Variant report

Variant	rs62228168
Chromosome Location	chr21:45596596-45596597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr21:45595732-45596725	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr21:45595796-45596614	MCF-7	breast:	n/a	n/a
3	JUND	chr21:45596541-45596739	HepG2	liver:	n/a	n/a
4	TCF12	chr21:45595920-45596623	ECC-1	luminal epithelium:	n/a	n/a
5	RCOR1	chr21:45596516-45596781	K562	blood:	n/a	n/a
6	ELF1	chr21:45596416-45597264	GM12878	blood:	n/a	n/a
7	POLR2A	chr21:45595794-45596705	GM12878	blood:	n/a	n/a
8	MTA3	chr21:45595948-45596736	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45551956..45555178-chr21:45594619..45596938,3	MCF-7	breast:
2	chr21:45546961..45549200-chr21:45595303..45598230,2	K562	blood:
3	chr21:45595936..45596637-chr21:45660422..45661271,3	MCF-7	breast:
4	chr21:45595676..45596652-chr21:45615636..45617063,9	MCF-7	breast:
5	chr21:45595723..45596653-chr21:45604850..45605608,2	MCF-7	breast:
6	chr21:45595676..45596715-chr21:45615636..45617128,25	MCF-7	breast:
7	chr21:45590531..45598113-chr21:45625237..45630055,9	MCF-7	breast:
8	chr21:45572891..45575841-chr21:45596465..45598354,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267913	TF binding region
ENSG00000160223	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000241945	Chromatin interaction
ENSG00000160221	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2838510	0.84[EUR][1000 genomes]
rs58954796	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59514931	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60750077	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61648450	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62228169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62228171	1.00[ASN][1000 genomes]
rs62228172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62228173	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62228182	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9980063	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv913893	chr21:45508561-45603746	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	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
9	nsv913896	chr21:45528919-45603746	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45584200-45598800	Weak transcription	Ovary	ovary
2	chr21:45592000-45598000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:45593200-45601000	Weak transcription	Right Atrium	heart
4	chr21:45593400-45602200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr21:45593400-45605000	Weak transcription	Small Intestine	intestine
6	chr21:45593600-45596600	Enhancers	Fetal Thymus	thymus
7	chr21:45593600-45604800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr21:45594400-45596600	Enhancers	Primary hematopoietic stem cells	blood
9	chr21:45594600-45596600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr21:45595000-45597600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr21:45595200-45597000	Enhancers	Placenta	Placenta
12	chr21:45595200-45597200	Enhancers	Gastric	stomach
13	chr21:45595200-45597600	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr21:45595400-45596600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr21:45595400-45597400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr21:45595400-45597600	Flanking Active TSS	GM12878-XiMat	blood
17	chr21:45595600-45596600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr21:45595800-45596600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr21:45595800-45596600	Enhancers	Esophagus	oesophagus
20	chr21:45595800-45597200	Enhancers	Spleen	Spleen
21	chr21:45595800-45597600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr21:45595800-45598000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:45595800-45598200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr21:45595800-45598400	Enhancers	Fetal Muscle Leg	muscle
25	chr21:45596000-45596600	Flanking Active TSS	Colonic Mucosa	Colon
26	chr21:45596000-45596600	Enhancers	Pancreas	Pancrea
27	chr21:45596000-45596600	Active TSS	Rectal Smooth Muscle	rectum
28	chr21:45596000-45596800	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr21:45596000-45597200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:45596000-45601400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr21:45596200-45596600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr21:45596200-45596800	Enhancers	Adipose Nuclei	Adipose
33	chr21:45596200-45597200	Active TSS	Brain Hippocampus Middle	brain
34	chr21:45596200-45597200	Enhancers	Lung	lung
35	chr21:45596400-45596600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr21:45596400-45596600	Flanking Active TSS	HepG2	liver
37	chr21:45596400-45597200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr21:45596400-45597400	Enhancers	Stomach Mucosa	stomach
39	chr21:45596400-45597800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr21:45596400-45600600	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links