Variant report

Variant	rs13319566
Chromosome Location	chr3:52095555-52095556
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr3:52095472-52095945	ECC-1	luminal epithelium:	n/a	n/a
2	YY1	chr3:52095555-52095841	GM12878	blood:	n/a	n/a
3	MYC	chr3:52095163-52095788	MCF10A-Er-Src	breast:	n/a	n/a
4	NR2C2	chr3:52095530-52095931	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52094254..52096500-chr3:52125955..52128876,2	MCF-7	breast:
2	chr3:52089468..52092661-chr3:52093229..52096649,5	K562	blood:
3	chr3:52093528..52096299-chr3:52098821..52100652,4	K562	blood:
4	chr3:52093207..52095585-chr3:52103069..52105025,2	K562	blood:
5	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:

No data

Variant related genes	Relation type
DUSP7	TF binding region
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12386365	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13314125	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164638	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs164639	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17051957	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17051977	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171294	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs183029	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304505	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452586	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28659792	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs352146	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352147	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352148	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352149	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352150	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352151	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352153	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55664415	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55834589	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56281986	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56322622	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57335685	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57466127	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59890038	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781635	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72964042	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72964044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638246	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs808787	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs876782	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs893056	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9809254	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9809977	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9811707	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815010	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9816434	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9817653	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9830293	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9841469	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843299	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843852	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9846049	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9847073	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9847092	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9857878	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9860982	0.89[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868101	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882775	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv590293	chr3:52089889-52097060	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv590299	chr3:52090344-52096432	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv590300	chr3:52090597-52096432	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
3	chr3:52092000-52095800	Weak transcription	Left Ventricle	heart
4	chr3:52092000-52096200	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52092000-52096400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:52092000-52096400	Weak transcription	HUVEC	blood vessel
7	chr3:52092000-52096400	Weak transcription	NH-A	brain
8	chr3:52092000-52096800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52092000-52097600	Enhancers	GM12878-XiMat	blood
10	chr3:52092000-52099200	Weak transcription	Right Atrium	heart
11	chr3:52092000-52102200	Enhancers	HMEC	breast
12	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:52092200-52095600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:52092200-52095800	Weak transcription	Primary B cells from cord blood	blood
15	chr3:52092200-52095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:52092200-52095800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:52092200-52096200	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:52092200-52096400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:52092200-52096400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:52092200-52096400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52092200-52096400	Weak transcription	Pancreas	Pancrea
22	chr3:52092200-52096400	Weak transcription	NHLF	lung
23	chr3:52092200-52096400	Weak transcription	Osteobl	bone
24	chr3:52092200-52096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52092200-52096600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:52092200-52096600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52092200-52096600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52092200-52096600	Weak transcription	Right Ventricle	heart
29	chr3:52092200-52096800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:52092200-52096800	Weak transcription	Fetal Brain Male	brain
31	chr3:52092200-52099200	Weak transcription	Gastric	stomach
32	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
35	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:52092400-52095600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:52092400-52095800	Weak transcription	Fetal Thymus	thymus
40	chr3:52092400-52096200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:52092400-52096400	Weak transcription	Hela-S3	cervix
42	chr3:52092400-52096400	Weak transcription	HSMM	muscle
43	chr3:52092400-52096400	Weak transcription	NHDF-Ad	bronchial
44	chr3:52092400-52096600	Weak transcription	Colonic Mucosa	Colon
45	chr3:52092400-52096600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:52092600-52095800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:52092600-52096400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:52093800-52095800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:52094000-52096400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links