Variant report

Variant	rs72902484
Chromosome Location	chr11:45934889-45934890
allele	A/G
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	RUNX3	chr11:45934585-45934960	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:45934715-45934920	GM12878	blood:	n/a	n/a
3	EBF1	chr11:45934697-45934891	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:45934574-45935356	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:45934678-45935355	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:45934570-45934919	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:45934656-45936909	GM12892	blood:	n/a	n/a
8	RUNX3	chr11:45934587-45934991	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45907546..45909448-chr11:45934193..45936568,2	MCF-7	breast:
2	chr11:45825326..45828118-chr11:45934084..45936499,2	K562	blood:

Variant related genes	Relation type
PEX16	TF binding region
ENSG00000181830	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11038708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1533613	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17847253	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35389927	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55644523	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72902474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72902480	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72902492	0.88[AMR][1000 genomes];0.96[EUR][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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1807609	chr11:45915859-45940195	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv1798496	chr11:45925495-45948304	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45922600-45938400	Weak transcription	Fetal Kidney	kidney
2	chr11:45923000-45938000	Weak transcription	NHDF-Ad	bronchial
3	chr11:45923000-45938400	Weak transcription	Right Atrium	heart
4	chr11:45923200-45935600	Weak transcription	NH-A	brain
5	chr11:45923600-45936600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:45924600-45936400	Strong transcription	Fetal Brain Female	brain
7	chr11:45926600-45935400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:45927000-45936200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:45927000-45936600	Weak transcription	K562	blood
10	chr11:45927200-45937600	Weak transcription	Stomach Mucosa	stomach
11	chr11:45927400-45935000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:45928000-45937800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:45929800-45938000	Strong transcription	Fetal Intestine Small	intestine
14	chr11:45930000-45935000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:45930000-45937400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:45930200-45935800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:45930200-45936200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:45930200-45936200	Weak transcription	HSMMtube	muscle
19	chr11:45930200-45937000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:45930200-45937200	Strong transcription	Thymus	Thymus
21	chr11:45930400-45937600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:45930400-45937600	Strong transcription	Fetal Stomach	stomach
23	chr11:45930400-45937800	Strong transcription	Fetal Intestine Large	intestine
24	chr11:45930400-45938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:45930400-45938000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:45930400-45938000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:45930400-45938000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:45930400-45938000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:45930600-45936200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:45930600-45936800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr11:45930600-45937000	Strong transcription	Lung	lung
32	chr11:45930600-45937200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:45930600-45937400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:45930600-45937600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:45930600-45937600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:45930600-45937600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:45930600-45937600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:45930600-45937600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:45930600-45937800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:45930600-45937800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr11:45930600-45937800	Strong transcription	Placenta	Placenta
42	chr11:45930600-45937800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr11:45930600-45937800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:45930600-45938000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:45930600-45938000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:45930600-45938000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:45930600-45938000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:45930800-45937000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:45930800-45937000	Strong transcription	Brain Hippocampus Middle	brain
50	chr11:45930800-45937000	Strong transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links