Variant report

Variant	rs62228216
Chromosome Location	chr21:45623518-45623519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45621565..45624005-chr21:45712576..45714212,3	MCF-7	breast:
2	chr21:45620341..45625358-chr21:45718389..45721509,5	MCF-7	breast:
3	chr21:45588739..45594310-chr21:45621185..45624296,6	MCF-7	breast:
4	chr21:45552930..45554458-chr21:45622046..45624839,2	MCF-7	breast:
5	chr21:45622629..45624491-chr21:45663848..45665509,2	MCF-7	breast:
6	chr21:45619816..45631884-chr21:45656529..45663802,30	MCF-7	breast:
7	chr21:45621014..45624737-chr21:45625090..45629806,7	K562	blood:
8	chr21:45580625..45582180-chr21:45622469..45623971,2	MCF-7	breast:
9	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
10	chr21:45621411..45624934-chr21:45718058..45721352,4	MCF-7	breast:
11	chr21:45621786..45624650-chr21:45632661..45635247,3	MCF-7	breast:
12	chr21:45622485..45624278-chr21:45668242..45670471,2	MCF-7	breast:
13	chr21:45621014..45626357-chr21:45626432..45630019,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000232010	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000160221	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs3746959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55708341	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55736164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132007	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56299324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58139755	0.80[AFR][1000 genomes]
rs58911644	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59380543	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62228209	0.80[EUR][1000 genomes]
rs62228210	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6518350	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6518351	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7282137	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
12	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
13	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	esv994385	chr21:45617619-45623578	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv587730	chr21:45619367-45627976	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv1794351	chr21:45619474-45627976	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	esv1798512	chr21:45619474-45629565	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	esv1834007	chr21:45619474-45629565	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv587738	chr21:45620353-45628374	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45616800-45626600	Weak transcription	Thymus	Thymus
2	chr21:45617000-45626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr21:45617200-45624000	Weak transcription	Gastric	stomach
4	chr21:45617200-45626200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr21:45617400-45624200	Weak transcription	Brain Substantia Nigra	brain
6	chr21:45617400-45624200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr21:45617400-45626000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr21:45620000-45623600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr21:45622000-45624200	Enhancers	Fetal Thymus	thymus
10	chr21:45622000-45625000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:45622000-45625600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:45622200-45623800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr21:45622200-45624600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr21:45622200-45624600	Weak transcription	Small Intestine	intestine
15	chr21:45622200-45625000	Enhancers	Spleen	Spleen
16	chr21:45622200-45625400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr21:45622200-45626200	Enhancers	Primary B cells from cord blood	blood
18	chr21:45622200-45626800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:45622200-45627000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr21:45622400-45623800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr21:45622400-45623800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr21:45622400-45624400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr21:45622400-45624600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr21:45622400-45625400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr21:45622400-45625400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr21:45622400-45627000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr21:45622600-45623800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr21:45622600-45623800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr21:45622600-45623800	Weak transcription	Pancreas	Pancrea
30	chr21:45622600-45624000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr21:45622600-45624200	Bivalent Enhancer	Fetal Stomach	stomach
32	chr21:45622600-45624400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr21:45622600-45624600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:45622600-45624600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr21:45622600-45624800	Enhancers	Primary hematopoietic stem cells	blood
36	chr21:45622600-45626000	Enhancers	Primary B cells from peripheral blood	blood
37	chr21:45622800-45629800	Enhancers	Placenta	Placenta
38	chr21:45623000-45623800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
39	chr21:45623000-45624000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:45623000-45624000	Weak transcription	Brain Anterior Caudate	brain
41	chr21:45623000-45624000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr21:45623000-45624000	Weak transcription	Esophagus	oesophagus
43	chr21:45623000-45624000	Weak transcription	Right Atrium	heart
44	chr21:45623000-45624000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr21:45623000-45624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr21:45623000-45624200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr21:45623000-45624200	Weak transcription	Fetal Lung	lung
48	chr21:45623000-45624400	Enhancers	Left Ventricle	heart
49	chr21:45623000-45624400	Enhancers	HMEC	breast
50	chr21:45623000-45624600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links