Variant report

Variant	rs9977309
Chromosome Location	chr21:47199202-47199203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 160 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1029014	0.84[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12151963	0.84[ASN][1000 genomes]
rs12329841	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12329855	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12481867	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12481913	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482094	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482377	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482405	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12482648	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12482750	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12483701	0.84[ASN][1000 genomes]
rs13051489	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1467758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17004799	0.84[ASN][1000 genomes]
rs17351433	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1964928	0.84[ASN][1000 genomes]
rs2065334	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2094888	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150460	0.84[ASN][1000 genomes]
rs2183595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2183596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2838974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2838976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2838978	0.84[ASN][1000 genomes]
rs2838981	0.84[ASN][1000 genomes]
rs2838982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838983	0.84[ASN][1000 genomes]
rs2838985	0.84[ASN][1000 genomes]
rs2838988	0.84[ASN][1000 genomes]
rs2838989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838990	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838994	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838995	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838996	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838997	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838998	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838999	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839000	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839001	0.88[ASN][1000 genomes]
rs2839002	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839003	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2839004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2839005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2839009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2839013	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2839014	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839026	0.85[CEU][hapmap];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	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28625750	0.84[ASN][1000 genomes]
rs3367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35781238	0.86[ASN][1000 genomes]
rs3788208	0.81[JPT][hapmap]
rs3788211	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.85[CEU][hapmap];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	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3920695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4347938	0.82[ASN][1000 genomes]
rs4434082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818795	0.81[ASN][1000 genomes]
rs4818797	0.84[ASN][1000 genomes]
rs4818798	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4819144	0.84[ASN][1000 genomes]
rs4819151	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4819152	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4819156	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs55707606	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780126	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55875620	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55912508	0.84[ASN][1000 genomes]
rs55923134	0.84[ASN][1000 genomes]
rs55957843	0.84[ASN][1000 genomes]
rs56012600	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56036552	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56256701	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56288252	0.82[ASN][1000 genomes]
rs56300316	0.84[ASN][1000 genomes]
rs56323347	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56347571	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56378934	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57057834	0.81[ASN][1000 genomes]
rs57282159	0.81[ASN][1000 genomes]
rs57328058	0.84[ASN][1000 genomes]
rs57501220	0.82[ASN][1000 genomes]
rs58925015	0.84[ASN][1000 genomes]
rs58952758	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59398815	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59785950	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60604183	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60988006	0.81[ASN][1000 genomes]
rs61100346	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61329313	0.84[ASN][1000 genomes]
rs62213277	0.82[ASN][1000 genomes]
rs62213555	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214592	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214596	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214597	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214599	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214604	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62215031	0.82[ASN][1000 genomes]
rs62215035	0.82[ASN][1000 genomes]
rs62215040	0.82[ASN][1000 genomes]
rs62215047	0.84[ASN][1000 genomes]
rs62215048	0.84[ASN][1000 genomes]
rs66552772	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66991496	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs725358	0.84[ASN][1000 genomes]
rs7276632	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7279909	0.84[ASN][1000 genomes]
rs7280560	0.84[ASN][1000 genomes]
rs7283803	0.82[ASN][1000 genomes]
rs7410008	0.81[ASN][1000 genomes]
rs744506	0.81[ASN][1000 genomes]
rs767137	0.84[ASN][1000 genomes]
rs8127369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8127428	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8127809	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128722	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8133966	0.84[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs914241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9306139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9637169	0.84[ASN][1000 genomes]
rs9637205	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637206	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637208	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9647229	0.84[ASN][1000 genomes]
rs9647230	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9974491	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976200	0.84[ASN][1000 genomes]
rs9976878	0.82[ASN][1000 genomes]
rs9977908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9978078	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978158	0.84[ASN][1000 genomes]
rs9978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978882	0.82[ASN][1000 genomes]
rs9981586	0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9977309	PCBP3	cis	Muscle Skeletal	GTEx
rs9977309	PCBP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:6 , 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	chr21:47198000-47199400	ZNF genes & repeats	Spleen	Spleen
4	chr21:47198200-47199400	Strong transcription	Thymus	Thymus
5	chr21:47199200-47199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:47199200-47212800	Weak transcription	Fetal Thymus	thymus

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