Variant report

Variant	rs17051957
Chromosome Location	chr3:52099441-52099442
allele	C/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	STAT3	chr3:52099197-52099713	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr3:52099066-52099874	MCF10A-Er-Src	breast:	n/a	chr3:52099517-52099528 chr3:52099145-52099154 chr3:52099518-52099528 chr3:52099519-52099528 chr3:52099518-52099528
3	MAX	chr3:52099355-52099760	K562	blood:	n/a	chr3:52099517-52099528 chr3:52099518-52099528 chr3:52099519-52099528 chr3:52099518-52099528
4	FOS	chr3:52099162-52099705	MCF10A-Er-Src	breast:	n/a	chr3:52099185-52099194
5	MYC	chr3:52099117-52099799	MCF10A-Er-Src	breast:	n/a	chr3:52099517-52099528 chr3:52099145-52099154 chr3:52099518-52099528 chr3:52099519-52099528 chr3:52099518-52099528
6	FOS	chr3:52099190-52099715	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:52099037-52099895	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr3:52099037-52099514	MCF10A-Er-Src	breast:	n/a	chr3:52099070-52099082
9	FOS	chr3:52099216-52099720	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:52099311-52099841	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr3:52099099-52099631	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:52099028-52099793	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr3:52099196-52099716	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:52099171-52099713	MCF10A-Er-Src	breast:	n/a	chr3:52099185-52099194

No.	Distal block	Cell Line	Cell type
1	chr3:52001214..52003642-chr3:52099197..52101063,2	K562	blood:
2	chr3:52087881..52090282-chr3:52097638..52100499,3	K562	blood:
3	chr3:52093528..52096299-chr3:52098821..52100652,4	K562	blood:
4	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:

Variant related genes	Relation type
LINC00696	TF binding region
ENSG00000164086	Chromatin interaction
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs123681	0.89[EUR][1000 genomes]
rs12386365	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13314125	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13319566	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164638	0.88[EUR][1000 genomes]
rs164639	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs17051977	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171294	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs183029	0.88[EUR][1000 genomes]
rs2304505	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28452586	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28659792	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs352146	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs352147	0.88[EUR][1000 genomes]
rs352148	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs352149	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs352150	0.88[EUR][1000 genomes]
rs352151	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs352153	0.91[EUR][1000 genomes]
rs3755797	0.82[CHB][hapmap]
rs55664415	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55834589	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56281986	0.89[EUR][1000 genomes]
rs56322622	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57335685	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57466127	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59890038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6781635	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72964042	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72964044	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7638246	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs808787	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs876782	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs893056	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9809254	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9809977	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811707	0.92[ASW][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9815010	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9816434	0.82[EUR][1000 genomes]
rs9817653	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9830293	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9841469	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9843299	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9843852	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9846049	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9847073	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9847092	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9857878	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860982	0.90[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865330	0.94[GIH][hapmap];0.88[TSI][hapmap]
rs9868101	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9882775	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
14	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

No data

Chromatin state (count:61 , 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	chr3:52092000-52102200	Enhancers	HMEC	breast
4	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
8	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:52094000-52102000	Enhancers	NHEK	skin
13	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52096200-52099600	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:52096200-52102000	Enhancers	Fetal Stomach	stomach
16	chr3:52096400-52106400	Weak transcription	Fetal Thymus	thymus
17	chr3:52096600-52100800	Enhancers	Spleen	Spleen
18	chr3:52096800-52104000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:52097000-52102000	Weak transcription	Colonic Mucosa	Colon
20	chr3:52097000-52102000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:52097000-52103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:52097000-52105000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:52097000-52105000	Weak transcription	Hela-S3	cervix
24	chr3:52097200-52103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:52097200-52104000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:52097400-52101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52097400-52101800	Weak transcription	NHDF-Ad	bronchial
28	chr3:52097400-52104000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:52097400-52105400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:52097600-52100000	Bivalent Enhancer	HepG2	liver
32	chr3:52097600-52101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:52097600-52103400	Weak transcription	Brain Substantia Nigra	brain
34	chr3:52097600-52108200	Weak transcription	NHLF	lung
35	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
36	chr3:52098800-52099800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:52098800-52100000	Enhancers	Pancreas	Pancrea
38	chr3:52098800-52106400	Enhancers	Fetal Muscle Leg	muscle
39	chr3:52099000-52100200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr3:52099200-52099600	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:52099200-52099800	Enhancers	HUVEC	blood vessel
42	chr3:52099200-52100000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:52099200-52100000	Enhancers	Gastric	stomach
44	chr3:52099200-52100000	Enhancers	Right Atrium	heart
45	chr3:52099200-52100200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:52099200-52100600	Enhancers	Lung	lung
47	chr3:52099200-52100600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:52099200-52101200	Enhancers	Right Ventricle	heart
49	chr3:52099400-52099600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:52099400-52099800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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