Variant report

Variant	rs1029014
Chromosome Location	chr21:47124173-47124174
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	chr21:47122343..47125254-chr21:47159876..47161705,2	MCF-7	breast:
2	chr21:47119012..47122239-chr21:47123124..47126324,3	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11089024	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12151963	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12381207	0.85[ASN][1000 genomes]
rs12481867	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12481913	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482094	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482377	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482750	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482853	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12483018	0.85[EUR][1000 genomes]
rs12483701	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051489	0.80[ASN][1000 genomes]
rs1467758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17004799	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351433	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1964928	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989537	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2065334	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2150460	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2183596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2183601	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838978	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838981	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838983	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838985	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838988	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838990	0.86[ASN][1000 genomes]
rs2838991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838994	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838995	0.84[ASN][1000 genomes]
rs2839004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839009	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839013	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2839014	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839026	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839029	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839032	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28583990	0.91[ASN][1000 genomes]
rs28625750	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28692915	0.83[EUR][1000 genomes]
rs3367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3788208	0.81[JPT][hapmap]
rs3788211	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788224	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3788227	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3920695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347938	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4434082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818795	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818797	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818798	0.83[ASN][1000 genomes]
rs4818801	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819134	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4819144	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs55707606	0.84[ASN][1000 genomes]
rs55912508	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923134	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957843	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012600	0.91[ASN][1000 genomes]
rs56213918	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56288252	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56300316	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323347	0.86[ASN][1000 genomes]
rs56378934	0.84[ASN][1000 genomes]
rs57057834	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57282159	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57328058	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57501220	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57990579	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58368336	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58925015	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60604183	0.86[ASN][1000 genomes]
rs60988006	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61100346	0.84[ASN][1000 genomes]
rs61329313	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61540945	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62213277	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215031	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215035	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215040	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215047	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215048	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62216072	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62216073	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66552772	0.84[ASN][1000 genomes]
rs67222545	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67565220	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725358	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276632	0.82[ASN][1000 genomes]
rs7279909	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280055	0.85[ASN][1000 genomes]
rs7280560	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283803	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7410008	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs744506	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs767137	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8133966	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs914241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9306139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637169	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637205	0.84[ASN][1000 genomes]
rs9637206	0.84[ASN][1000 genomes]
rs9637208	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9647229	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647230	0.86[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9974491	0.86[ASN][1000 genomes]
rs9975404	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976200	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976878	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9977309	0.84[ASN][1000 genomes]
rs9977908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9978078	0.86[ASN][1000 genomes]
rs9978158	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9978882	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981586	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1029014	PCBP3	cis	Nerve Tibial	GTEx
rs1029014	PCBP3	cis	Heart Left Ventricle	GTEx
rs1029014	PCBP3	cis	Muscle Skeletal	GTEx
rs1029014	PCBP3	cis	lung	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47102600-47138400	Weak transcription	Fetal Thymus	thymus
2	chr21:47118600-47125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:47119000-47128800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47119400-47133200	Weak transcription	Thymus	Thymus
5	chr21:47119400-47134800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:47120600-47126200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:47121000-47126400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:47123800-47124600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr21:47123800-47124600	Enhancers	Fetal Stomach	stomach
10	chr21:47124000-47124400	Enhancers	Spleen	Spleen
11	chr21:47124000-47124600	Enhancers	Fetal Muscle Trunk	muscle

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