Variant report

Variant	rs62254273
Chromosome Location	chr3:53178658-53178659
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	chr3:53176620..53178879-chr3:53179713..53181872,2	MCF-7	breast:
2	chr3:53177843..53180443-chr3:53877021..53879242,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016391	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs35292588	1.00[ASN][1000 genomes]
rs55685362	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254272	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254274	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62254276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254280	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087762	0.96[AMR][1000 genomes];0.95[EUR][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	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	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
4	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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
2	chr3:53169200-53179000	Weak transcription	Fetal Lung	lung
3	chr3:53169200-53183800	Weak transcription	Right Ventricle	heart
4	chr3:53174000-53182400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:53174800-53189600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:53175000-53183800	Weak transcription	Esophagus	oesophagus
7	chr3:53175200-53183800	Weak transcription	Right Atrium	heart
8	chr3:53175400-53183600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:53175600-53179200	Weak transcription	Hela-S3	cervix
10	chr3:53175600-53180600	Weak transcription	Adipose Nuclei	Adipose
11	chr3:53175600-53184000	Weak transcription	NHDF-Ad	bronchial
12	chr3:53175800-53180600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:53175800-53183800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:53176400-53188000	Enhancers	Stomach Mucosa	stomach
15	chr3:53176600-53180800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:53177000-53179000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:53177000-53180200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:53177200-53181600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:53177200-53182400	Enhancers	Pancreas	Pancrea
20	chr3:53177800-53190200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:53178000-53179000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:53178000-53181200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:53178000-53181400	Weak transcription	GM12878-XiMat	blood
24	chr3:53178000-53181600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:53178000-53182200	Enhancers	Gastric	stomach
26	chr3:53178000-53189600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr3:53178200-53184400	Weak transcription	Placenta	Placenta
28	chr3:53178600-53179400	Enhancers	Lung	lung
29	chr3:53178600-53190200	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links