Variant report

Variant	rs10084560
Chromosome Location	chr21:45341186-45341187
allele	C/T
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	EBF1	chr21:45341171-45342328	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
2	MTA3	chr21:45340954-45342916	GM12878	blood:	n/a	n/a
3	EBF1	chr21:45341130-45342390	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
4	POLR2A	chr21:45340945-45342783	GM12878	blood:	n/a	n/a
5	EBF1	chr21:45341152-45342483	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
6	POLR2A	chr21:45341093-45342803	K562	blood:	n/a	n/a
7	POLR2A	chr21:45339849-45343820	GM12878	blood:	n/a	n/a
8	CHD1	chr21:45341093-45342359	GM12878	blood:	n/a	n/a
9	POLR2A	chr21:45341113-45341213	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45320627..45322266-chr21:45340238..45342463,2	MCF-7	breast:
2	chr21:45340959..45342900-chr21:45429415..45431633,2	K562	blood:
3	chr21:45340526..45342218-chr21:45368922..45371693,3	K562	blood:
4	chr21:45341019..45344772-chr21:45346724..45351005,5	MCF-7	breast:
5	chr21:45280312..45282784-chr21:45340621..45342718,2	K562	blood:
6	chr21:45277545..45279138-chr21:45340639..45343236,2	K562	blood:
7	chr21:45283298..45287513-chr21:45338855..45343382,5	K562	blood:
8	chr21:45302191..45305898-chr21:45340704..45344205,3	K562	blood:
9	chr21:45284242..45287080-chr21:45339493..45341946,2	MCF-7	breast:
10	chr21:45340007..45343701-chr21:45343921..45347389,3	MCF-7	breast:
11	chr21:45228155..45231014-chr21:45339166..45342042,3	K562	blood:
12	chr21:45334570..45338840-chr21:45339112..45343099,4	MCF-7	breast:
13	chr21:45340582..45343200-chr21:45355048..45357219,2	MCF-7	breast:
14	chr21:45283663..45287678-chr21:45338795..45345768,12	K562	blood:
15	chr21:45194660..45196232-chr21:45340700..45342794,3	K562	blood:

Variant related genes	Relation type
AGPAT3	TF binding region
RNU6-859P	TF binding region
ENSG00000215458	Chromatin interaction
ENSG00000160216	Chromatin interaction
ENSG00000160213	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10084623	1.00[AMR][1000 genomes]
rs11909584	1.00[AMR][1000 genomes]
rs60998087	1.00[AMR][1000 genomes]
rs9306170	1.00[AMR][1000 genomes]
rs9974773	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9977077	1.00[AMR][1000 genomes]
rs9977718	1.00[AMR][1000 genomes]
rs9981524	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9981945	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9982231	1.00[AMR][1000 genomes]
rs9983454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9984820	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1066284	chr21:45249549-45343314	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45333000-45341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr21:45334200-45341200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:45336000-45344400	Enhancers	Liver	Liver
4	chr21:45336400-45351600	Weak transcription	Fetal Brain Female	brain
5	chr21:45336800-45341200	Weak transcription	Fetal Lung	lung
6	chr21:45337000-45342000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr21:45337200-45341200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr21:45337200-45342400	Weak transcription	Colon Smooth Muscle	Colon
9	chr21:45337200-45350800	Weak transcription	Fetal Brain Male	brain
10	chr21:45337400-45341200	Weak transcription	Brain Anterior Caudate	brain
11	chr21:45337400-45342200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr21:45337400-45342200	Weak transcription	Brain Hippocampus Middle	brain
13	chr21:45337400-45342200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr21:45337400-45343200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:45337400-45344400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr21:45337600-45341200	Weak transcription	Ovary	ovary
17	chr21:45337600-45341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:45337600-45341600	Weak transcription	Fetal Heart	heart
19	chr21:45337600-45341600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr21:45337600-45342000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr21:45337600-45342200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr21:45337600-45342600	Weak transcription	Brain Substantia Nigra	brain
23	chr21:45337600-45343200	Weak transcription	NHEK	skin
24	chr21:45337600-45344200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr21:45337600-45344400	Weak transcription	Dnd41	blood
26	chr21:45337600-45358600	Weak transcription	Osteobl	bone
27	chr21:45337800-45341200	Weak transcription	Pancreas	Pancrea
28	chr21:45338200-45341200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr21:45338200-45341200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr21:45338200-45341200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr21:45338200-45343200	Weak transcription	HSMM	muscle
32	chr21:45338400-45341600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr21:45338400-45341600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:45338400-45341600	Weak transcription	Small Intestine	intestine
35	chr21:45338600-45341400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr21:45338800-45341200	Weak transcription	Primary B cells from cord blood	blood
37	chr21:45338800-45341400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr21:45338800-45341600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr21:45338800-45342200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr21:45338800-45342200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr21:45338800-45358600	Weak transcription	Hela-S3	cervix
42	chr21:45339600-45341600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr21:45339600-45342000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr21:45339600-45342600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:45339600-45342600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr21:45339600-45342600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr21:45339600-45342800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr21:45339600-45344000	Enhancers	Gastric	stomach
49	chr21:45339600-45344400	Enhancers	Fetal Intestine Large	intestine
50	chr21:45339800-45341200	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links