Variant report

Variant	rs11709002
Chromosome Location	chr3:120471429-120471430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120469262..120472636-chr3:120473122..120476515,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10511403	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11706997	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11709661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485282	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12491957	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12493166	0.81[ASN][1000 genomes]
rs1505700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1505701	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs16831698	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2331541	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35108870	0.84[ASN][1000 genomes]
rs378759	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs55741444	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57704109	0.82[ASN][1000 genomes]
rs6772101	0.86[ASN][1000 genomes]
rs6787364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829072	0.91[ASN][1000 genomes]
rs9857158	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv1797756	chr3:120464660-120473719	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120462600-120495200	Weak transcription	Aorta	Aorta
2	chr3:120462800-120472200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:120462800-120473000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:120462800-120483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:120462800-120485600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:120462800-120499800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:120462800-120500000	Weak transcription	Gastric	stomach
8	chr3:120462800-120503000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:120463000-120472000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:120463000-120472000	Weak transcription	Stomach Mucosa	stomach
11	chr3:120463000-120472600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:120463000-120473200	Weak transcription	NHLF	lung
13	chr3:120463000-120477800	Weak transcription	Spleen	Spleen
14	chr3:120463000-120482400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:120463000-120484800	Weak transcription	K562	blood
16	chr3:120463000-120485600	Weak transcription	Pancreas	Pancrea
17	chr3:120463000-120485600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:120463000-120485600	Weak transcription	HMEC	breast
19	chr3:120463000-120493600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:120463000-120496000	Weak transcription	Fetal Lung	lung
21	chr3:120463000-120499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:120463000-120502000	Weak transcription	Colonic Mucosa	Colon
23	chr3:120463000-120504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:120463000-120504800	Weak transcription	Fetal Brain Male	brain
25	chr3:120463200-120472600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:120463200-120473200	Weak transcription	Fetal Heart	heart
27	chr3:120463200-120474600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:120463200-120484600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:120463200-120485400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:120463200-120492000	Weak transcription	Thymus	Thymus
31	chr3:120463200-120494000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:120463200-120495200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:120463400-120472800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:120463400-120474000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:120463400-120476800	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:120463400-120478800	Weak transcription	NH-A	brain
37	chr3:120463400-120482800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:120463400-120485000	Weak transcription	Brain Angular Gyrus	brain
39	chr3:120463400-120497000	Weak transcription	Fetal Kidney	kidney
40	chr3:120463400-120503000	Weak transcription	Small Intestine	intestine
41	chr3:120464000-120489600	Weak transcription	NHDF-Ad	bronchial
42	chr3:120466800-120473400	Weak transcription	Brain Germinal Matrix	brain
43	chr3:120466800-120481400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:120469200-120471600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:120469200-120472000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:120469200-120472200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:120469200-120472400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:120469200-120472600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:120469200-120473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:120469200-120474000	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links