Variant report

Variant	rs59785950
Chromosome Location	chr21:47225742-47225743
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	chr21:47224097..47226924-chr21:47229345..47232171,3	K562	blood:
2	chr21:47220341..47222961-chr21:47224438..47226331,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10854472	0.82[ASN][1000 genomes]
rs11089024	0.82[ASN][1000 genomes]
rs12329841	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12329855	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12481867	0.82[ASN][1000 genomes]
rs12481913	0.80[ASN][1000 genomes]
rs12481970	0.81[ASN][1000 genomes]
rs12481977	0.82[ASN][1000 genomes]
rs12482010	0.81[ASN][1000 genomes]
rs12482094	0.82[ASN][1000 genomes]
rs12482377	0.82[ASN][1000 genomes]
rs12482405	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12482648	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12482853	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17351419	0.82[ASN][1000 genomes]
rs17351433	0.82[ASN][1000 genomes]
rs2094888	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2183595	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2183596	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838989	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838990	0.86[ASN][1000 genomes]
rs2838991	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838992	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838993	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838994	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838995	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838996	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838997	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838998	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838999	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839000	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839001	1.00[ASN][1000 genomes]
rs2839002	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839003	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839004	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839005	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839009	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839013	0.82[ASN][1000 genomes]
rs2839014	0.86[ASN][1000 genomes]
rs2839026	0.82[ASN][1000 genomes]
rs28583990	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3367	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35781238	0.95[ASN][1000 genomes]
rs3788209	0.82[ASN][1000 genomes]
rs3788211	0.82[ASN][1000 genomes]
rs3788215	0.80[ASN][1000 genomes]
rs3788216	0.82[ASN][1000 genomes]
rs3788220	0.82[ASN][1000 genomes]
rs3788227	0.82[ASN][1000 genomes]
rs4818798	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818801	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818802	0.82[ASN][1000 genomes]
rs4818803	0.82[ASN][1000 genomes]
rs4819151	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819152	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819154	0.83[ASN][1000 genomes]
rs4819155	0.82[ASN][1000 genomes]
rs4819156	0.82[ASN][1000 genomes]
rs4819157	0.82[ASN][1000 genomes]
rs55707606	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55780126	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55856400	0.82[ASN][1000 genomes]
rs55875620	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55912352	0.82[ASN][1000 genomes]
rs55927540	0.86[ASN][1000 genomes]
rs56012600	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56036552	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56256701	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56323347	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56347571	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56378934	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58952758	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59398815	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60604183	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61063225	0.80[ASN][1000 genomes]
rs61100346	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62211883	0.82[ASN][1000 genomes]
rs62211885	0.82[ASN][1000 genomes]
rs62211886	0.82[ASN][1000 genomes]
rs62211895	0.82[ASN][1000 genomes]
rs62211925	0.82[ASN][1000 genomes]
rs62211926	0.82[ASN][1000 genomes]
rs62213555	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214592	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214596	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214599	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214604	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66523344	0.82[ASN][1000 genomes]
rs66552772	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66991496	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67055992	0.82[ASN][1000 genomes]
rs67878041	0.82[ASN][1000 genomes]
rs72497640	0.84[AMR][1000 genomes]
rs7276632	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7280173	0.82[ASN][1000 genomes]
rs8127369	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8127428	0.82[ASN][1000 genomes]
rs8127809	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8128722	0.85[ASN][1000 genomes]
rs914241	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9637205	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9637206	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9637208	0.82[ASN][1000 genomes]
rs9647230	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964975	0.82[ASN][1000 genomes]
rs9974491	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9977309	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9977908	0.85[EUR][1000 genomes]
rs9978078	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9978740	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9983770	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv3515526	chr21:47223277-47225849	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
13	esv3515527	chr21:47223407-47225851	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59785950	PCBP3	cis	lung	GTEx
rs59785950	PCBP3	cis	Muscle Skeletal	GTEx
rs59785950	PCBP3	cis	Heart Left Ventricle	GTEx
rs59785950	PCBP3	cis	Nerve Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47226200	Weak transcription	Gastric	stomach
2	chr21:47217800-47229400	Weak transcription	Esophagus	oesophagus
3	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
4	chr21:47218000-47231000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr21:47218000-47240200	Weak transcription	Pancreas	Pancrea
6	chr21:47221000-47236400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:47221200-47239800	Weak transcription	Spleen	Spleen
8	chr21:47224000-47239000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:47225400-47226800	Strong transcription	Thymus	Thymus
10	chr21:47225600-47226800	Genic enhancers	Fetal Thymus	thymus

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