Variant report

Variant	rs11086440
Chromosome Location	chr20:52405793-52405794
allele	C/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52404288..52406884-chr20:52421776..52423435,2	K562	blood:
2	chr20:52403941..52405869-chr8:146051670..146054549,2	MCF-7	breast:
3	chr17:56703908..56706201-chr20:52403227..52406128,2	MCF-7	breast:
4	chr15:52262547..52265504-chr20:52405082..52406713,2	MCF-7	breast:
5	chr1:114471357..114473665-chr20:52405177..52406948,2	MCF-7	breast:
6	chr20:52404657..52409301-chr20:55839674..55843108,6	MCF-7	breast:
7	chr17:59474142..59479097-chr20:52403146..52407414,5	MCF-7	breast:
8	chr17:58754040..58755910-chr20:52405124..52406880,2	MCF-7	breast:
9	chr20:52404454..52406653-chr20:60640164..60641703,2	MCF-7	breast:
10	chr1:243512538..243513041-chr20:52405648..52406496,2	MCF-7	breast:
11	chr20:52403779..52405878-chr20:52738578..52741634,3	MCF-7	breast:
12	chr2:39345656..39348295-chr20:52403967..52406506,2	MCF-7	breast:
13	chr20:52404639..52407466-chr20:55822538..55824308,2	MCF-7	breast:
14	chr20:46352698..46355620-chr20:52405700..52407569,2	MCF-7	breast:
15	chr20:52405785..52406558-chr20:52486542..52487158,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000147789	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000130699	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000121068	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11086439	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13045415	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4399775	0.86[CHB][hapmap]
rs4811465	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4811466	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6068667	0.84[ASN][1000 genomes]
rs6123313	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6126949	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6126951	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6126953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv965888	chr20:52394959-52410541	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	33 gene(s)	inside rSNPs	diseases
7	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
8	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52402000-52407600	Enhancers	Placenta	Placenta
2	chr20:52402200-52409400	Weak transcription	Esophagus	oesophagus
3	chr20:52403000-52406200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:52403400-52406000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr20:52403400-52406200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr20:52403400-52407200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr20:52403400-52407200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:52403600-52406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:52403600-52406200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr20:52403600-52406200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:52403600-52407400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr20:52403800-52405800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr20:52403800-52405800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr20:52403800-52405800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:52403800-52405800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:52403800-52405800	Weak transcription	GM12878-XiMat	blood
17	chr20:52403800-52406000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr20:52403800-52406000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:52403800-52406000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr20:52403800-52406000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:52403800-52406200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr20:52403800-52406200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:52403800-52406200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr20:52403800-52406200	Weak transcription	Fetal Lung	lung
25	chr20:52403800-52406200	Weak transcription	K562	blood
26	chr20:52403800-52406800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:52403800-52407400	Weak transcription	Stomach Mucosa	stomach
28	chr20:52403800-52409400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr20:52403800-52409600	Weak transcription	Pancreas	Pancrea
30	chr20:52404000-52405800	Enhancers	A549	lung
31	chr20:52404000-52405800	Weak transcription	HMEC	breast
32	chr20:52404000-52406200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr20:52404000-52406600	Enhancers	HepG2	liver
34	chr20:52404200-52405800	Weak transcription	NHEK	skin
35	chr20:52404200-52406200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr20:52404200-52406200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr20:52404200-52407400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr20:52404200-52414400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr20:52404200-52415600	Weak transcription	Fetal Intestine Large	intestine
40	chr20:52404400-52406000	Weak transcription	HUVEC	blood vessel
41	chr20:52404400-52406200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:52404400-52407400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr20:52404400-52407400	Weak transcription	Fetal Stomach	stomach
44	chr20:52404600-52406000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:52405000-52407400	Weak transcription	Fetal Intestine Small	intestine
46	chr20:52405400-52405800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr20:52405400-52405800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links