Variant report

Variant	rs16998468
Chromosome Location	chr20:52444402-52444403
allele	A/C
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52367432..52369907-chr20:52444310..52447312,3	K562	blood:
2	chr17:79479762..79482602-chr20:52444194..52446135,2	MCF-7	breast:
3	chr17:57917983..57919742-chr20:52443624..52445975,2	MCF-7	breast:
4	chr19:12904144..12906645-chr20:52443752..52446655,2	MCF-7	breast:
5	chr20:52194902..52196178-chr20:52444038..52445704,6	MCF-7	breast:
6	chr1:116005229..116007431-chr20:52444362..52446929,2	MCF-7	breast:
7	chr20:52442966..52445864-chr20:55839139..55841212,2	MCF-7	breast:
8	chr17:57917840..57922874-chr20:52444092..52449259,5	MCF-7	breast:
9	chr17:56708142..56710971-chr20:52444323..52447306,3	MCF-7	breast:
10	chr17:65374754..65375398-chr20:52444383..52445136,2	MCF-7	breast:
11	chr1:112486408..112487122-chr20:52444338..52445114,2	MCF-7	breast:
12	chr17:56735072..56736721-chr20:52444117..52446150,2	MCF-7	breast:
13	chr17:58602315..58604454-chr20:52443406..52445937,2	MCF-7	breast:
14	chr15:69817146..69817999-chr20:52444013..52444987,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199004	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000229947	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000229848	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000154217	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2079278	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34193630	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34219895	0.86[ASN][1000 genomes]
rs35479532	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022784	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097591	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73912496	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52440000-52444800	Weak transcription	Thymus	Thymus
3	chr20:52440800-52445400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:52441000-52445000	Enhancers	Fetal Stomach	stomach
5	chr20:52441200-52446000	Enhancers	HepG2	liver
6	chr20:52441600-52444600	Weak transcription	Colon Smooth Muscle	Colon
7	chr20:52441600-52445200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:52442000-52444600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:52442400-52444800	Weak transcription	Stomach Mucosa	stomach
10	chr20:52442400-52445000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr20:52442600-52445400	Enhancers	Primary B cells from peripheral blood	blood
12	chr20:52442800-52444600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:52442800-52445400	Enhancers	Fetal Thymus	thymus
14	chr20:52443000-52445200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr20:52443200-52444600	Enhancers	Primary B cells from cord blood	blood
16	chr20:52443200-52444600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:52443200-52444600	Enhancers	GM12878-XiMat	blood
18	chr20:52443200-52445400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr20:52443200-52445400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr20:52443200-52445400	Enhancers	Fetal Intestine Small	intestine
21	chr20:52443200-52445600	Flanking Active TSS	A549	lung
22	chr20:52443400-52444600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr20:52443400-52445400	Enhancers	Primary T cells from cord blood	blood
24	chr20:52443400-52445400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr20:52443400-52445800	Enhancers	Fetal Intestine Large	intestine
26	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:52443600-52444600	Weak transcription	Brain Hippocampus Middle	brain
28	chr20:52443600-52444600	Enhancers	HSMMtube	muscle
29	chr20:52443600-52444800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:52443600-52444800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:52443600-52445000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr20:52443600-52445000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr20:52443600-52445000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr20:52443600-52445000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr20:52443600-52445000	Enhancers	Rectal Smooth Muscle	rectum
36	chr20:52443600-52445200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:52443600-52445200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr20:52443600-52445200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr20:52443600-52445200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr20:52443600-52445600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:52443600-52447000	Enhancers	Placenta	Placenta
42	chr20:52443600-52447200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr20:52443800-52444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr20:52443800-52444600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr20:52443800-52444600	Enhancers	Psoas Muscle	Psoas
46	chr20:52443800-52444600	Enhancers	NHLF	lung
47	chr20:52443800-52444800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr20:52443800-52444800	Enhancers	NH-A	brain
49	chr20:52443800-52445000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr20:52443800-52445000	Enhancers	Adipose Nuclei	Adipose

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