Variant report

Variant	rs28515553
Chromosome Location	chr21:47310565-47310566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr21:47310511-47310852	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47308979..47311967-chr21:47312189..47314453,2	MCF-7	breast:
2	chr21:47308842..47311490-chr21:47321844..47323697,2	MCF-7	breast:
3	chr21:47304723..47306559-chr21:47309917..47311783,2	MCF-7	breast:
4	chr21:47307528..47310993-chr21:47318183..47321905,4	K562	blood:

Variant related genes	Relation type
PCBP3	TF binding region
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1033366	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12626343	0.92[ASN][1000 genomes]
rs13048129	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839036	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819162	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4819163	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4819164	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57691792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62211942	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7277818	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128715	0.81[ASN][1000 genomes]
rs8130949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8132062	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8133743	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS 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	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
21	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
22	esv3415114	chr21:47310350-47310944	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47303800-47313200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr21:47304200-47313400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr21:47304200-47313400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr21:47304400-47311200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr21:47304400-47311600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr21:47304400-47311800	Enhancers	Primary T cells from cord blood	blood
7	chr21:47305000-47314200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr21:47306200-47311600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr21:47306400-47311600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr21:47306400-47311800	Enhancers	Fetal Muscle Leg	muscle
11	chr21:47306800-47311600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr21:47307000-47311200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr21:47307200-47311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr21:47307200-47313400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr21:47307400-47313400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr21:47307600-47311400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr21:47307600-47311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:47307600-47313600	Weak transcription	NHDF-Ad	bronchial
19	chr21:47307600-47313800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr21:47308000-47311600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr21:47308000-47312800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
23	chr21:47308200-47314000	Weak transcription	Left Ventricle	heart
24	chr21:47309400-47311800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr21:47309600-47311400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:47309600-47311600	Weak transcription	Thymus	Thymus
27	chr21:47309800-47311600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr21:47310000-47310600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr21:47310000-47311000	Weak transcription	Spleen	Spleen
30	chr21:47310000-47311400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr21:47310000-47313600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr21:47310200-47311400	Weak transcription	Fetal Thymus	thymus
33	chr21:47310200-47311800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr21:47310200-47313200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr21:47310200-47313600	Weak transcription	Brain Substantia Nigra	brain
36	chr21:47310200-47313800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:47310200-47313800	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:47310400-47310800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr21:47310400-47311400	Weak transcription	Placenta	Placenta
40	chr21:47310400-47311800	Weak transcription	Colonic Mucosa	Colon
41	chr21:47310400-47312000	Weak transcription	Adipose Nuclei	Adipose
42	chr21:47310400-47312600	Weak transcription	HSMMtube	muscle
43	chr21:47310400-47313200	Weak transcription	HSMM	muscle

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