Variant report

Variant	rs11039159
Chromosome Location	chr11:47294021-47294022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr11:47293513-47294118	K562	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778 chr11:47293763-47293778
2	MEF2A	chr11:47293424-47294098	K562	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778 chr11:47293763-47293778
3	WRNIP1	chr11:47293892-47294095	GM12878	blood:	n/a	n/a
4	MXI1	chr11:47293807-47294619	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:47293371-47294177	K562	blood:	n/a	n/a
6	ZMIZ1	chr11:47293761-47294070	K562	blood:	n/a	n/a
7	CBX3	chr11:47293481-47294111	K562	blood:	n/a	n/a
8	BHLHE40	chr11:47293716-47294073	K562	blood:	n/a	chr11:47293993-47294009
9	REST	chr11:47293798-47294917	ECC-1	luminal epithelium:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
10	REST	chr11:47293917-47294874	SK-N-SH	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
11	MAX	chr11:47293905-47294165	K562	blood:	n/a	n/a
12	POLR2A	chr11:47293582-47294110	K562	blood:	n/a	n/a
13	REST	chr11:47293942-47294127	K562	blood:	n/a	n/a
14	REST	chr11:47293898-47294947	PFSK-1	brain:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
15	RCOR1	chr11:47293593-47294069	K562	blood:	n/a	n/a
16	TEAD4	chr11:47293411-47294226	K562	blood:	n/a	n/a
17	REST	chr11:47293529-47294141	K562	blood:	n/a	n/a
18	REST	chr11:47293894-47294905	GM12878	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
19	REST	chr11:47293901-47294187	Hela-S3	cervix:	n/a	n/a
20	REST	chr11:47293955-47294880	ECC-1	luminal epithelium:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
21	TAL1	chr11:47293537-47294190	K562	blood:	n/a	n/a
22	REST	chr11:47293506-47294886	HL-60	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
23	REST	chr11:47293917-47294740	Hela-S3	cervix:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463

No.	Distal block	Cell Line	Cell type
1	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
2	chr11:47194502..47201735-chr11:47289181..47294156,14	K562	blood:
3	chr11:47289567..47294786-chr11:47310778..47315538,7	MCF-7	breast:
4	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
5	chr11:47293111..47295014-chr11:47788351..47790710,2	MCF-7	breast:
6	chr11:47291588..47294118-chr11:47313687..47316370,3	K562	blood:
7	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
8	chr11:47290389..47294105-chr11:47428413..47432863,5	MCF-7	breast:

Variant related genes	Relation type
MADD	TF binding region
ENSG00000256746	TF binding region
ENSG00000165915	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000109920	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10838696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039138	1.00[CHB][hapmap]
rs11039139	0.89[ASN][1000 genomes]
rs11039149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039162	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11039182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606683	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12802374	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2167080	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2596407	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2697923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2856653	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7116451	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs749067	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944419	0.94[ASN][1000 genomes]
rs7944584	0.83[ASN][1000 genomes]

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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47292200-47294200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:47292200-47294200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr11:47292200-47294200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr11:47292200-47294400	Flanking Active TSS	K562	blood
8	chr11:47292400-47294200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr11:47292600-47294200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:47292600-47294200	Enhancers	Gastric	stomach
11	chr11:47292600-47294200	Enhancers	Small Intestine	intestine
12	chr11:47292600-47294600	Enhancers	Liver	Liver
13	chr11:47292600-47294800	Enhancers	Psoas Muscle	Psoas
14	chr11:47292600-47294800	Enhancers	Stomach Mucosa	stomach
15	chr11:47292600-47295800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:47292600-47296000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:47292600-47296000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:47292600-47296000	Weak transcription	Ovary	ovary
19	chr11:47292600-47296200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47292800-47294200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:47292800-47294200	Enhancers	Fetal Lung	lung
22	chr11:47292800-47294200	Enhancers	Fetal Stomach	stomach
23	chr11:47292800-47294600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:47292800-47294600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:47292800-47294800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:47292800-47294800	Flanking Active TSS	GM12878-XiMat	blood
27	chr11:47292800-47295200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:47292800-47296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:47292800-47296200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:47293000-47294200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr11:47293000-47294200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:47293000-47294200	Enhancers	Aorta	Aorta
33	chr11:47293000-47294200	Enhancers	Colonic Mucosa	Colon
34	chr11:47293000-47294200	Enhancers	Right Ventricle	heart
35	chr11:47293000-47294400	Enhancers	Fetal Brain Male	brain
36	chr11:47293000-47294600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr11:47293000-47294600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:47293000-47294600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:47293000-47294800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:47293000-47294800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:47293000-47294800	Enhancers	Adipose Nuclei	Adipose
42	chr11:47293000-47294800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr11:47293000-47294800	Enhancers	Fetal Muscle Leg	muscle
44	chr11:47293000-47295200	Enhancers	Primary B cells from peripheral blood	blood
45	chr11:47293000-47295400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:47293000-47295600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:47293000-47295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr11:47293000-47296000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:47293000-47296200	Weak transcription	Fetal Kidney	kidney
50	chr11:47293000-47296400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links