Variant report

Variant	rs17040306
Chromosome Location	chr2:113483153-113483154
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:113483020-113483170	GM12867	blood:	n/a	n/a
2	RUNX3	chr2:113483052-113483978	GM12878	blood:	n/a	n/a
3	ZNF143	chr2:113483132-113483900	GM12878	blood:	n/a	n/a
4	CTCF	chr2:113483040-113483190	GM12871	blood:	n/a	n/a
5	CTCF	chr2:113483040-113483190	GM12873	blood:	n/a	n/a
6	ZEB1	chr2:113483141-113484524	GM12878	blood:	n/a	chr2:113483982-113483990 chr2:113483843-113483852 chr2:113483609-113483616
7	CTCF	chr2:113483020-113483170	GM12870	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
2	chr2:113380065..113382456-chr2:113480700..113483703,3	MCF-7	breast:
3	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
4	chr2:113475474..113478098-chr2:113481097..113483249,3	MCF-7	breast:
5	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
6	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
7	chr2:113482871..113484637-chr2:113485555..113488424,2	K562	blood:
8	chr2:113237844..113240182-chr2:113482913..113484469,2	MCF-7	breast:
9	chr2:113480533..113482697-chr2:113482909..113484492,2	K562	blood:
10	chr2:113478980..113481125-chr2:113482565..113484434,2	MCF-7	breast:
11	chr2:113340774..113345524-chr2:113480391..113485957,9	MCF-7	breast:
12	chr2:113339955..113341936-chr2:113481777..113484601,3	MCF-7	breast:
13	chr2:113298665..113301106-chr2:113481233..113484131,2	MCF-7	breast:
14	chr2:113384015..113385213-chr2:113482175..113483476,11	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC4	TF binding region
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17042289	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17042293	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17042296	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17042298	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55712130	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55900444	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56152754	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60255523	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6542099	1.00[AMR][1000 genomes]
rs6744790	1.00[AMR][1000 genomes]
rs72952103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952128	0.81[AFR][1000 genomes]
rs73955242	1.00[AMR][1000 genomes]
rs7597191	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3458160	chr2:113460280-113484749	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3458161	chr2:113460322-113484724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3458162	chr2:113460460-113484652	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113464200-113486400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:113469400-113484200	Weak transcription	Right Atrium	heart
3	chr2:113477600-113487000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr2:113478400-113483800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:113478600-113488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:113479400-113485200	Enhancers	K562	blood
7	chr2:113480000-113488200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:113481200-113487600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:113481800-113484400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:113481800-113486600	Enhancers	Placenta	Placenta
11	chr2:113482000-113483200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:113482000-113483600	Enhancers	GM12878-XiMat	blood
13	chr2:113482000-113483800	Weak transcription	Colonic Mucosa	Colon
14	chr2:113482200-113484400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:113482200-113484800	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:113482200-113485000	Enhancers	Hela-S3	cervix
17	chr2:113482200-113485200	Enhancers	HMEC	breast
18	chr2:113482400-113484000	Flanking Bivalent TSS/Enh	HepG2	liver
19	chr2:113482400-113484800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:113482400-113484800	Enhancers	Fetal Intestine Large	intestine
21	chr2:113482400-113484800	Enhancers	Fetal Intestine Small	intestine
22	chr2:113482600-113483600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:113482600-113484000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:113482600-113484200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:113482600-113484400	Enhancers	A549	lung
26	chr2:113482600-113484800	Enhancers	NHEK	skin
27	chr2:113482800-113483600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:113482800-113483800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:113482800-113483800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:113482800-113484000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:113482800-113484800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:113483000-113483200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:113483000-113484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:113483000-113484000	Weak transcription	Fetal Thymus	thymus
35	chr2:113483000-113484200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:113483000-113488200	Enhancers	Spleen	Spleen

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