Variant report

Variant	rs28438591
Chromosome Location	chr21:47165946-47165947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr21:47165631-47167012	GM12878	blood:	n/a	n/a
2	POU2F2	chr21:47165703-47166984	GM12878	blood:	n/a	n/a
3	CTCF	chr21:47165755-47165969	GM12891	blood:	n/a	n/a
4	MYC	chr21:47165800-47165955	MCF-7	breast:	n/a	n/a
5	REST	chr21:47165811-47166968	PANC-1	pancreas:	n/a	n/a
6	BCL3	chr21:47165600-47166169	GM12878	blood:	n/a	n/a
7	CTCF	chr21:47165741-47165963	MCF-7	breast:	n/a	n/a
8	POLR2A	chr21:47165519-47167135	GM12892	blood:	n/a	n/a
9	BCL3	chr21:47165608-47166182	GM12878	blood:	n/a	n/a
10	POLR2A	chr21:47165714-47167019	GM12878	blood:	n/a	n/a
11	MYC	chr21:47165687-47166182	MCF-7	breast:	n/a	n/a
12	SIX5	chr21:47165802-47166339	GM12878	blood:	n/a	n/a
13	PAX5	chr21:47165798-47166929	GM12878	blood:	n/a	n/a
14	HEY1	chr21:47165751-47166447	K562	blood:	n/a	n/a
15	IRF4	chr21:47165874-47166936	GM12878	blood:	n/a	n/a
16	POLR2A	chr21:47165739-47166948	H1-hESC	embryonic stem cell:	n/a	n/a
17	PBX3	chr21:47165711-47166962	GM12878	blood:	n/a	n/a
18	POLR2A	chr21:47165645-47166108	MCF-7	breast:	n/a	n/a
19	POLR2A	chr21:47165787-47166087	Gliobla	brain:	n/a	n/a
20	MYC	chr21:47165731-47166020	MCF-7	breast:	n/a	n/a
21	CTCF	chr21:47165732-47166014	GM19239	blood:	n/a	n/a
22	TCF3	chr21:47165717-47166172	GM12878	blood:	n/a	n/a
23	NFATC1	chr21:47165656-47166014	GM12878	blood:	n/a	n/a
24	ZBTB33	chr21:47165869-47166925	GM12878	blood:	n/a	n/a
25	NFIC	chr21:47165680-47166145	GM12878	blood:	n/a	n/a
26	POU2F2	chr21:47165680-47167042	GM12891	blood:	n/a	n/a
27	POLR2A	chr21:47165686-47166977	GM12891	blood:	n/a	n/a
28	MYC	chr21:47165706-47166119	MCF-7	breast:	n/a	n/a
29	PBX3	chr21:47165771-47166048	GM12878	blood:	n/a	n/a
30	CTCF	chr21:47165742-47166043	MCF-7	breast:	n/a	n/a
31	CTCF	chr21:47165740-47165950	MCF-7	breast:	n/a	n/a
32	CTCF	chr21:47165756-47165962	NHEK	skin:	n/a	n/a
33	BCL11A	chr21:47165800-47166974	GM12878	blood:	n/a	n/a
34	TCF3	chr21:47165596-47167097	GM12878	blood:	n/a	n/a
35	POLR2A	chr21:47165622-47166179	MCF-7	breast:	n/a	n/a
36	NFATC1	chr21:47165554-47166182	GM12878	blood:	n/a	n/a
37	CTCF	chr21:47165731-47166079	MCF-7	breast:	n/a	n/a
38	IRF4	chr21:47165926-47166909	GM12878	blood:	n/a	n/a
39	CTCF	chr21:47165718-47166018	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr21:47165748-47165955	GM12892	blood:	n/a	n/a
41	POLR2A	chr21:47165694-47166982	GM12891	blood:	n/a	n/a
42	POU2F2	chr21:47165679-47167041	GM12891	blood:	n/a	n/a
43	POU2F2	chr21:47165766-47166957	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47163262..47166071-chr21:47166179..47167744,2	MCF-7	breast:
2	chr21:47155045..47157882-chr21:47165789..47168073,2	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11702850	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11911839	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2150452	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2297293	0.81[ASN][1000 genomes]
rs2330245	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2838984	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819146	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819150	0.81[EUR][1000 genomes]
rs62213280	0.83[ASN][1000 genomes]
rs7278438	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7281669	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129304	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9306138	0.80[ASN][1000 genomes]
rs9306141	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs971977	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977795	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9978181	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9979633	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
11	esv3438685	chr21:47163624-47168822	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	esv3377547	chr21:47164324-47167922	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3395748	chr21:47164324-47168022	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:47156600-47168000	Weak transcription	Brain Angular Gyrus	brain
3	chr21:47157000-47168200	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:47157800-47167400	Weak transcription	HSMMtube	muscle
5	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr21:47159000-47168000	Weak transcription	Brain Anterior Caudate	brain
7	chr21:47162400-47167200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:47162400-47167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:47162400-47167600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:47163000-47167400	Weak transcription	NHDF-Ad	bronchial
11	chr21:47164200-47167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:47164600-47166200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:47164600-47168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr21:47164800-47166200	ZNF genes & repeats	Thymus	Thymus
15	chr21:47165000-47166200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr21:47165000-47166200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr21:47165000-47169000	Strong transcription	Primary T cells from cord blood	blood
18	chr21:47165200-47166000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
19	chr21:47165400-47166000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:47165400-47166000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:47165400-47166000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:47165400-47166200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:47165400-47166200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:47165400-47166200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:47165400-47166200	ZNF genes & repeats	Dnd41	blood
26	chr21:47165600-47166000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:47165600-47166000	ZNF genes & repeats	Gastric	stomach
28	chr21:47165600-47166000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
29	chr21:47165600-47166200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:47165600-47166200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
31	chr21:47165600-47166200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr21:47165600-47166200	ZNF genes & repeats	HSMM	muscle
33	chr21:47165600-47167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr21:47165800-47166000	ZNF genes & repeats	Adipose Nuclei	Adipose
35	chr21:47165800-47166200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr21:47165800-47166200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr21:47165800-47166200	ZNF genes & repeats	Spleen	Spleen
38	chr21:47165800-47167600	Strong transcription	Fetal Thymus	thymus
39	chr21:47165800-47171000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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