Variant report

Variant	rs16998533
Chromosome Location	chr20:52516232-52516233
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:63755678..63757317-chr20:52515698..52518258,2	MCF-7	breast:
2	chr20:52514216..52516428-chr20:52534749..52536551,2	K562	blood:
3	chr20:52498095..52500309-chr20:52514634..52517144,2	K562	blood:
4	chr20:52367603..52371397-chr20:52514347..52517077,3	K562	blood:
5	chr17:56735130..56737677-chr20:52513678..52516608,2	MCF-7	breast:
6	chr16:88877114..88879697-chr20:52516225..52518277,2	MCF-7	breast:
7	chr17:59494603..59496146-chr20:52514075..52516283,2	MCF-7	breast:
8	chr20:52515942..52518179-chr20:55845896..55847637,2	MCF-7	breast:
9	chr20:46413154..46415404-chr20:52515491..52518113,2	MCF-7	breast:
10	chr2:230537937..230540661-chr20:52513696..52516538,2	MCF-7	breast:
11	chr20:52514689..52517854-chr20:55839715..55843096,5	MCF-7	breast:
12	chr12:89746081..89748324-chr20:52514638..52517176,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198931	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000139318	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000196562	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16998499	1.00[EUR][1000 genomes]
rs16998502	1.00[EUR][1000 genomes]
rs55655714	1.00[AMR][1000 genomes]
rs55973940	1.00[AMR][1000 genomes]
rs57886257	1.00[EUR][1000 genomes]
rs58979406	1.00[EUR][1000 genomes]
rs59046998	1.00[EUR][1000 genomes]
rs6091815	1.00[AMR][1000 genomes]
rs6097744	1.00[AMR][1000 genomes]
rs6097746	1.00[AMR][1000 genomes]
rs61484939	1.00[AMR][1000 genomes]
rs7262342	1.00[EUR][1000 genomes]
rs73275816	1.00[EUR][1000 genomes]
rs73275820	1.00[EUR][1000 genomes]
rs73914417	1.00[EUR][1000 genomes]
rs73914419	1.00[EUR][1000 genomes]
rs73914429	1.00[EUR][1000 genomes]
rs73914430	1.00[EUR][1000 genomes]
rs73914434	1.00[EUR][1000 genomes]
rs73914475	1.00[AMR][1000 genomes]
rs8114189	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52507800-52518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:52507800-52522800	Weak transcription	Placenta	Placenta
3	chr20:52514400-52516600	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr20:52514400-52518600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr20:52514400-52518800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr20:52514400-52519000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr20:52514400-52521000	Enhancers	HMEC	breast
8	chr20:52514600-52516400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:52514600-52516600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:52514600-52517200	Enhancers	Thymus	Thymus
11	chr20:52514600-52517400	Enhancers	NHEK	skin
12	chr20:52514600-52518000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr20:52514600-52518600	Enhancers	Stomach Mucosa	stomach
14	chr20:52514600-52518800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr20:52514600-52518800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr20:52514600-52518800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr20:52514600-52519000	Enhancers	Fetal Intestine Small	intestine
18	chr20:52514600-52520600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr20:52514600-52520600	Enhancers	NHDF-Ad	bronchial
20	chr20:52514800-52516400	Enhancers	Fetal Heart	heart
21	chr20:52514800-52516800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr20:52514800-52517200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr20:52514800-52517400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:52514800-52517400	Enhancers	Dnd41	blood
25	chr20:52514800-52518600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr20:52514800-52518800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr20:52514800-52519000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr20:52514800-52520600	Enhancers	NHLF	lung
29	chr20:52514800-52521000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:52515000-52516600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr20:52515000-52516600	Enhancers	Fetal Thymus	thymus
32	chr20:52515000-52516600	Enhancers	Lung	lung
33	chr20:52515000-52517400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:52515000-52517400	Enhancers	Duodenum Mucosa	Duodenum
35	chr20:52515000-52518400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr20:52515000-52518800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr20:52515000-52518800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr20:52515000-52519000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:52515000-52519400	Enhancers	Fetal Muscle Leg	muscle
40	chr20:52515000-52520800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:52515200-52516600	Enhancers	Esophagus	oesophagus
42	chr20:52515200-52516600	Enhancers	Gastric	stomach
43	chr20:52515200-52516600	Enhancers	Left Ventricle	heart
44	chr20:52515200-52516600	Enhancers	Pancreas	Pancrea
45	chr20:52515200-52516800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr20:52515200-52516800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr20:52515200-52517000	Enhancers	K562	blood
48	chr20:52515200-52517200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr20:52515200-52517200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr20:52515200-52517200	Weak transcription	Fetal Lung	lung

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