Variant report

Variant	rs2838996
Chromosome Location	chr21:47214060-47214061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47208812..47212516-chr21:47213678..47217597,6	K562	blood:
2	chr21:47212372..47214255-chr21:47215488..47217482,2	MCF-7	breast:
3	chr21:47212074..47214311-chr21:47223664..47225574,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11089024	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12329841	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12329855	0.87[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	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12482648	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1467758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17351433	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2065334	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2094888	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2183596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838990	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838994	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838995	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838997	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838998	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838999	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839001	0.93[ASN][1000 genomes]
rs2839002	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839003	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35781238	0.91[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]
rs4434082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4818798	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4819151	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4819152	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55780126	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55875620	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56012600	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56036552	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56256701	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56323347	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56347571	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56378934	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58952758	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59398815	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59785950	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60604183	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61100346	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62213555	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214592	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214596	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214597	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214599	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214604	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66552772	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66991496	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7276632	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8127369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127428	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8127809	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8128722	0.84[EUR][1000 genomes];0.92[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];0.91[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9306139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9637205	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637206	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637208	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9647230	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9974491	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9977309	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9977908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9978078	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[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
rs2838996	PCBP3	cis	Heart Left Ventricle	GTEx
rs2838996	PCBP3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47197400-47214200	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47199400-47217200	Weak transcription	Spleen	Spleen
3	chr21:47208000-47217200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:47209200-47217200	Weak transcription	Gastric	stomach
5	chr21:47209600-47217200	Weak transcription	Pancreas	Pancrea
6	chr21:47213400-47217200	Weak transcription	Thymus	Thymus
7	chr21:47213400-47219800	Weak transcription	Fetal Thymus	thymus
8	chr21:47213600-47214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr21:47213600-47215000	Enhancers	HepG2	liver
10	chr21:47213800-47217000	Weak transcription	Fetal Kidney	kidney

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