Variant report

Variant	rs28438743
Chromosome Location	chr21:46330580-46330581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46330559-46332504	GM12878	blood:	n/a	n/a
2	BHLHE40	chr21:46330425-46330604	K562	blood:	n/a	chr21:46330478-46330487 chr21:46330478-46330487
3	STAT5A	chr21:46330289-46332278	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:46330287-46332619	GM19099	blood:	n/a	n/a
5	POLR2A	chr21:46330081-46332394	HL-60	blood:	n/a	n/a
6	BHLHE40	chr21:46330150-46330669	HepG2	liver:	n/a	chr21:46330478-46330487 chr21:46330478-46330487

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46220308..46222402-chr21:46328701..46333083,4	MCF-7	breast:
2	chr21:46233435..46239577-chr21:46329843..46334353,8	MCF-7	breast:
3	chr21:46292072..46295985-chr21:46328607..46334685,5	MCF-7	breast:
4	chr21:46329082..46330961-chr21:46492504..46494830,2	MCF-7	breast:
5	chr21:46328608..46330967-chr21:46493545..46495065,2	K562	blood:
6	chr21:46220726..46223224-chr21:46328113..46331561,4	K562	blood:
7	chr21:46235459..46240790-chr21:46329963..46334235,7	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf67-8	chr21:46330515-46330656	NONHSAT082892
2	lnc-C21orf67-8	chr21:46330199-46330603	NONHSAT082893
3	lnc-C21orf67-8	chr21:46330236-46330700	NONHSAT082894

No data

Variant related genes	Relation type
ITGB2	TF binding region
ENSG00000268856	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs58645077	1.00[AMR][1000 genomes]
rs73380573	1.00[AMR][1000 genomes]
rs73382608	1.00[AMR][1000 genomes]
rs73382614	1.00[AMR][1000 genomes]
rs9976146	1.00[AMR][1000 genomes]
rs9980891	1.00[AMR][1000 genomes]
rs9983887	1.00[AMR][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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv470908	chr21:46298869-46335580	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv913970	chr21:46305175-46487831	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv933240	chr21:46305956-46371518	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv913974	chr21:46306161-46430792	Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv913975	chr21:46306161-46459432	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv913976	chr21:46306161-46487831	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
13	nsv1064518	chr21:46317690-46413159	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46295600-46338800	Weak transcription	Right Atrium	heart
2	chr21:46320000-46331000	Weak transcription	Brain Substantia Nigra	brain
3	chr21:46322000-46331400	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr21:46322600-46330800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr21:46322800-46330600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr21:46322800-46330600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr21:46322800-46330800	Weak transcription	Brain Anterior Caudate	brain
8	chr21:46323000-46330800	Weak transcription	Esophagus	oesophagus
9	chr21:46324400-46330600	Weak transcription	Stomach Mucosa	stomach
10	chr21:46324800-46330600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr21:46324800-46330800	Weak transcription	Gastric	stomach
12	chr21:46324800-46335400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr21:46325000-46331200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:46326200-46330800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr21:46326800-46331000	Genic enhancers	Fetal Thymus	thymus
16	chr21:46326800-46331600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr21:46326800-46335200	Enhancers	Placenta	Placenta
18	chr21:46327000-46330800	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr21:46327000-46332400	Bivalent Enhancer	Fetal Stomach	stomach
20	chr21:46327800-46331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr21:46328200-46331000	Weak transcription	HUVEC	blood vessel
22	chr21:46328200-46331600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr21:46328400-46330800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr21:46328600-46332400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr21:46328600-46335400	Enhancers	Liver	Liver
26	chr21:46328800-46331200	Genic enhancers	Spleen	Spleen
27	chr21:46328800-46331600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr21:46329000-46331200	Weak transcription	GM12878-XiMat	blood
29	chr21:46329200-46330600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr21:46329200-46330600	Weak transcription	Lung	lung
31	chr21:46329200-46330800	Enhancers	Stomach Smooth Muscle	stomach
32	chr21:46329200-46331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr21:46329200-46331000	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr21:46329400-46330800	Genic enhancers	Dnd41	blood
35	chr21:46329400-46331200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr21:46329400-46332400	Enhancers	Colon Smooth Muscle	Colon
37	chr21:46329600-46330600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr21:46329600-46331000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr21:46329600-46334200	Enhancers	Fetal Muscle Leg	muscle
40	chr21:46329800-46330600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr21:46329800-46330800	Enhancers	Primary B cells from cord blood	blood
42	chr21:46329800-46330800	Enhancers	Primary T cells from cord blood	blood
43	chr21:46329800-46331000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr21:46329800-46331000	Enhancers	Fetal Brain Male	brain
45	chr21:46329800-46331400	Bivalent Enhancer	Fetal Lung	lung
46	chr21:46330000-46330600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr21:46330000-46330600	Flanking Active TSS	HepG2	liver
48	chr21:46330000-46330800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr21:46330000-46330800	Enhancers	Hela-S3	cervix
50	chr21:46330000-46331000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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