Variant report

Variant	rs2838990
Chromosome Location	chr21:47171964-47171965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47170584..47173101-chr21:47174695..47177329,2	K562	blood:

Extended variants
information (count: 168 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1029014	0.86[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12151963	0.86[ASN][1000 genomes]
rs12329855	0.80[ASN][1000 genomes]
rs12381207	0.81[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]
rs12482405	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12482648	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12482750	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12483701	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13051489	0.82[ASN][1000 genomes]
rs1467758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17004790	1.00[YRI][hapmap]
rs17004799	0.86[ASN][1000 genomes]
rs17351433	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1964928	0.86[ASN][1000 genomes]
rs1989537	0.82[ASN][1000 genomes]
rs2065334	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2094888	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2150460	0.86[ASN][1000 genomes]
rs2183595	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183596	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183601	0.81[ASN][1000 genomes]
rs2838973	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838974	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838978	0.86[ASN][1000 genomes]
rs2838981	0.86[ASN][1000 genomes]
rs2838982	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838983	0.86[ASN][1000 genomes]
rs2838985	0.86[ASN][1000 genomes]
rs2838988	0.86[ASN][1000 genomes]
rs2838989	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838991	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838992	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838994	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838995	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838996	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838997	0.91[ASN][1000 genomes]
rs2838998	0.88[ASN][1000 genomes]
rs2838999	0.86[ASN][1000 genomes]
rs2839000	0.86[ASN][1000 genomes]
rs2839001	0.86[ASN][1000 genomes]
rs2839002	0.86[ASN][1000 genomes]
rs2839003	0.82[ASN][1000 genomes]
rs2839004	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839005	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839009	0.92[CEU][hapmap];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	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28625750	0.86[ASN][1000 genomes]
rs3367	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35781238	0.84[ASN][1000 genomes]
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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4347938	0.84[ASN][1000 genomes]
rs4434082	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4818795	0.84[ASN][1000 genomes]
rs4818797	0.86[ASN][1000 genomes]
rs4818798	0.96[ASN][1000 genomes]
rs4818801	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs4819134	0.81[ASN][1000 genomes]
rs4819144	0.86[ASN][1000 genomes]
rs4819151	0.86[ASN][1000 genomes]
rs4819152	0.86[ASN][1000 genomes]
rs4819156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs55707606	0.98[ASN][1000 genomes]
rs55780126	0.82[ASN][1000 genomes]
rs55875620	0.82[ASN][1000 genomes]
rs55912508	0.86[ASN][1000 genomes]
rs55923134	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55957843	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56012600	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56036552	0.84[ASN][1000 genomes]
rs56213918	0.81[ASN][1000 genomes]
rs56256701	0.85[ASN][1000 genomes]
rs56288252	0.84[ASN][1000 genomes]
rs56300316	0.86[ASN][1000 genomes]
rs56323347	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347571	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56378934	0.98[ASN][1000 genomes]
rs57057834	0.83[ASN][1000 genomes]
rs57282159	0.83[ASN][1000 genomes]
rs57328058	0.86[ASN][1000 genomes]
rs57501220	0.84[ASN][1000 genomes]
rs58925015	0.86[ASN][1000 genomes]
rs58952758	0.86[ASN][1000 genomes]
rs59398815	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59785950	0.86[ASN][1000 genomes]
rs60604183	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60988006	0.83[ASN][1000 genomes]
rs61100346	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61329313	0.86[ASN][1000 genomes]
rs61540945	0.81[ASN][1000 genomes]
rs62213277	0.84[ASN][1000 genomes]
rs62213555	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214592	0.86[ASN][1000 genomes]
rs62214596	0.86[ASN][1000 genomes]
rs62214597	0.86[ASN][1000 genomes]
rs62214599	0.86[ASN][1000 genomes]
rs62214604	0.82[ASN][1000 genomes]
rs62215031	0.84[ASN][1000 genomes]
rs62215035	0.84[ASN][1000 genomes]
rs62215040	0.84[ASN][1000 genomes]
rs62215047	0.86[ASN][1000 genomes]
rs62215048	0.86[ASN][1000 genomes]
rs62216072	0.81[ASN][1000 genomes]
rs66552772	0.98[ASN][1000 genomes]
rs66991496	0.86[ASN][1000 genomes]
rs67222545	0.81[ASN][1000 genomes]
rs67565220	0.81[ASN][1000 genomes]
rs725358	0.86[ASN][1000 genomes]
rs7276632	0.95[ASN][1000 genomes]
rs7279909	0.86[ASN][1000 genomes]
rs7280055	0.81[ASN][1000 genomes]
rs7280560	0.86[ASN][1000 genomes]
rs7283803	0.84[ASN][1000 genomes]
rs7410008	0.83[ASN][1000 genomes]
rs744506	0.83[ASN][1000 genomes]
rs767137	0.86[ASN][1000 genomes]
rs8127369	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8127428	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8127809	0.87[ASN][1000 genomes]
rs8128722	0.85[ASN][1000 genomes]
rs8133966	0.86[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs914241	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306139	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9637169	0.86[ASN][1000 genomes]
rs9637205	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637206	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637208	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9647229	0.86[ASN][1000 genomes]
rs9647230	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9974491	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975404	0.81[ASN][1000 genomes]
rs9976200	0.86[ASN][1000 genomes]
rs9976878	0.84[ASN][1000 genomes]
rs9977309	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9977908	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978078	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978158	0.86[ASN][1000 genomes]
rs9978740	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9978882	0.84[ASN][1000 genomes]
rs9981586	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838990	PCBP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47166200-47174400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr21:47166200-47176800	Weak transcription	Dnd41	blood
3	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr21:47167800-47176200	Weak transcription	NH-A	brain
5	chr21:47168400-47172000	Weak transcription	Brain Anterior Caudate	brain
6	chr21:47168400-47172400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:47168600-47187000	Weak transcription	NHDF-Ad	bronchial
8	chr21:47168800-47172400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:47168800-47183000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:47169000-47176000	Weak transcription	Primary T cells from cord blood	blood
11	chr21:47169200-47174200	Weak transcription	HSMMtube	muscle
12	chr21:47169400-47175800	Weak transcription	HSMM	muscle
13	chr21:47169800-47172000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:47169800-47172400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr21:47170000-47179800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:47170200-47188800	Weak transcription	Spleen	Spleen
17	chr21:47170600-47174600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:47170800-47188200	Weak transcription	Right Atrium	heart
19	chr21:47171800-47179400	Weak transcription	Fetal Thymus	thymus
20	chr21:47171800-47180000	Weak transcription	Thymus	Thymus
21	chr21:47171800-47186600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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