Variant report

Variant	rs2839006
Chromosome Location	chr21:47240514-47240515
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47239959..47242449-chr21:47264107..47266678,2	K562	blood:
2	chr21:46712083..46713107-chr21:47240205..47240763,3	K562	blood:
3	chr21:47240324..47241096-chr21:47342788..47343697,3	MCF-7	breast:
4	chr21:47240141..47240932-chr21:47300508..47301042,2	MCF-7	breast:
5	chr21:46974512..46975479-chr21:47240182..47241018,3	MCF-7	breast:
6	chr21:47237629..47240751-chr21:47286627..47289424,3	MCF-7	breast:
7	chr21:46961701..46963309-chr21:47239137..47240693,2	K562	blood:
8	chr21:47160450..47161017-chr21:47239857..47240766,2	MCF-7	breast:
9	chr21:46973106..46978237-chr21:47237804..47242212,8	MCF-7	breast:
10	chr21:46961245..46963279-chr21:47238506..47240896,2	MCF-7	breast:
11	chr21:47062419..47066562-chr21:47239039..47241901,3	MCF-7	breast:
12	chr21:46369368..46370314-chr21:47240169..47241031,2	K562	blood:
13	chr21:46871841..46874571-chr21:47238507..47240724,2	MCF-7	breast:
14	chr21:46975702..46976554-chr21:47240286..47241105,4	MCF-7	breast:
15	chr21:46973481..46977035-chr21:47238682..47244036,11	MCF-7	breast:
16	chr21:47114783..47115552-chr21:47240377..47241099,2	K562	blood:
17	chr21:47240289..47241171-chr21:47342639..47343656,4	MCF-7	breast:
18	chr21:47059881..47063838-chr21:47238507..47241456,3	MCF-7	breast:
19	chr21:46897608..46898629-chr21:47240205..47241125,3	K562	blood:
20	chr21:46974481..46976891-chr21:47239576..47241145,21	MCF-7	breast:
21	chr21:46975863..46976683-chr21:47240184..47241118,3	K562	blood:
22	chr21:46974938..46975481-chr21:47240107..47241154,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173638	Chromatin interaction
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11089022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11089023	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11702443	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11702478	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11702552	0.84[ASN][1000 genomes]
rs12627257	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1556335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2075885	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2150452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839007	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839012	0.89[ASN][1000 genomes]
rs2839015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839016	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2839027	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2839028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2839034	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3788219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4819145	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4819150	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61496907	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7276396	0.85[ASN][1000 genomes]
rs7281669	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs741955	0.87[ASN][1000 genomes]
rs743352	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8129118	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs8134872	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs914243	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs9306138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs971977	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9979633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47236400-47243800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:47237200-47241200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47237200-47241400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr21:47237400-47240600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr21:47237600-47240800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr21:47238000-47240600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr21:47238000-47240600	Enhancers	HMEC	breast
9	chr21:47238200-47240600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr21:47238200-47240800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:47238200-47241000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr21:47238200-47241000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:47238200-47241000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr21:47238200-47241000	Enhancers	HSMM	muscle
15	chr21:47238400-47241000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:47238400-47241000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr21:47238400-47241600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:47238600-47240800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr21:47238600-47241000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr21:47238600-47241000	Enhancers	Fetal Muscle Leg	muscle
21	chr21:47238600-47241000	Enhancers	GM12878-XiMat	blood
22	chr21:47238800-47241000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr21:47238800-47241000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr21:47238800-47241000	Enhancers	Brain Germinal Matrix	brain
25	chr21:47238800-47241800	Enhancers	Fetal Thymus	thymus
26	chr21:47239000-47240600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr21:47239000-47241000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr21:47239000-47241000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr21:47239000-47241000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:47239000-47241000	Enhancers	NH-A	brain
31	chr21:47239000-47241200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr21:47239200-47241000	Enhancers	Fetal Brain Female	brain
33	chr21:47239200-47241000	Enhancers	Fetal Stomach	stomach
34	chr21:47239200-47241000	Enhancers	A549	lung
35	chr21:47239400-47240600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr21:47239400-47240600	Enhancers	Fetal Intestine Large	intestine
37	chr21:47239400-47241000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr21:47239400-47241000	Enhancers	Fetal Brain Male	brain
39	chr21:47239400-47247200	Weak transcription	Primary T cells from cord blood	blood
40	chr21:47239600-47240600	Genic enhancers	Thymus	Thymus
41	chr21:47239600-47240600	Enhancers	HSMMtube	muscle
42	chr21:47239600-47240800	Weak transcription	NHEK	skin
43	chr21:47239800-47240600	Weak transcription	NHLF	lung
44	chr21:47239800-47240600	Enhancers	Osteobl	bone
45	chr21:47239800-47240800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr21:47240000-47240600	Enhancers	Fetal Intestine Small	intestine
47	chr21:47240200-47240600	Enhancers	Pancreas	Pancrea
48	chr21:47240200-47240600	Flanking Active TSS	HepG2	liver
49	chr21:47240200-47240800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr21:47240200-47241000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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