Variant report

Variant	rs62254280
Chromosome Location	chr3:53188062-53188063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53187108..53189082-chr3:53208380..53210944,2	MCF-7	breast:
2	chr3:53187844..53191099-chr3:53288490..53291420,3	MCF-7	breast:
3	chr3:53187180..53188996-chr3:53201461..53203249,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs35292588	1.00[ASN][1000 genomes]
rs55685362	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254272	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254273	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254274	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62254276	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254277	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254278	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254279	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777221	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087762	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53174800-53189600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:53177800-53190200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:53178000-53189600	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr3:53178600-53190200	Enhancers	Colonic Mucosa	Colon
5	chr3:53179000-53190000	Enhancers	Duodenum Mucosa	Duodenum
6	chr3:53182400-53193400	Weak transcription	Psoas Muscle	Psoas
7	chr3:53182400-53193800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:53183200-53194600	Enhancers	Gastric	stomach
9	chr3:53183400-53189000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:53183400-53194600	Enhancers	Pancreas	Pancrea
11	chr3:53183600-53190600	Enhancers	Liver	Liver
12	chr3:53183800-53189000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:53184200-53194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:53184400-53193800	Enhancers	Adipose Nuclei	Adipose
15	chr3:53184600-53190000	Weak transcription	Spleen	Spleen
16	chr3:53184800-53188600	Weak transcription	Right Ventricle	heart
17	chr3:53185000-53188400	Weak transcription	Left Ventricle	heart
18	chr3:53185600-53188600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:53186000-53189200	Weak transcription	Hela-S3	cervix
20	chr3:53186200-53188800	Bivalent Enhancer	HepG2	liver
21	chr3:53186800-53190200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:53187000-53189200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:53187400-53189400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:53187600-53189000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:53187600-53189600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:53187600-53189800	Enhancers	Lung	lung
27	chr3:53187600-53190400	Enhancers	Brain Anterior Caudate	brain
28	chr3:53187800-53188400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:53187800-53189400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:53187800-53189400	Enhancers	HSMM	muscle
31	chr3:53187800-53189400	Enhancers	Osteobl	bone
32	chr3:53187800-53189600	Enhancers	Fetal Lung	lung
33	chr3:53187800-53190200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr3:53187800-53190400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:53187800-53190800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:53187800-53191800	Enhancers	HMEC	breast
37	chr3:53187800-53194600	Enhancers	Esophagus	oesophagus
38	chr3:53188000-53188200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:53188000-53188200	Enhancers	Brain Hippocampus Middle	brain
40	chr3:53188000-53188200	Flanking Active TSS	Stomach Mucosa	stomach
41	chr3:53188000-53188400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:53188000-53188400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
43	chr3:53188000-53188600	Enhancers	HSMMtube	muscle
44	chr3:53188000-53189400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:53188000-53189600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:53188000-53189600	Enhancers	Fetal Intestine Large	intestine
47	chr3:53188000-53192000	Enhancers	Right Atrium	heart
48	chr3:53188000-53192800	Weak transcription	Small Intestine	intestine

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