Variant report

Variant	rs13039563
Chromosome Location	chr20:52296849-52296850
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52295687..52298139-chr5:10358029..10359596,2	MCF-7	breast:
2	chr20:52210434..52211153-chr20:52296368..52297289,2	MCF-7	breast:
3	chr20:52295776..52297405-chr3:64088907..64090515,2	MCF-7	breast:
4	chr20:52277654..52278913-chr20:52296328..52297068,3	MCF-7	breast:
5	chr17:56788439..56788984-chr20:52296323..52296866,2	MCF-7	breast:
6	chr17:56735351..56738135-chr20:52295745..52298144,2	MCF-7	breast:
7	chr20:45989203..45991635-chr20:52294610..52297437,2	MCF-7	breast:
8	chr20:52293539..52297422-chr20:55838657..55844085,6	MCF-7	breast:
9	chr20:52294764..52297312-chr20:52368038..52369565,2	K562	blood:
10	chr17:57915331..57918284-chr20:52296594..52299022,2	MCF-7	breast:
11	chr14:23008348..23010148-chr20:52295113..52296975,2	MCF-7	breast:
12	chr20:52296496..52297267-chr20:52307610..52308510,2	MCF-7	breast:
13	chr11:62608889..62610568-chr20:52296380..52298644,2	MCF-7	breast:
14	chr20:46412861..46415421-chr20:52295698..52298036,2	MCF-7	breast:
15	chr19:49339053..49339570-chr20:52296712..52297315,2	MCF-7	breast:
16	chr20:52236780..52239010-chr20:52294987..52297314,2	K562	blood:
17	chr12:7070485..7072610-chr20:52295836..52297427,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000087076	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000241101	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000211884	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12481286	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624860	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13036868	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6013752	0.95[ASN][1000 genomes]
rs6022654	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6022656	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6063975	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6068614	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6068620	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834006	chr20:52182498-52309366	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	193 gene(s)	inside rSNPs	diseases
4	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
5	nsv912935	chr20:52221906-52337118	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	101 gene(s)	inside rSNPs	diseases
6	nsv912936	chr20:52250876-52344962	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
7	nsv912937	chr20:52251863-52344962	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
9	nsv518277	chr20:52276452-52315311	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv912938	chr20:52276452-52328338	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52293400-52299600	Enhancers	Placenta	Placenta
2	chr20:52294000-52297400	Enhancers	Fetal Kidney	kidney
3	chr20:52294200-52297000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr20:52294200-52297200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:52294200-52297200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:52294200-52297400	Enhancers	Stomach Mucosa	stomach
7	chr20:52294400-52297000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr20:52294400-52297600	Enhancers	Fetal Lung	lung
9	chr20:52294600-52297000	Enhancers	NHLF	lung
10	chr20:52295000-52297000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr20:52295200-52297000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr20:52295200-52297000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr20:52295200-52297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:52295200-52297400	Enhancers	Thymus	Thymus
15	chr20:52295200-52297400	Enhancers	Dnd41	blood
16	chr20:52295400-52297000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr20:52295400-52297400	Enhancers	Fetal Thymus	thymus
18	chr20:52295400-52297800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr20:52295400-52298600	Weak transcription	GM12878-XiMat	blood
20	chr20:52295400-52302200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr20:52295800-52297400	Enhancers	Fetal Stomach	stomach
22	chr20:52295800-52298200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr20:52296000-52297600	Enhancers	Fetal Heart	heart
24	chr20:52296200-52297000	Enhancers	Brain Substantia Nigra	brain
25	chr20:52296200-52297400	Enhancers	Brain Hippocampus Middle	brain
26	chr20:52296200-52297600	Enhancers	Colon Smooth Muscle	Colon
27	chr20:52296200-52298000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr20:52296200-52298600	Weak transcription	Primary B cells from cord blood	blood
29	chr20:52296400-52297000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:52296400-52297000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr20:52296400-52297000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:52296400-52297000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr20:52296400-52297000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr20:52296600-52297000	Enhancers	Primary T cells from cord blood	blood
35	chr20:52296600-52297400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr20:52296600-52297400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:52296600-52301800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:52296800-52297600	Enhancers	A549	lung
39	chr20:52296800-52298400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr20:52296800-52298800	Enhancers	HepG2	liver
41	chr20:52296800-52301400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr20:52296800-52301400	Weak transcription	K562	blood
43	chr20:52296800-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr20:52296800-52301800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr20:52296800-52302200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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