Variant report

Variant	rs1865711
Chromosome Location	chr3:24531567-24531568
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	POLR2A	chr3:24531547-24531602	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr3:24531562-24532009	T-47D	breast:	n/a	n/a
3	SIN3AK20	chr3:24531512-24532235	MCF-7	breast:	n/a	n/a
4	CEBPB	chr3:24531530-24532109	MCF-7	breast:	n/a	chr3:24531835-24531846
5	GATA3	chr3:24531557-24531994	T-47D	breast:	n/a	n/a
6	EP300	chr3:24531473-24531992	T-47D	breast:	n/a	chr3:24531832-24531846
7	POLR2A	chr3:24531493-24531970	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr3:24531556-24532072	HepG2	liver:	n/a	chr3:24531835-24531846

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24400228..24405741-chr3:24531182..24533191,4	MCF-7	breast:

Variant related genes	Relation type
THRB-AS1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12488078	0.90[EUR][1000 genomes]
rs13078191	0.96[ASN][1000 genomes]
rs1865710	0.96[ASN][1000 genomes]
rs3749376	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs55929411	0.85[ASN][1000 genomes]
rs56783261	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57622980	0.81[ASN][1000 genomes]
rs57751578	0.94[ASN][1000 genomes]
rs58274299	0.90[EUR][1000 genomes]
rs58388581	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58932894	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60502621	0.90[EUR][1000 genomes]
rs61063562	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764938	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6765048	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6789815	1.00[JPT][hapmap]
rs73152119	0.96[ASN][1000 genomes]
rs73823308	0.95[EUR][1000 genomes]
rs73823340	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73823342	0.93[ASN][1000 genomes]
rs73823348	0.85[ASN][1000 genomes]
rs73823356	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24515600-24533200	Weak transcription	Stomach Mucosa	stomach
2	chr3:24519400-24532800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:24523000-24534000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:24525200-24531800	Enhancers	Liver	Liver
5	chr3:24525600-24531800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:24525600-24533800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:24526800-24534000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:24527600-24535400	Weak transcription	Lung	lung
9	chr3:24527800-24531600	Weak transcription	Brain Germinal Matrix	brain
10	chr3:24527800-24531600	Weak transcription	Right Atrium	heart
11	chr3:24527800-24531800	Weak transcription	Pancreas	Pancrea
12	chr3:24527800-24533600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:24528000-24531800	Weak transcription	Gastric	stomach
14	chr3:24528000-24532000	Weak transcription	Left Ventricle	heart
15	chr3:24529000-24532400	Enhancers	Psoas Muscle	Psoas
16	chr3:24529400-24535000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:24529800-24531800	Weak transcription	Aorta	Aorta
18	chr3:24529800-24533000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:24529800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:24529800-24534400	Weak transcription	NHDF-Ad	bronchial
21	chr3:24529800-24535200	Weak transcription	NHEK	skin
22	chr3:24530400-24533000	Enhancers	Fetal Intestine Small	intestine
23	chr3:24530400-24534600	Enhancers	Adipose Nuclei	Adipose
24	chr3:24530600-24531800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:24530600-24532000	Enhancers	HMEC	breast
26	chr3:24530800-24531800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:24530800-24532000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:24530800-24532000	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:24530800-24532000	Enhancers	Spleen	Spleen
30	chr3:24530800-24532600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:24530800-24533200	Enhancers	Fetal Intestine Large	intestine
32	chr3:24530800-24533600	Enhancers	HepG2	liver
33	chr3:24530800-24534400	Enhancers	Colon Smooth Muscle	Colon
34	chr3:24530800-24534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:24531000-24531800	Enhancers	K562	blood
36	chr3:24531000-24532200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:24531000-24532600	Enhancers	Fetal Lung	lung
38	chr3:24531000-24533200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:24531200-24531600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:24531200-24531600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:24531200-24532200	Enhancers	Hela-S3	cervix
42	chr3:24531200-24533000	Weak transcription	Right Ventricle	heart
43	chr3:24531200-24533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:24531400-24531800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links