Variant report

Variant	rs147088199
Chromosome Location	chr20:52556993-52556994
allele	G/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:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
2	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
3	chr17:56706658..56709234-chr20:52552890..52557689,4	MCF-7	breast:
4	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
5	chr20:52556025..52558052-chr4:57843937..57845567,2	MCF-7	breast:
6	chr17:48157159..48157813-chr20:52556453..52557192,2	MCF-7	breast:
7	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
8	chr17:56707751..56710392-chr20:52555190..52558925,4	MCF-7	breast:
9	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
10	chr20:49347041..49349298-chr20:52555192..52557887,2	MCF-7	breast:
11	chr17:56736212..56737922-chr20:52556344..52558393,2	MCF-7	breast:
12	chr17:59485646..59489353-chr20:52553682..52557868,4	MCF-7	breast:
13	chr20:52452353..52453193-chr20:52556867..52557776,2	MCF-7	breast:
14	chr20:52556047..52557092-chr3:64008811..64009718,4	MCF-7	breast:
15	chr20:45825065..45825605-chr20:52556876..52557527,2	MCF-7	breast:
16	chr20:52554600..52557238-chr20:55797829..55800165,3	MCF-7	breast:
17	chr20:52553226..52558762-chr20:55837122..55843874,19	MCF-7	breast:
18	chr20:52224289..52226213-chr20:52555088..52557591,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFDN4-1	chr20:52556699-52557137	XLOC_013571

No data

Variant related genes	Relation type
ENSG00000064787	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000005884	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000121068	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	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
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:52550400-52557400	Enhancers	Placenta	Placenta
3	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr20:52552200-52557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52552600-52557400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr20:52552600-52557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr20:52552800-52560200	Weak transcription	Primary T cells from cord blood	blood
12	chr20:52552800-52560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr20:52553800-52558600	Enhancers	HepG2	liver
14	chr20:52554000-52557000	Weak transcription	Fetal Stomach	stomach
15	chr20:52554200-52559200	Enhancers	K562	blood
16	chr20:52554600-52560000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
19	chr20:52555000-52557600	Enhancers	Colonic Mucosa	Colon
20	chr20:52555000-52557600	Enhancers	Stomach Mucosa	stomach
21	chr20:52555200-52559400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr20:52555400-52557000	Enhancers	HSMM	muscle
23	chr20:52555400-52557000	Enhancers	NHEK	skin
24	chr20:52555400-52557200	Enhancers	Brain Hippocampus Middle	brain
25	chr20:52555400-52557400	Enhancers	NHLF	lung
26	chr20:52555400-52557600	Enhancers	Brain Cingulate Gyrus	brain
27	chr20:52555400-52557600	Enhancers	Duodenum Mucosa	Duodenum
28	chr20:52555400-52557800	Enhancers	HMEC	breast
29	chr20:52555400-52559400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:52555400-52561000	Enhancers	Fetal Heart	heart
31	chr20:52555600-52557000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr20:52555600-52557000	Weak transcription	Right Atrium	heart
33	chr20:52555600-52557200	Enhancers	Brain Angular Gyrus	brain
34	chr20:52555600-52557400	Enhancers	Osteobl	bone
35	chr20:52555600-52557600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr20:52555800-52557200	Enhancers	Hela-S3	cervix
37	chr20:52555800-52557600	Enhancers	Brain Substantia Nigra	brain
38	chr20:52555800-52559000	Enhancers	Colon Smooth Muscle	Colon
39	chr20:52556000-52557000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr20:52556000-52557000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:52556000-52557200	Enhancers	Fetal Brain Male	brain
42	chr20:52556000-52557200	Enhancers	Fetal Kidney	kidney
43	chr20:52556000-52557200	Enhancers	Left Ventricle	heart
44	chr20:52556000-52557400	Enhancers	Liver	Liver
45	chr20:52556000-52557400	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr20:52556000-52557600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr20:52556000-52557600	Enhancers	HUVEC	blood vessel
48	chr20:52556000-52558000	Flanking Active TSS	A549	lung
49	chr20:52556000-52558000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr20:52556000-52558400	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links