Variant report

Variant	rs62273780
Chromosome Location	chr3:111484375-111484376
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	chr3:111482636..111484637-chr3:111486491..111489104,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10212300	0.90[ASN][1000 genomes]
rs10470303	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10934106	0.96[ASN][1000 genomes]
rs10934107	0.97[ASN][1000 genomes]
rs11710738	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711582	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12330761	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12490166	1.00[ASN][1000 genomes]
rs12490595	0.96[ASN][1000 genomes]
rs12496925	0.96[ASN][1000 genomes]
rs12496971	0.96[ASN][1000 genomes]
rs12497012	0.87[ASN][1000 genomes]
rs13069980	0.95[ASN][1000 genomes]
rs13074817	0.94[ASN][1000 genomes]
rs13079085	0.96[ASN][1000 genomes]
rs2137595	0.82[EUR][1000 genomes]
rs4284954	0.96[ASN][1000 genomes]
rs4413291	0.82[EUR][1000 genomes]
rs4431081	1.00[ASN][1000 genomes]
rs4682057	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682299	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4682303	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682305	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028731	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62275532	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438008	0.96[ASN][1000 genomes]
rs6438009	0.96[ASN][1000 genomes]
rs6764720	0.85[ASN][1000 genomes]
rs6768713	0.97[ASN][1000 genomes]
rs6777540	1.00[ASN][1000 genomes]
rs6784753	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786386	1.00[ASN][1000 genomes]
rs6786612	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788543	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6790072	0.96[ASN][1000 genomes]
rs6790079	1.00[ASN][1000 genomes]
rs6792493	0.84[ASN][1000 genomes]
rs6796087	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6802995	0.99[ASN][1000 genomes]
rs7427201	1.00[ASN][1000 genomes]
rs7609653	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614443	1.00[ASN][1000 genomes]
rs955381	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs959540	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9818574	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823974	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825915	1.00[ASN][1000 genomes]
rs9834030	0.96[ASN][1000 genomes]
rs9838371	1.00[ASN][1000 genomes]
rs9863403	1.00[ASN][1000 genomes]
rs9868171	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868909	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9870823	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111477600-111484600	Enhancers	HMEC	breast
2	chr3:111478000-111484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111478800-111484800	Enhancers	Rectal Smooth Muscle	rectum
4	chr3:111479800-111484400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:111479800-111484800	Enhancers	Osteobl	bone
6	chr3:111480000-111484400	Enhancers	Colon Smooth Muscle	Colon
7	chr3:111480000-111484400	Enhancers	Hela-S3	cervix
8	chr3:111480200-111484400	Enhancers	NHLF	lung
9	chr3:111480200-111484600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:111480200-111492000	Enhancers	Liver	Liver
11	chr3:111480400-111484400	Enhancers	NHEK	skin
12	chr3:111480600-111484400	Enhancers	HSMMtube	muscle
13	chr3:111480600-111484800	Enhancers	NHDF-Ad	bronchial
14	chr3:111480600-111486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:111480800-111484400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:111480800-111484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:111480800-111484400	Enhancers	HSMM	muscle
18	chr3:111480800-111484600	Enhancers	Adipose Nuclei	Adipose
19	chr3:111481000-111487400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:111481000-111487400	Weak transcription	Right Atrium	heart
21	chr3:111481600-111484400	Enhancers	Fetal Intestine Small	intestine
22	chr3:111481800-111484400	Enhancers	Stomach Mucosa	stomach
23	chr3:111481800-111485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:111482000-111487400	Weak transcription	Pancreas	Pancrea
25	chr3:111482200-111487200	Weak transcription	Fetal Heart	heart
26	chr3:111482200-111487400	Weak transcription	Left Ventricle	heart
27	chr3:111482600-111484400	Enhancers	Fetal Intestine Large	intestine
28	chr3:111482600-111484400	Enhancers	HepG2	liver
29	chr3:111482600-111487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:111482800-111484600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:111482800-111487200	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:111482800-111487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:111483000-111487400	Weak transcription	Fetal Stomach	stomach
34	chr3:111483200-111487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:111483200-111489200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:111483400-111484600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:111483400-111487200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:111483400-111487400	Weak transcription	Fetal Lung	lung
39	chr3:111483800-111484400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:111483800-111484600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:111483800-111484600	Flanking Active TSS	A549	lung
42	chr3:111483800-111487600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:111484000-111486800	Weak transcription	NH-A	brain
44	chr3:111484000-111487400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:111484200-111486000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:111484200-111487000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:111484200-111487000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:111484200-111487200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:111484200-111487200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:111484200-111487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links