Variant report

Variant	rs28400288
Chromosome Location	chr11:62560785-62560786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62560628-62561081	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62557524..62562234-chr11:62648109..62651861,7	MCF-7	breast:
2	chr11:62552943..62561747-chr11:62616572..62625876,31	K562	blood:
3	chr1:149223443..149226268-chr11:62558578..62560961,2	MCF-7	breast:
4	chr11:62432613..62435010-chr11:62559783..62562446,3	MCF-7	breast:
5	chr11:62358650..62362308-chr11:62559226..62561722,3	MCF-7	breast:
6	chr11:62527671..62530483-chr11:62558571..62560981,2	K562	blood:
7	chr11:62494172..62498821-chr11:62557548..62561455,7	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM223	TF binding region
ENSG00000162194	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000214756	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11231220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12270342	1.00[AMR][1000 genomes]
rs12288417	1.00[AMR][1000 genomes]
rs12290152	1.00[AMR][1000 genomes]
rs12292281	1.00[AMR][1000 genomes]
rs12295052	1.00[AMR][1000 genomes]
rs12295516	1.00[AMR][1000 genomes]
rs56994557	1.00[AMR][1000 genomes]
rs58003814	1.00[AMR][1000 genomes]
rs58505493	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58792209	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59143369	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61088491	1.00[AMR][1000 genomes]
rs73483955	1.00[AMR][1000 genomes]
rs73483965	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73483978	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73485621	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73485634	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73485689	1.00[AMR][1000 genomes]
rs73487820	1.00[AMR][1000 genomes]
rs73487823	1.00[AMR][1000 genomes]
rs73487824	1.00[AMR][1000 genomes]
rs73487852	1.00[AMR][1000 genomes]
rs73487868	1.00[AMR][1000 genomes]
rs73502144	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
7	nsv897624	chr11:62549593-62563341	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62559400-62571200	Genic enhancers	Placenta	Placenta
2	chr11:62559400-62572000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62559600-62561600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:62559600-62561800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:62559600-62565400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:62559800-62560800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:62559800-62561000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:62559800-62561400	Weak transcription	Ovary	ovary
9	chr11:62559800-62571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:62560000-62561200	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr11:62560000-62561600	Weak transcription	Small Intestine	intestine
12	chr11:62560000-62561600	Weak transcription	HMEC	breast
13	chr11:62560000-62563200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:62560000-62563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:62560000-62570400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr11:62560000-62571000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:62560000-62571200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:62560000-62571400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr11:62560000-62571400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:62560200-62560800	Weak transcription	Primary B cells from cord blood	blood
21	chr11:62560200-62560800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:62560200-62560800	Genic enhancers	Monocytes-CD14+_RO01746	blood
23	chr11:62560200-62561000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:62560200-62561000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:62560200-62561400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:62560200-62561400	Weak transcription	Pancreas	Pancrea
27	chr11:62560200-62561400	Weak transcription	Psoas Muscle	Psoas
28	chr11:62560200-62561600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:62560200-62561600	Weak transcription	Aorta	Aorta
30	chr11:62560200-62561600	Weak transcription	Gastric	stomach
31	chr11:62560200-62562000	Genic enhancers	Dnd41	blood
32	chr11:62560200-62562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:62560200-62563200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:62560200-62564800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:62560200-62568800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:62560200-62569000	Strong transcription	GM12878-XiMat	blood
37	chr11:62560200-62569800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:62560200-62570000	Strong transcription	Right Ventricle	heart
39	chr11:62560200-62570200	Strong transcription	Esophagus	oesophagus
40	chr11:62560200-62570200	Strong transcription	NHDF-Ad	bronchial
41	chr11:62560200-62570400	Strong transcription	Brain Angular Gyrus	brain
42	chr11:62560200-62570400	Strong transcription	Colonic Mucosa	Colon
43	chr11:62560200-62570800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:62560200-62570800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:62560200-62570800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:62560200-62570800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:62560200-62570800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:62560200-62570800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr11:62560200-62570800	Strong transcription	Spleen	Spleen
50	chr11:62560200-62571000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links