Variant report

Variant	rs16998584
Chromosome Location	chr20:52554513-52554514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr20:52554372-52558599	A549	lung:	n/a	n/a
2	IRF1	chr20:52554370-52554555	K562	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52195063..52195597-chr20:52554502..52555063,2	MCF-7	breast:
2	chr20:52367473..52369879-chr20:52554123..52556023,3	K562	blood:
3	chr20:49411382..49413304-chr20:52553862..52556702,3	MCF-7	breast:
4	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
5	chr17:56706658..56709234-chr20:52552890..52557689,4	MCF-7	breast:
6	chr20:52199312..52199876-chr20:52554468..52555262,2	MCF-7	breast:
7	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
8	chr20:52554429..52556366-chr20:55834185..55835777,2	MCF-7	breast:
9	chr14:50359132..50359652-chr20:52554409..52554981,2	MCF-7	breast:
10	chr20:52553633..52555661-chr20:55821269..55822979,2	MCF-7	breast:
11	chr12:81102346..81103912-chr20:52553556..52556381,2	MCF-7	breast:
12	chr20:52553803..52556220-chr20:55831106..55834849,4	MCF-7	breast:
13	chr20:52553947..52555886-chr20:52679638..52682394,3	MCF-7	breast:
14	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
15	chr17:59485646..59489353-chr20:52553682..52557868,4	MCF-7	breast:
16	chr20:52552477..52556062-chr3:64098052..64101134,3	MCF-7	breast:
17	chr20:45985786..45987562-chr20:52552557..52555043,2	MCF-7	breast:
18	chr20:52553226..52558762-chr20:55837122..55843874,19	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFDN4-3	chr20:52553902-52554760	NONHSAT080410

No data

Variant related genes	Relation type
ENSG00000236352	TF binding region
ENSG00000226308	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16998572	0.83[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4809945	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4811485	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6013838	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52543600-52556000	Weak transcription	Aorta	Aorta
2	chr20:52543800-52555000	Weak transcription	Stomach Mucosa	stomach
3	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
5	chr20:52550200-52555000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:52550400-52557400	Enhancers	Placenta	Placenta
7	chr20:52550800-52555400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52551200-52556200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr20:52551200-52556400	Weak transcription	Psoas Muscle	Psoas
10	chr20:52551600-52555800	Weak transcription	Colon Smooth Muscle	Colon
11	chr20:52551800-52555400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:52551800-52555400	Weak transcription	NHEK	skin
13	chr20:52551800-52556200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:52552000-52555000	Weak transcription	A549	lung
16	chr20:52552000-52555200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr20:52552000-52555400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:52552000-52555400	Weak transcription	HMEC	breast
19	chr20:52552000-52555600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:52552000-52555600	Weak transcription	Brain Angular Gyrus	brain
21	chr20:52552000-52556000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:52552000-52556000	Weak transcription	NH-A	brain
23	chr20:52552000-52556800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:52552200-52555400	Weak transcription	Brain Hippocampus Middle	brain
26	chr20:52552200-52555400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr20:52552200-52555400	Weak transcription	NHLF	lung
28	chr20:52552200-52555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:52552200-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr20:52552200-52555600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr20:52552200-52555800	Weak transcription	Brain Substantia Nigra	brain
32	chr20:52552200-52556000	Weak transcription	Fetal Kidney	kidney
33	chr20:52552200-52556000	Weak transcription	Small Intestine	intestine
34	chr20:52552200-52556000	Weak transcription	Thymus	Thymus
35	chr20:52552200-52556000	Enhancers	GM12878-XiMat	blood
36	chr20:52552200-52556200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:52552200-52557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr20:52552400-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr20:52552400-52555600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:52552600-52554800	Weak transcription	HSMMtube	muscle
43	chr20:52552600-52555000	Weak transcription	Colonic Mucosa	Colon
44	chr20:52552600-52555200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr20:52552600-52555400	Weak transcription	Right Atrium	heart
46	chr20:52552600-52555400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr20:52552600-52555600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr20:52552600-52555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr20:52552600-52555800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr20:52552600-52555800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links