUR][1000 genomes]
rs2838995	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838996	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838997	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2838998	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2838999	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2839000	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2839002	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2839003	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2839004	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2839005	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2839009	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28583990	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3367	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818798	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818801	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4819151	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4819152	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55707606	0.82[ASN][1000 genomes]
rs55780126	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55875620	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56012600	0.80[ASN][1000 genomes]
rs56036552	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56256701	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56323347	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56347571	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56378934	0.82[ASN][1000 genomes]
rs58952758	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59398815	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59785950	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60604183	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61100346	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62213555	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214592	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62214596	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62214597	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62214599	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62214604	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66552772	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66991496	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7276632	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8127369	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8127809	0.80[ASN][1000 genomes]
rs8128722	0.83[ASN][1000 genomes]
rs914241	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9637205	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9637206	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9647230	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9974491	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9977309	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9977908	0.80[EUR][1000 genomes]
rs9978078	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9978740	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	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
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12329855	PCBP3	cis	Heart Left Ventricle	GTEx
rs12329855	PCBP3	cis	Muscle Skeletal	GTEx
rs12329855	PCBP3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47188800-47208000	Weak transcription	NHDF-Ad	bronchial
2	chr21:47197400-47214200	Weak transcription	Primary T cells from cord blood	blood
3	chr21:47199200-47212800	Weak transcription	Fetal Thymus	thymus
4	chr21:47199400-47206600	Weak transcription	Thymus	Thymus
5	chr21:47199400-47217200	Weak transcription	Spleen	Spleen

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